diff --git a/.Rproj.user/BAB4038F/pcs/files-pane.pper b/.Rproj.user/BAB4038F/pcs/files-pane.pper
index ff84e24..b260829 100644
--- a/.Rproj.user/BAB4038F/pcs/files-pane.pper
+++ b/.Rproj.user/BAB4038F/pcs/files-pane.pper
@@ -5,5 +5,5 @@
             "ascending": true
         }
     ],
-    "path": "~/git/pf.memory/R"
+    "path": "~/git/pf.memory"
 }
\ No newline at end of file
diff --git a/.Rproj.user/BAB4038F/pcs/source-pane.pper b/.Rproj.user/BAB4038F/pcs/source-pane.pper
index b074a4f..bc7dc99 100644
--- a/.Rproj.user/BAB4038F/pcs/source-pane.pper
+++ b/.Rproj.user/BAB4038F/pcs/source-pane.pper
@@ -1,3 +1,3 @@
 {
-    "activeTab": 1
+    "activeTab": 4
 }
\ No newline at end of file
diff --git a/_pkgdown.yml b/_pkgdown.yml
index b258094..1d5c025 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -15,8 +15,8 @@ navbar:
       href: articles/Hybrid.html
   - text: Parasite
     menu:
-    - text: Simple Infections
-      href: articles/Simple_Infections.html
+    - text: Parasite Densities
+      href: articles/Parasite_Densities.html
   right:
   - icon: fa-github
     href: https://github.com/dd-harp/pf.memory/
diff --git a/docs/404.html b/docs/404.html
index dbd40c1..0a2a4b9 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -47,7 +47,7 @@
 <li class="nav-item dropdown">
   <a href="https://dd-harp.github.io/pf.memory/#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="https://dd-harp.github.io/pf.memory/articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="https://dd-harp.github.io/pf.memory/articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul>
diff --git a/docs/articles/Dynamics.html b/docs/articles/Dynamics.html
index 5bf797f..e571b11 100644
--- a/docs/articles/Dynamics.html
+++ b/docs/articles/Dynamics.html
@@ -49,7 +49,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul>
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 4813c2a..ff9b4e2 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/articles/plotCounts.html b/docs/articles/plotCounts.html
index 9ca3256..599b72b 100644
--- a/docs/articles/plotCounts.html
+++ b/docs/articles/plotCounts.html
@@ -49,7 +49,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul>
diff --git a/docs/authors.html b/docs/authors.html
index b4e669f..dcc9da8 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/index.html b/docs/index.html
index 9c6321c..78904eb 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -49,7 +49,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul>
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index bdf0021..8d7ab76 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -9,7 +9,7 @@ articles:
   Parasite_Densities: Parasite_Densities.html
   plotCounts: plotCounts.html
   prevalence: prevalence.html
-last_built: 2024-02-13T23:35Z
+last_built: 2024-02-13T23:57Z
 urls:
   reference: https://dd-harp.github.io/pf.memory/reference
   article: https://dd-harp.github.io/pf.memory/articles
diff --git a/docs/reference/Detect.html b/docs/reference/Detect.html
index 35c949e..b2923d3 100644
--- a/docs/reference/Detect.html
+++ b/docs/reference/Detect.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/Detect.nb.html b/docs/reference/Detect.nb.html
index e661ab4..ed16adc 100644
--- a/docs/reference/Detect.nb.html
+++ b/docs/reference/Detect.nb.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/Detect.pois.html b/docs/reference/Detect.pois.html
index ea74648..6b9008e 100644
--- a/docs/reference/Detect.pois.html
+++ b/docs/reference/Detect.pois.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/DetectBda.html b/docs/reference/DetectBda.html
index e475430..1e0f163 100644
--- a/docs/reference/DetectBda.html
+++ b/docs/reference/DetectBda.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/DetectPM.html b/docs/reference/DetectPM.html
index c282cd9..130e9d7 100644
--- a/docs/reference/DetectPM.html
+++ b/docs/reference/DetectPM.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/DetectPa.html b/docs/reference/DetectPa.html
index be6fff5..fec4748 100644
--- a/docs/reference/DetectPa.html
+++ b/docs/reference/DetectPa.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/FoI.html b/docs/reference/FoI.html
index 57d846b..dce4563 100644
--- a/docs/reference/FoI.html
+++ b/docs/reference/FoI.html
@@ -36,7 +36,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/MoIDistPlot.html b/docs/reference/MoIDistPlot.html
index f0e07a6..1c13cd8 100644
--- a/docs/reference/MoIDistPlot.html
+++ b/docs/reference/MoIDistPlot.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/MoIPM.html b/docs/reference/MoIPM.html
index 7770224..f946f31 100644
--- a/docs/reference/MoIPM.html
+++ b/docs/reference/MoIPM.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/Wda.delta.html b/docs/reference/Wda.delta.html
index a7ae398..75a5ae4 100644
--- a/docs/reference/Wda.delta.html
+++ b/docs/reference/Wda.delta.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/Wda.html b/docs/reference/Wda.html
index c4ca0d0..948f697 100644
--- a/docs/reference/Wda.html
+++ b/docs/reference/Wda.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/Wda.none.html b/docs/reference/Wda.none.html
index 220be71..bede844 100644
--- a/docs/reference/Wda.none.html
+++ b/docs/reference/Wda.none.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/ageFoI.flat.html b/docs/reference/ageFoI.flat.html
index f756842..6a70d5b 100644
--- a/docs/reference/ageFoI.flat.html
+++ b/docs/reference/ageFoI.flat.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/ageFoI.html b/docs/reference/ageFoI.html
index b408b32..29364f1 100644
--- a/docs/reference/ageFoI.html
+++ b/docs/reference/ageFoI.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/ageFoI.type2.html b/docs/reference/ageFoI.type2.html
index 1dbeb79..857b30d 100644
--- a/docs/reference/ageFoI.type2.html
+++ b/docs/reference/ageFoI.type2.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/alpha2mu.W.html b/docs/reference/alpha2mu.W.html
index 943f2d1..45d46bc 100644
--- a/docs/reference/alpha2mu.W.html
+++ b/docs/reference/alpha2mu.W.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/alpha2mu.base.html b/docs/reference/alpha2mu.base.html
index c1e0ef7..657cafe 100644
--- a/docs/reference/alpha2mu.base.html
+++ b/docs/reference/alpha2mu.base.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/alpha2mu.html b/docs/reference/alpha2mu.html
index fd01b37..1189bad 100644
--- a/docs/reference/alpha2mu.html
+++ b/docs/reference/alpha2mu.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/binnedCounts.html b/docs/reference/binnedCounts.html
index 5e2857a..360c431 100644
--- a/docs/reference/binnedCounts.html
+++ b/docs/reference/binnedCounts.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/binnedCounts.nb.html b/docs/reference/binnedCounts.nb.html
index 7084dbf..a559550 100644
--- a/docs/reference/binnedCounts.nb.html
+++ b/docs/reference/binnedCounts.nb.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/binnedCounts.pois.html b/docs/reference/binnedCounts.pois.html
index 7aae29c..3fd9285 100644
--- a/docs/reference/binnedCounts.pois.html
+++ b/docs/reference/binnedCounts.pois.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/cdfConvolve2.html b/docs/reference/cdfConvolve2.html
index 1148b2e..7b0c68a 100644
--- a/docs/reference/cdfConvolve2.html
+++ b/docs/reference/cdfConvolve2.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/cdfConvolve2a.html b/docs/reference/cdfConvolve2a.html
index 2cd27d4..f7f4959 100644
--- a/docs/reference/cdfConvolve2a.html
+++ b/docs/reference/cdfConvolve2a.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/cdfConvolve2b.html b/docs/reference/cdfConvolve2b.html
index e3bda02..208c01b 100644
--- a/docs/reference/cdfConvolve2b.html
+++ b/docs/reference/cdfConvolve2b.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/dAoI.html b/docs/reference/dAoI.html
index cb5ead0..b37626d 100644
--- a/docs/reference/dAoI.html
+++ b/docs/reference/dAoI.html
@@ -34,7 +34,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/dAoIda.html b/docs/reference/dAoIda.html
index 2e7f5f1..e39de35 100644
--- a/docs/reference/dAoIda.html
+++ b/docs/reference/dAoIda.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/dAoY.html b/docs/reference/dAoY.html
index c22dca2..5a6db45 100644
--- a/docs/reference/dAoY.html
+++ b/docs/reference/dAoY.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/dAoYN.html b/docs/reference/dAoYN.html
index babfa64..be7dc55 100644
--- a/docs/reference/dAoYN.html
+++ b/docs/reference/dAoYN.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/dAoYda.html b/docs/reference/dAoYda.html
index 107deb2..15cc107 100644
--- a/docs/reference/dAoYda.html
+++ b/docs/reference/dAoYda.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/dCounts.html b/docs/reference/dCounts.html
index 26bece0..6b30eed 100644
--- a/docs/reference/dCounts.html
+++ b/docs/reference/dCounts.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/dCounts.nb.html b/docs/reference/dCounts.nb.html
index 00ae339..4dba8e9 100644
--- a/docs/reference/dCounts.nb.html
+++ b/docs/reference/dCounts.nb.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/dCounts.pois.html b/docs/reference/dCounts.pois.html
index 36702c7..cf050e5 100644
--- a/docs/reference/dCounts.pois.html
+++ b/docs/reference/dCounts.pois.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/dCountsBa.html b/docs/reference/dCountsBa.html
index 9e9a607..4332759 100644
--- a/docs/reference/dCountsBa.html
+++ b/docs/reference/dCountsBa.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/dCountsPa.html b/docs/reference/dCountsPa.html
index 6b38825..492f30f 100644
--- a/docs/reference/dCountsPa.html
+++ b/docs/reference/dCountsPa.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/dDensityPaConvolve2.html b/docs/reference/dDensityPaConvolve2.html
index ab85085..00b7702 100644
--- a/docs/reference/dDensityPaConvolve2.html
+++ b/docs/reference/dDensityPaConvolve2.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/dMoIda.html b/docs/reference/dMoIda.html
index d407036..6f1ead4 100644
--- a/docs/reference/dMoIda.html
+++ b/docs/reference/dMoIda.html
@@ -50,7 +50,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/dbeta1.html b/docs/reference/dbeta1.html
index 9152776..2aa2259 100644
--- a/docs/reference/dbeta1.html
+++ b/docs/reference/dbeta1.html
@@ -34,7 +34,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/dmda.html b/docs/reference/dmda.html
index ccae10c..1238a3a 100644
--- a/docs/reference/dmda.html
+++ b/docs/reference/dmda.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/dpda.html b/docs/reference/dpda.html
index 280c256..98780f1 100644
--- a/docs/reference/dpda.html
+++ b/docs/reference/dpda.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/index.html b/docs/reference/index.html
index e14f769..e568e54 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/log10RBC.html b/docs/reference/log10RBC.html
index 10ed3c1..eb9937f 100644
--- a/docs/reference/log10RBC.html
+++ b/docs/reference/log10RBC.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/log10RBC.static.html b/docs/reference/log10RBC.static.html
index 78ebe01..1fbf718 100644
--- a/docs/reference/log10RBC.static.html
+++ b/docs/reference/log10RBC.static.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/meanCountsBa.html b/docs/reference/meanCountsBa.html
index 35286c0..3389981 100644
--- a/docs/reference/meanCountsBa.html
+++ b/docs/reference/meanCountsBa.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/meanCountsPa.html b/docs/reference/meanCountsPa.html
index 449e015..02f7d1d 100644
--- a/docs/reference/meanCountsPa.html
+++ b/docs/reference/meanCountsPa.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/meanMoI.html b/docs/reference/meanMoI.html
index 0492aae..5ea83ee 100644
--- a/docs/reference/meanMoI.html
+++ b/docs/reference/meanMoI.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/momentAoI.html b/docs/reference/momentAoI.html
index f862049..e19715e 100644
--- a/docs/reference/momentAoI.html
+++ b/docs/reference/momentAoI.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/momentAoY.html b/docs/reference/momentAoY.html
index 58d838a..20b3f02 100644
--- a/docs/reference/momentAoY.html
+++ b/docs/reference/momentAoY.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/nzPois.html b/docs/reference/nzPois.html
index a388d27..69311f0 100644
--- a/docs/reference/nzPois.html
+++ b/docs/reference/nzPois.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/pAoI.html b/docs/reference/pAoI.html
index 7af47aa..f7a6062 100644
--- a/docs/reference/pAoI.html
+++ b/docs/reference/pAoI.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/pAoY.html b/docs/reference/pAoY.html
index acdfeff..24a3147 100644
--- a/docs/reference/pAoY.html
+++ b/docs/reference/pAoY.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/pAoYN.html b/docs/reference/pAoYN.html
index 5dad85a..174b707 100644
--- a/docs/reference/pAoYN.html
+++ b/docs/reference/pAoYN.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/pAoY_long.html b/docs/reference/pAoY_long.html
index 5f71612..035e726 100644
--- a/docs/reference/pAoY_long.html
+++ b/docs/reference/pAoY_long.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/pCounts.html b/docs/reference/pCounts.html
index 3e790eb..e606642 100644
--- a/docs/reference/pCounts.html
+++ b/docs/reference/pCounts.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/pCounts.nb.html b/docs/reference/pCounts.nb.html
index 066f415..691552f 100644
--- a/docs/reference/pCounts.nb.html
+++ b/docs/reference/pCounts.nb.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/pCounts.pois.html b/docs/reference/pCounts.pois.html
index 534daf6..5027783 100644
--- a/docs/reference/pCounts.pois.html
+++ b/docs/reference/pCounts.pois.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/pCountsBa.html b/docs/reference/pCountsBa.html
index fe869b1..b4abb3e 100644
--- a/docs/reference/pCountsBa.html
+++ b/docs/reference/pCountsBa.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/pCountsPa.html b/docs/reference/pCountsPa.html
index 113a533..93e5a3e 100644
--- a/docs/reference/pCountsPa.html
+++ b/docs/reference/pCountsPa.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/par_Wda_delta.html b/docs/reference/par_Wda_delta.html
index 93ec3db..1af8a39 100644
--- a/docs/reference/par_Wda_delta.html
+++ b/docs/reference/par_Wda_delta.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/par_Wda_none.html b/docs/reference/par_Wda_none.html
index 92712bd..4274e6c 100644
--- a/docs/reference/par_Wda_none.html
+++ b/docs/reference/par_Wda_none.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/par_expSeason.html b/docs/reference/par_expSeason.html
index d358e59..48672ad 100644
--- a/docs/reference/par_expSeason.html
+++ b/docs/reference/par_expSeason.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/par_flatAge.html b/docs/reference/par_flatAge.html
index e4f0cfe..25f4fa0 100644
--- a/docs/reference/par_flatAge.html
+++ b/docs/reference/par_flatAge.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/par_flatSeason.html b/docs/reference/par_flatSeason.html
index dae580d..e768e34 100644
--- a/docs/reference/par_flatSeason.html
+++ b/docs/reference/par_flatSeason.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/par_flatTrend.html b/docs/reference/par_flatTrend.html
index e5c8060..8896810 100644
--- a/docs/reference/par_flatTrend.html
+++ b/docs/reference/par_flatTrend.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/par_lRBC_static.html b/docs/reference/par_lRBC_static.html
index a558b43..418917d 100644
--- a/docs/reference/par_lRBC_static.html
+++ b/docs/reference/par_lRBC_static.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/par_nbCounts.html b/docs/reference/par_nbCounts.html
index b5dfe88..6d36d66 100644
--- a/docs/reference/par_nbCounts.html
+++ b/docs/reference/par_nbCounts.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/par_poisCounts.html b/docs/reference/par_poisCounts.html
index 2420264..5844612 100644
--- a/docs/reference/par_poisCounts.html
+++ b/docs/reference/par_poisCounts.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/par_sigma_abc.html b/docs/reference/par_sigma_abc.html
index 13bdf84..3d0ff09 100644
--- a/docs/reference/par_sigma_abc.html
+++ b/docs/reference/par_sigma_abc.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/par_sinSeason.html b/docs/reference/par_sinSeason.html
index a0e4716..fa8eb8b 100644
--- a/docs/reference/par_sinSeason.html
+++ b/docs/reference/par_sinSeason.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/par_type2Age.html b/docs/reference/par_type2Age.html
index e7f45d6..67c011a 100644
--- a/docs/reference/par_type2Age.html
+++ b/docs/reference/par_type2Age.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/pbeta1.html b/docs/reference/pbeta1.html
index 4fdd2e6..56c212d 100644
--- a/docs/reference/pbeta1.html
+++ b/docs/reference/pbeta1.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/qbeta1.html b/docs/reference/qbeta1.html
index 0569881..bc50d29 100644
--- a/docs/reference/qbeta1.html
+++ b/docs/reference/qbeta1.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/rAoI.html b/docs/reference/rAoI.html
index 549532e..c7b371a 100644
--- a/docs/reference/rAoI.html
+++ b/docs/reference/rAoI.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/rAoY.html b/docs/reference/rAoY.html
index 41f1731..06f1fc5 100644
--- a/docs/reference/rAoY.html
+++ b/docs/reference/rAoY.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/rAoYN.html b/docs/reference/rAoYN.html
index 95bdedf..19f2be6 100644
--- a/docs/reference/rAoYN.html
+++ b/docs/reference/rAoYN.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/rRda.html b/docs/reference/rRda.html
index 4af70b3..2b6bd3a 100644
--- a/docs/reference/rRda.html
+++ b/docs/reference/rRda.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/rbeta1.html b/docs/reference/rbeta1.html
index 213550e..0d7414b 100644
--- a/docs/reference/rbeta1.html
+++ b/docs/reference/rbeta1.html
@@ -36,7 +36,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/salpha2mu.html b/docs/reference/salpha2mu.html
index f57eba5..69d6248 100644
--- a/docs/reference/salpha2mu.html
+++ b/docs/reference/salpha2mu.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/seasonalFoI.exp.html b/docs/reference/seasonalFoI.exp.html
index 46cf703..2ff1015 100644
--- a/docs/reference/seasonalFoI.exp.html
+++ b/docs/reference/seasonalFoI.exp.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/seasonalFoI.flat.html b/docs/reference/seasonalFoI.flat.html
index a4432c8..e60639a 100644
--- a/docs/reference/seasonalFoI.flat.html
+++ b/docs/reference/seasonalFoI.flat.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/seasonalFoI.html b/docs/reference/seasonalFoI.html
index ac15503..419c0f4 100644
--- a/docs/reference/seasonalFoI.html
+++ b/docs/reference/seasonalFoI.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/seasonalFoI.sin.html b/docs/reference/seasonalFoI.sin.html
index c92baed..ac79cbd 100644
--- a/docs/reference/seasonalFoI.sin.html
+++ b/docs/reference/seasonalFoI.sin.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/solveMMinfty.html b/docs/reference/solveMMinfty.html
index 82f3ca4..434eb57 100644
--- a/docs/reference/solveMMinfty.html
+++ b/docs/reference/solveMMinfty.html
@@ -38,7 +38,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/solve_dAoI.html b/docs/reference/solve_dAoI.html
index 15ba055..c4a4297 100644
--- a/docs/reference/solve_dAoI.html
+++ b/docs/reference/solve_dAoI.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/solve_dAoYda.html b/docs/reference/solve_dAoYda.html
index 55ccf00..25ed064 100644
--- a/docs/reference/solve_dAoYda.html
+++ b/docs/reference/solve_dAoYda.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/solve_dm.html b/docs/reference/solve_dm.html
index c1ee79c..d38dd2c 100644
--- a/docs/reference/solve_dm.html
+++ b/docs/reference/solve_dm.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/solve_dpda.html b/docs/reference/solve_dpda.html
index 9207193..e03b38c 100644
--- a/docs/reference/solve_dpda.html
+++ b/docs/reference/solve_dpda.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/trendFoI.flat.html b/docs/reference/trendFoI.flat.html
index c48df69..40d3050 100644
--- a/docs/reference/trendFoI.flat.html
+++ b/docs/reference/trendFoI.flat.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/trendFoI.html b/docs/reference/trendFoI.html
index c9928af..1b7aa88 100644
--- a/docs/reference/trendFoI.html
+++ b/docs/reference/trendFoI.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/truePRa.html b/docs/reference/truePRa.html
index 56456a9..dfeeb9e 100644
--- a/docs/reference/truePRa.html
+++ b/docs/reference/truePRa.html
@@ -32,7 +32,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/reference/zda.html b/docs/reference/zda.html
index db7c4f4..a83bb64 100644
--- a/docs/reference/zda.html
+++ b/docs/reference/zda.html
@@ -38,7 +38,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-parasite">Parasite</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-parasite">
-    <a class="dropdown-item" href="../articles/Simple_Infections.html">Simple Infections</a>
+    <a class="dropdown-item" href="../articles/Parasite_Densities.html">Parasite Densities</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/search.json b/docs/search.json
index d4b5447..0840f35 100644
--- a/docs/search.json
+++ b/docs/search.json
@@ -1 +1 @@
-[{"path":"https://dd-harp.github.io/pf.memory/articles/AoI-Hybrid.html","id":"hybrid-model","dir":"Articles","previous_headings":"","what":"Hybrid Model","title":"Hybrid Model for the Age of Infection","text":"function solve_dAoI computes first three moments AoI default. plot \\(n^{th}\\) root first three moments. ## Numerical Verification solving hybrid model variables track moments, using equations derived :","code":"aa = seq(5, 3*365, by = 5)  moment1y = momentAoY(aa, foiP3) par(mar = c(7, 4, 2, 2)) solve_dAoI(5/365, foiP3) -> mt  plot(mt$time, mt$xn1, type = \"l\", xlab = \"Age (in Days)\", ylab = expression(list(x, sqrt(x[paste(\"[2]\")]), sqrt(x[paste(\"[3]\")], 3))), ylim = range(mt$xn3^(1/3)))  lines(mt$time, mt$xn2^(1/2), col = \"purple\") lines(mt$time, mt$xn3^(1/3), col = \"darkgreen\") aa = seq(1, 5*365, by = 5)  moment1 = momentAoI(aa, foiP3) moment2 = momentAoI(aa, foiP3, n=2) moment3 = momentAoI(aa, foiP3, n=3) solve_dAoI(5/365, foiP3, Tmax = 5*365, dt=5) -> mt par(mfrow = c(2,2), mar = c(7, 4, 2, 2)) # Top Left plot(mt$time, mt$xn1, type = \"l\", xlab = \"Age (in Days)\", ylab = expression(x), lwd=3)  lines(aa, moment1, col = \"yellow\", lwd=2, lty=2)  # Top Right  plot(mt$time, mt$xn2, type = \"l\", xlab = \"Age (in Days)\", ylab = expression(x[paste(\"[2]\")]), lwd=3, col = \"purple\")  lines(aa, moment2, col = \"yellow\", lwd=2, lty=2) plot(mt$time, mt$xn3, type = \"l\", lwd=3, col = \"darkgreen\",      xlab = \"Age (in Days)\", ylab = expression(x[paste(\"[3]\")])) lines(aa, moment3, col = \"yellow\", lwd=2, lty=2) par(mar = c(7, 4, 2, 2)) solve_dAoI(5/365, foiP3) -> mt  plot(mt$time, mt$xn1, type = \"l\", xlab = \"Age (in Days)\", ylab = expression(list(x, sqrt(x[paste(\"[2]\")]), sqrt(x[paste(\"[3]\")], 3))), lwd=3, ylim = range(mt$xn3^(1/3)))  lines(mt$time, mt$xn2^(1/2), col = \"purple\", lwd=3) lines(mt$time, mt$xn3^(1/3), col = \"darkgreen\", lwd=3)  lines(aa, moment1, col = \"yellow\", lwd=2, lty=2) lines(aa, moment2^(1/2), col = \"yellow\", lwd=2, lty=2) lines(aa, moment3^(1/3), col = \"yellow\", lwd=2, lty=2)"},{"path":"https://dd-harp.github.io/pf.memory/articles/AoI.html","id":"the-density-function","dir":"Articles","previous_headings":"","what":"The Density Function","title":"Age of Infection","text":"following shows distribution AoI looks like cohort age 2.  , plot distributions 12 cohorts age 2, born one month apart.","code":"plot(a2years, dAoI(a2years, max(a2years), foiP3), type =\"l\", xlab = \"Parasite Age\", ylab = expression(F[A](alpha, a, tau)), ylim = c(0,0.009)) plot(a2years, dAoI(a2years, max(a2years), foiP3), type = \"n\", xlab = \"Parasite Age\", ylab = expression(F[A](alpha, a, tau)), ylim = c(0,0.013)) for(i in 1:12)   lines(a2years, dAoI(a2years,max(a2years),foiP3, tau=30*i), col = clrs[i])"},{"path":"https://dd-harp.github.io/pf.memory/articles/AoI.html","id":"the-distribution-function","dir":"Articles","previous_headings":"","what":"The Distribution Function","title":"Age of Infection","text":"","code":"plot(a2years, cumsum(dAoI(a2years, max(a2years), foiP3)), type = \"l\", xlab = \"Parasite Cohort Age\", ylab = expression(1-F[X](alpha, a, tau)), lwd=2) lines(a2years, pAoI(a2years, max(a2years), foiP3), col = \"red\", lwd=2, lty =2) par(mar = c(5,4,1,2))  plot(a2years, pAoI(a2years, max(a2years), foiP3), type = \"n\", xlab =  expression(list(alpha, \" Parasite Age\")), ylab = expression(F[X](alpha, a, tau)))  for(i in 1:12)   lines(a2years, pAoI(a2years,max(a2years), foiP3, tau=30*i), col = clrs[i])"},{"path":"https://dd-harp.github.io/pf.memory/articles/AoI.html","id":"random-numbers","dir":"Articles","previous_headings":"","what":"Random Numbers","title":"Age of Infection","text":"","code":"par(mar = c(5,4,1,2)) a5years = 0:(5*365) rhx = rAoI(10000, 5*365, foiP3) hist(rhx, breaks = c(0:c(5*365)), right=F, probability=T, main = \"\", xlab = expression(alpha), border = grey(0.5)) cdf1 = pAoI(a5years, 5*365, foiP3) pdf1 = dAoI(a5years, 5*365, foiP3)  lines(a5years, pdf1, col=\"red\", lwd=2) par(mar = c(5,4,1,2)) plot(ecdf(rhx), xlim = c(0,1825), cex=0.2, main = \"\", xlab = expression(alpha)) lines(a5years, cdf1, col = \"red\", lty = 2, lwd=2)"},{"path":"https://dd-harp.github.io/pf.memory/articles/AoI.html","id":"moments","dir":"Articles","previous_headings":"","what":"Moments","title":"Age of Infection","text":"Let \\(x\\) denote first moment \\(A_\\tau()\\): \\[x_\\tau() = \\left< A_\\tau() \\right> = \\int_0^\\infty \\alpha \\frac{z_\\tau(\\alpha, )} {m_\\tau()}\\] Similarly, let \\(x_\\tau()[n]\\) denote higher order moments \\(A_\\tau()\\): \\[x_{n}(, \\tau) = \\int_0^\\infty \\alpha^n \\frac{z_\\tau(\\alpha, )} {m_\\tau()}\\] first three moments AoY plotted time. top plot, ’ve also plotted \\(n^{th}\\) root \\(n^{th}\\) moment.","code":"aa = seq(1, 5*365, by = 5)  moment1 = momentAoI(aa, foiP3) moment2 = momentAoI(aa, foiP3, n=2) moment3 = momentAoI(aa, foiP3, n=3) par(mfrow = c(3,1), mar = c(0.5, 4, 0.5, 2)) plot(aa, moment1, type = \"l\", xlab = \"\", ylab = expression(E(A)), lwd=2, xaxt=\"n\", ylim = range((moment3)^(1/3)) )  lines(aa, sqrt(moment2), col = \"darkgreen\") lines(aa, (moment3)^(1/3), col = \"purple\") plot(aa, moment2, type = \"l\", xlab = \"\", ylab = expression(E(A^2)), lwd=2, xaxt=\"n\", col = \"darkgreen\")  plot(aa, moment3, type = \"l\", xlab = \"\", ylab = expression(E(A^2)), lwd=2, col = \"purple\")  mtext(\"Age (in Days)\", 1, 3)"},{"path":"https://dd-harp.github.io/pf.memory/articles/AoY-Hybrid.html","id":"derivation-for-dyda","dir":"Articles","previous_headings":"","what":"Derivation for \\(dy/da\\)","title":"AoY Hybrid Model","text":"start multiplying \\(\\alpha\\) integrating respect \\(\\alpha\\): \\[ \\int_0^\\alpha \\frac{\\partial y(\\alpha, )}{\\partial } d \\alpha + \\int_0^\\alpha \\frac{\\partial y(\\alpha, )}{\\partial \\alpha} d\\alpha = - \\left(F(r,m)  + h \\right) \\int_0^\\alpha y(\\alpha, ) d\\alpha \\] \\[\\int_0^\\alpha y(\\alpha, ) d\\alpha =  \\left<Y \\right> p\\] \\[ \\frac{d \\left< Y \\right> p}{da} + \\int_0^\\alpha dy = - p \\left(F(r,m) + h \\right) \\left< Y \\right>    \\] Using chain rule: \\[ \\frac{\\partial \\left<\\right> p}{\\partial }= p \\frac{\\partial \\left<\\right>}{\\partial }  + \\left<\\right> \\frac{\\partial p}{\\partial }   \\] substituting: \\[ p \\frac{d \\left< Y \\right>}{da} + \\left<Y \\right> \\frac{dp}{da}  + \\int_0^\\alpha dy = - p \\left(F(r,m) + h \\right) \\left<Y \\right> \\] \\(dp/da = h(1-p) - R(m) p\\) \\[ p \\frac{d \\left< Y \\right>}{da} = - \\left[h (1-p) - R(m) p \\right] \\left<Y \\right>   - p \\left(F(r,m) + h \\right) \\left<Y \\right>  - \\int_0^\\alpha dy   \\] now lots things cancel, : \\[ p \\frac{d \\left< Y \\right>}{da} = - h \\left<Y \\right> -(F(r,m)-R(m)) \\left<Y \\right> - \\int_0^\\alpha dy   \\] last term, integrate parts: \\[ \\int_0^\\alpha \\partial z = \\alpha y(,\\alpha) \\big|_{\\alpha = } - \\alpha y(,\\alpha) \\big|_{\\alpha = 0} - \\int_0^y d\\alpha \\] simplifies : (first terms wrong, think wrong) \\[ \\int_0^\\alpha \\partial y =  h_d(0)e^{-ra} \\] \\[ \\frac{dy}{da} = 1 - \\frac{h}{p} y  - \\left( F(r,m) - R(m) \\right) y \\]","code":""},{"path":"https://dd-harp.github.io/pf.memory/articles/AoY-Hybrid.html","id":"frm","dir":"Articles","previous_headings":"","what":"\\(F(r,m)\\)","title":"AoY Hybrid Model","text":"intuition changes AoY worked treating MoI cases. arrived function: \\[F(r, \\zeta) = R(m) \\left( 1 + \\frac{\\zeta^{\\sqrt{2}}}{4} + \\sum_{k \\geq 3} \\frac{1}{k} \\frac{\\zeta^3}{k!} \\right). \\] \\[F(r, \\zeta) = r \\frac{\\mbox{Pr}(\\zeta=1; m(t))}{\\mbox{Pr}(\\zeta>0; m(t))} \\left( 1 + \\frac{\\zeta^{\\sqrt{2}}}{4} + \\sum_{k \\geq 3} \\frac{1}{k} \\frac{\\zeta^3}{k!} \\right). \\] Performance seem improve adding terms \\(k>5.\\) \\(\\zeta=1\\) MoI=1, term clear. cancels \\(R(m)\\) term. reasoned MoI 2 greater, change occur probability \\(1/\\zeta\\), increasing AoY something close \\(y\\). \\(\\zeta=2\\): Somehow, made mistake wrote first term, didn’t notice much later. fiddling around exponent, found \\(\\zeta^{\\sqrt{2}}\\) worked better \\(\\zeta\\) (started, mistake), curiously, better \\(\\zeta^2\\) \\(\\zeta>2\\): seemed work reasonably well. Ultimately, justification using formula seems work quite well.","code":""},{"path":"https://dd-harp.github.io/pf.memory/articles/AoY.html","id":"aoy-density","dir":"Articles","previous_headings":"","what":"AoY Density","title":"Age of the Youngest Infection (AoY)","text":"","code":"aoy = dAoY(1:1825, 5*365, foiP3) raoy = rAoY(10^5, 5*365, foiP3) hist(raoy, breaks=c(0:(5*365)), right=F, plot=F)->daoy plot(daoy$mids, daoy$density, type = \"l\") lines(1:1825, aoy, type = \"l\", col = \"red\")"},{"path":"https://dd-harp.github.io/pf.memory/articles/AoY.html","id":"moments","dir":"Articles","previous_headings":"","what":"Moments","title":"Age of the Youngest Infection (AoY)","text":"first three moments AoY plotted time. top plot, ’ve also plotted \\(n^{th}\\) root \\(n^{th}\\) moment.","code":"aa = seq(5, 5*365, by = 5)  moment1y = momentAoY(aa, foiP3) moment2y = momentAoY(aa, foiP3, n=2) moment3y = momentAoY(aa, foiP3, n=3) par(mfrow = c(4,1), mar = c(0.5, 4, 0.5, 2)) plot(aa, moment1y, type = \"l\", xlab = \"\", ylab = expression(E(Y)), lwd=2, xaxt=\"n\", ylim = range((moment3y)^(1/3)) )  lines(aa, sqrt(moment2y), col = \"darkgreen\") lines(aa, (moment3y)^(1/3), col = \"purple\") plot(aa, moment2y, type = \"l\", xlab = \"\", ylab = expression(E(Y^2)), lwd=2, xaxt=\"n\", col = \"darkgreen\")  plot(aa, moment3y, type = \"l\", xlab = \"\", ylab = expression(E(Y^2)), lwd=2, col = \"purple\")  mtext(\"Age (in Days)\", 1, 3)"},{"path":"https://dd-harp.github.io/pf.memory/articles/AoY.html","id":"derivation","dir":"Articles","previous_headings":"","what":"Derivation","title":"Age of the Youngest Infection (AoY)","text":"First, note CDF minimum \\(n\\) random values AoI cohort : \\[1-(1-F_A(\\alpha,,\\tau))^n\\] Using , can compute CDF full distribution AoY across population: \\[F_Y(\\alpha, , \\tau) = \\frac{1}{p_\\tau()} \\sum_{\\zeta>0} \\mbox{dpois}\\left(\\zeta,m_\\tau()\\right) \\left( 1-(1-F_A(\\alpha,,\\tau))^\\zeta \\right)\\] rewriting slightly: \\[F_Y(\\alpha, , \\tau)  p_\\tau() = \\sum_{\\zeta>0} \\frac{m_\\tau()^\\zeta}{\\zeta!} e^{-m_\\tau()} \\left(1- \\left(1-F_A \\left(\\alpha,, \\tau\\right)\\right)^\\zeta\\right)\\] pulling \\(e^{-m_\\tau()}\\) recombining terms, get: \\[F_Y (\\alpha, , \\tau) p_\\tau()= p_\\tau() - e^{-m_\\tau()} \\sum_{\\zeta>0} \\frac{ \\left[m_\\tau() \\left(1-F_A \\left(\\alpha,, \\tau\\right)\\right)\\right]^\\zeta}{\\zeta!}\\] sum \\(\\zeta=0\\ldots\\infty,\\) expression inside simple, sum \\(M>0\\), add term \\(M=0\\) sum, subtract outside: \\[F_Y(\\alpha, ,\\tau) p_\\tau() = p_\\tau() - e^{-m_\\tau()} \\left(-1+ \\sum_{\\zeta>=0} \\frac{ \\left[m_\\tau() \\left(1-F_A \\left(\\alpha,\\right)\\right)\\right]^\\zeta}{\\zeta!} \\right)\\] \\(e^{-m_\\tau()} = 1-p_\\tau()\\) infinite sum simply exponential, : \\[F_Y(\\alpha, , \\tau) p_\\tau() = p_\\tau() + 1-p_\\tau() - e^{-m_\\tau()} e^{m_\\tau() (1-F_A(\\alpha, , \\tau))}  \\] \\[F_Y(\\alpha, ,\\tau) p_\\tau() = 1-e^{-m_\\tau()F_a(\\alpha, )}\\] \\[F_Y(\\alpha, ,\\tau) = \\frac{1-e^{-m_\\tau()F_A(\\alpha, ,\\tau)}}{p_\\tau()}.\\] PDF AoY found taking derivative \\(F_Y\\): \\[ \\begin{array}{rcl} Y \\sim f_Y(\\alpha, , \\tau) & = & \\frac{d F_Y(\\alpha, ,\\tau)}{d\\alpha} \\\\ &=&  \\; f_A(\\alpha, ) e^{-m_\\tau() F_A(\\alpha, ,\\tau)}   \\frac{\\textstyle{m_\\tau()}}{\\textstyle{p_\\tau()}}\\\\ \\end{array} \\]","code":""},{"path":"https://dd-harp.github.io/pf.memory/articles/Dynamics.html","id":"formulas-and-computation","dir":"Articles","previous_headings":"","what":"Formulas and Computation","title":"Random Variables for Parasite Infection Dynamics","text":"Let \\(z_\\tau(\\alpha,)\\) denote density infections age \\(\\alpha\\) host cohort age \\(\\) born day \\(\\tau\\). dynamics \\(z(\\alpha,)\\) described following: \\[ \\frac{\\partial z}{\\partial } + \\frac{\\partial z}{\\partial \\alpha} = - r z \\label{dzda} \\] boundary condition: \\[ \\begin{equation} z_\\tau(0,) = h_\\tau(). \\end{equation} \\] solutions given : \\[ z_\\tau(\\alpha,) = h_\\tau(-\\alpha) e^{-r \\alpha} \\] function zda computes \\(z_\\tau(\\alpha, ).\\) mean MoI given formula: \\[ m_\\tau() = \\int_0^z_\\tau(\\alpha, ) d \\alpha \\] distribution MoI Poisson (Nåsell , 1985)2 mean \\(m_\\tau().\\) function meanMoI computes \\(m_\\tau()\\) using zda true prevalence \\[ p_\\tau() = 1 - e^{-m_\\tau()} \\] function truePRa computes true prevalence using meanMoI density function age infection (AoI) \\[ A_\\tau() \\sim f_A(\\alpha, , \\tau) = \\frac{z_\\tau(\\alpha,)}{m_\\tau()} \\] moments \\[ x_n(, \\tau | h) = \\int_0^ \\alpha^n f_A(\\alpha, , \\tau) d \\alpha \\] age youngest infection (AoY) defined : \\[ Y_\\tau() \\sim f_Y(\\alpha, , \\tau) = \\min_{\\zeta \\sim M_\\tau()} \\left\\{ \\alpha_i \\right\\}_{=1}^\\zeta,  \\alpha_i \\sim A_\\tau() \\] density function can expressed terms density distribution functions AoI MoI. \\[ f_Y(\\alpha; , \\tau) = f_A(\\alpha, ,\\tau) e^{-m_\\tau() F_A(\\alpha, ,\\tau)} \\frac{m_\\tau()}{p_\\tau()}. \\] distribution function AoY : \\[ F_Y() \\sim \\frac{1-e^{-m_\\tau()F_A(\\alpha, ,\\tau)}}{1-e^{-m_\\tau()}} = \\frac{1-e^{-m_\\tau()F_A(\\alpha, ,\\tau)}}{p_\\tau()} \\label{FY} \\] moments : \\[ y_n(, \\tau | h) = \\int_0^ \\alpha^n f_Y(\\alpha | , \\tau, h) d \\alpha \\] also developed functions compute age youngest \\(N\\) infections, called AoYN \\[ N_\\tau() \\sim \\min_{N} \\left\\{ \\alpha_i \\right\\}_{=1}^N \\mbox { }  \\alpha_i \\sim A_\\tau() \\] distribution function AoYN, \\(N_\\tau()\\), \\[F_N(\\alpha, , t) \\sim 1- (1-F_A(\\alpha, , \\tau))^N\\] following summary table functions compute MoI, AoI, AoY, moments. density function AoYN found differentiating: \\[f_N(\\alpha, , t) \\sim N (1-F_A(\\alpha, , \\tau))^{N-1}\\frac{f_A(\\alpha, , \\tau)}{m_\\tau()}\\]","code":""},{"path":"https://dd-harp.github.io/pf.memory/articles/Dynamics.html","id":"quick-reference","dir":"Articles","previous_headings":"","what":"Quick Reference","title":"Random Variables for Parasite Infection Dynamics","text":"following summary table functions compute MoI, AoI, AoY, AoYN, moments.","code":""},{"path":[]},{"path":"https://dd-harp.github.io/pf.memory/articles/Dynamics.html","id":"force-of-infection-foi","dir":"Articles","previous_headings":"Demonstration","what":"Force of Infection (FoI)","title":"Random Variables for Parasite Infection Dynamics","text":"compute anything, must first set function describe exposure (see FoI vignette). define functions plot FoI cohort ages (red), can also compute population average FoI (black). Different cohorts experience different histories exposure.","code":""},{"path":"https://dd-harp.github.io/pf.memory/articles/Dynamics.html","id":"computing-zda","dir":"Articles","previous_headings":"Demonstration","what":"Computing zda","title":"Random Variables for Parasite Infection Dynamics","text":"function pf.memory::zda(alpha, , FoIpar, ...) uses formula Eq. 1 compute density parasite infections cohort humans ages. Using zda, can compute density parasites cohort age without solving full system equations. Given function describing FoI population, \\(h(t)\\), cohort birthday, \\(\\tau.\\) following computes density infections every age cohort age 3. plot \\(z_\\tau(\\alpha, )\\), note \\(\\alpha\\) grows larger, parasite cohort gets older. plot parasite cohorts age, time going backwards x-axis.  Now, can imagine zda look like several different host cohorts age three, born different times. effect, taking snapshot cohorts age, different times. curves different hosts born different months, thus experienced different levels exposure first two years life. annual FoI 5 infections, per person, per year (\\(\\bar h = 5/365\\)):","code":"alpha = 60 a = 6*365 zda(60, 6*365, foiP3) ## [1] 0.001601196 zz = zda(a3years, max(a3years), foiP3)"},{"path":"https://dd-harp.github.io/pf.memory/articles/Dynamics.html","id":"multiplicity-of-infection-moi","dir":"Articles","previous_headings":"","what":"Multiplicity of Infection (MoI)","title":"Random Variables for Parasite Infection Dynamics","text":"define random variable \\(M\\) describing multiplicity infection (MoI). distribution MoI Poisson (see MoI vignette). \\[M_\\tau() \\sim f_M(\\zeta; , \\tau) = \\mbox{Pois}(m_\\tau())\\] Since \\(z_\\tau(\\alpha, )\\) describes density infections age \\(\\alpha\\) cohort age \\(\\), density infections must MoI. Since \\(0 \\leq \\alpha < \\), must true : \\[\\begin{equation} \\tag{2} m_\\tau() = \\int_0^z_\\tau(\\alpha, ) d \\alpha \\end{equation}\\] function computes \\(m_\\tau()\\) called meanMoI. , plot average MoI host cohort ages:","code":"mm = meanMoI(a3years, foiP3, hhat=5/365)"},{"path":"https://dd-harp.github.io/pf.memory/articles/Dynamics.html","id":"age-of-infection-aoi","dir":"Articles","previous_headings":"","what":"Age of Infection (AoI)","title":"Random Variables for Parasite Infection Dynamics","text":"define random variable \\(A_\\tau()\\) describes age infection (AoI), given formula \\[ A_\\tau() \\sim f_A(\\alpha; , \\tau) = \\frac{z_\\tau(\\alpha,)}{m_\\tau()} \\]","code":""},{"path":"https://dd-harp.github.io/pf.memory/articles/Dynamics.html","id":"the-density-function-daoi","dir":"Articles","previous_headings":"Age of Infection (AoI)","what":"The Density Function, dAoI","title":"Random Variables for Parasite Infection Dynamics","text":"can compute \\(A_\\tau()\\) using density function dAoI:  Now, plot distribution AoI cohorts age two, born different months (), notice distributions changed shapes:","code":"f_A = dAoI(a3years, max(a3years), foiP3)"},{"path":"https://dd-harp.github.io/pf.memory/articles/Dynamics.html","id":"the-distribution-function-paoi","dir":"Articles","previous_headings":"Age of Infection (AoI)","what":"The Distribution Function, pAoI","title":"Random Variables for Parasite Infection Dynamics","text":"distribution function \\(A_\\tau()\\) : \\[ F_A() \\sim \\int_0^\\alpha f_A(\\alpha; , \\tau) d\\alpha \\] functions work correctly, get approximately answer computing cumulative sum dAoI. shouldn’t expect answers exactly , close, pAoI black.","code":"F_A = pAoI(a3years, max(a3years), foiP3) F_A_alt = cumsum(f_A) par(mar = c(5,4,1,1))  plot(a3years, F_A, type = \"l\",       xlab = \"Parasite Cohort Age\",       ylab = expression(1-F[X](alpha, a, tau)), lwd=3)  lines(a3years, F_A_alt, col = \"red\", lwd=2, lty =2)"},{"path":"https://dd-harp.github.io/pf.memory/articles/Dynamics.html","id":"random-numbers-raoi","dir":"Articles","previous_headings":"Age of Infection (AoI)","what":"Random Numbers, rAoI","title":"Random Variables for Parasite Infection Dynamics","text":"function rAoI uses pAoI generate random numbers \\(F_A(\\alpha)\\) simple visual check computes empirical CDF random variates \\(F_A(\\alpha)\\) computed using pAoI  can also plot distribution functions.","code":"rhx = rAoI(10000, 3*365, foiP3) par(mar = c(5,4,1,2)) plot(stats::ecdf(rhx), xlim = c(0,1095), cex=0.2, main = \"\",       xlab = expression(list(alpha, paste(\"Parasite Age (in Days)\"))),       ylab = expression(list(F[A](alpha), paste(\"ecdf\")))) lines(a3years, F_A, col = \"red\", lty = 2, lwd=2)"},{"path":"https://dd-harp.github.io/pf.memory/articles/Dynamics.html","id":"aoi-moments","dir":"Articles","previous_headings":"Age of Infection (AoI)","what":"AoI Moments","title":"Random Variables for Parasite Infection Dynamics","text":"Let \\(x\\) denote first moment \\(A_\\tau()\\): \\[x_\\tau() = \\left< A_\\tau() \\right> = \\int_0^\\infty \\alpha \\frac{z_\\tau(\\alpha, )} {m_\\tau()}\\] Similarly, let \\(x_\\tau()[n]\\) denote higher order moments \\(A_\\tau()\\): \\[x_{[n]}(, \\tau) = \\int_0^\\infty \\alpha^n \\frac{z_\\tau(\\alpha, )} {m_\\tau()}\\] first three moments AoY plotted time. top plot, ’ve also plotted \\(n^{th}\\) root \\(n^{th}\\) moment. ## Age Youngest Infection (AoY) derived random variable \\(Y_\\tau()\\) describing age youngest infection (AoY). density function AoY : \\[Y_\\tau() \\sim f_Y(\\alpha; , \\tau) = f_A(\\alpha, ,\\tau) e^{-m_\\tau() F_A(\\alpha, ,\\tau)} \\frac{m_\\tau()}{p_\\tau()}\\] distribution function : \\[F_Y() \\sim \\frac{1-e^{-m_\\tau()F_A(\\alpha, ,\\tau)}}{1-e^{-m_\\tau()}} = \\frac{1-e^{-m_\\tau()F_A(\\alpha, ,\\tau)}}{p_\\tau()} \\] derivations found Suppplement Henry JM, et al. (2024)3 mean AoY : \\[ \\left< Y_\\tau() \\right> = \\int_0^\\alpha \\; f_Y(\\alpha, , \\tau) \\; d\\alpha \\] higher order moments AoY : \\[\\left< Y_\\tau()^n \\right> = \\int_0^n \\alpha^n \\; f_y(\\alpha, , \\tau) \\; d\\alpha \\]","code":"moment1 = momentAoI(a3years, foiP3) moment2 = momentAoI(a3years, foiP3, n=2) moment3 = momentAoI(a3years, foiP3, n=3)"},{"path":"https://dd-harp.github.io/pf.memory/articles/Dynamics.html","id":"aoy-density-daoy","dir":"Articles","previous_headings":"Age of Infection (AoI)","what":"AoY Density, dAoY","title":"Random Variables for Parasite Infection Dynamics","text":"density function computed function dAoY. can compare \\(f_Y(\\alpha)\\) (black) \\(f_A(alpha)\\) (grey).","code":"f_Y = dAoY(a3years, 3*365, foiP3)"},{"path":"https://dd-harp.github.io/pf.memory/articles/Dynamics.html","id":"random-variables-raoy","dir":"Articles","previous_headings":"Age of Infection (AoI)","what":"Random Variables, rAoY","title":"Random Variables for Parasite Infection Dynamics","text":"","code":"raoy = rAoY(10^5, 3*365, foiP3) hist(raoy, breaks=seq(0, 1095, by = 15),       right=F, probability=T, main = \"\",       xlab = expression(list(alpha, paste(\"Parasite Age (in Days)\"))),       border = grey(0.5)) -> out lines(a3years, f_Y, type = \"l\", col = \"red\")"},{"path":"https://dd-harp.github.io/pf.memory/articles/Dynamics.html","id":"aoy-moments","dir":"Articles","previous_headings":"Age of Infection (AoI)","what":"AoY Moments","title":"Random Variables for Parasite Infection Dynamics","text":"first three moments AoY plotted time. top plot, ’ve also plotted \\(n^{th}\\) root \\(n^{th}\\) moment.  Next: vignette Multiplicity Infection: Hybrid Models, Queuing Models, Verification, show mean MoI computed using formula Eq. 2 gives answer approaches.","code":"aa = seq(5, 3*365, by = 5)  moment1y = momentAoY(aa, foiP3) moment2y = momentAoY(aa, foiP3, n=2) moment3y = momentAoY(aa, foiP3, n=3)"},{"path":"https://dd-harp.github.io/pf.memory/articles/FoI-TraceFunctions.html","id":"references","dir":"Articles","previous_headings":"","what":"References","title":"FoI Trace Functions","text":"G. R. Port, P. F. L. Boreham, J. H. Bryan, relationship host size feeding mosquitoes Anopheles Gambiae Giles complex (Diptera: Culicidae). Bulletin Entomological Research 70, 133–144 (1980). P. Carnevale, J. L. Frézil, M. F. Bosseno, F. Le Pont, J. Lancien, [aggressiveness Anopheles gambiae relation age sex human subjects]. Bull. World Health Organ. 56, 147–154 (1978). K. . Liebman, et al., Determinants Heterogeneous Blood Feeding Patterns Aedes Aegypti Iquitos, Peru. PLoS Negl. Trop. Dis. 8, e2702 (2014).","code":""},{"path":"https://dd-harp.github.io/pf.memory/articles/FoI.html","id":"references","dir":"Articles","previous_headings":"","what":"References","title":"The Force of Infection (FoI)","text":"G. R. Port, P. F. L. Boreham, J. H. Bryan, relationship host size feeding mosquitoes Anopheles Gambiae Giles complex (Diptera: Culicidae). Bulletin Entomological Research 70, 133–144 (1980). P. Carnevale, J. L. Frézil, M. F. Bosseno, F. Le Pont, J. Lancien, [aggressiveness Anopheles gambiae relation age sex human subjects]. Bull. World Health Organ. 56, 147–154 (1978). K. . Liebman, et al., Determinants Heterogeneous Blood Feeding Patterns Aedes Aegypti Iquitos, Peru. PLoS Negl. Trop. Dis. 8, e2702 (2014).","code":""},{"path":"https://dd-harp.github.io/pf.memory/articles/Guide.html","id":"dynamics","dir":"Articles","previous_headings":"","what":"Dynamics","title":"Memory and Malaria","text":"derived mathematical formulas describe dynamics malaria infections random variables cohorts humans age (Henry JM, et al., 2024)1 R package computational companion.","code":""},{"path":"https://dd-harp.github.io/pf.memory/articles/Guide.html","id":"formulas","dir":"Articles","previous_headings":"Dynamics","what":"Formulas","title":"Memory and Malaria","text":"Let \\(z_\\tau(\\alpha,)\\) denote density infections age \\(\\alpha\\) host cohort age \\(\\) born day \\(\\tau\\). dynamics \\(z(\\alpha,)\\) described following: \\[ \\frac{\\partial z}{\\partial } + \\frac{\\partial z}{\\partial \\alpha} = - r z \\label{dzda} \\] boundary condition: \\[ \\begin{equation} z_\\tau(0,) = h_\\tau(). \\end{equation} \\] solutions given : \\[ z_\\tau(\\alpha,) = h_\\tau(-\\alpha) e^{-r \\alpha} \\] function zda computes \\(z_\\tau(\\alpha, ).\\) mean MoI given formula: \\[ m_\\tau() = \\int_0^z_\\tau(\\alpha, ) d \\alpha \\] distribution MoI Poisson (Nåsell , 1985)2 mean \\(m_\\tau().\\) function meanMoI computes \\(m_\\tau()\\) using zda true prevalence \\[ p_\\tau() = 1 - e^{-m_\\tau()} \\] function truePRa computes true prevalence using meanMoI. density function age infection (AoI) \\[ A_\\tau() \\sim f_A(\\alpha, , \\tau) = \\frac{z_\\tau(\\alpha,)}{m_\\tau()} \\] age youngest infection (AoY) defined : \\[ Y_\\tau() \\sim f_Y(\\alpha, , \\tau) = \\min_{\\zeta \\sim M_\\tau()} \\left\\{ \\alpha_i \\right\\}_{=1}^\\zeta,  \\alpha_i \\sim A_\\tau() \\] density function can expressed terms density distribution functions AoI MoI. \\[ f_Y(\\alpha; , \\tau) = f_A(\\alpha, ,\\tau) e^{-m_\\tau() F_A(\\alpha, ,\\tau)} \\frac{m_\\tau()}{p_\\tau()}. \\] distribution function AoY : \\[ F_Y() \\sim \\frac{1-e^{-m_\\tau()F_A(\\alpha, ,\\tau)}}{1-e^{-m_\\tau()}} = \\frac{1-e^{-m_\\tau()F_A(\\alpha, ,\\tau)}}{p_\\tau()} \\label{FY} \\] also developed functions compute age youngest \\(N\\) infections, called AoYN \\[ \\min_{N} \\left\\{ \\alpha_i \\right\\}_{=1}^N,  \\alpha_i \\sim A_\\tau() \\] distribution function AoYN \\[F_N(\\alpha, , t) \\sim 1- (1-F_A(\\alpha, , \\tau))^N\\] following summary table functions compute MoI, AoI, AoY, moments.","code":""},{"path":"https://dd-harp.github.io/pf.memory/articles/Guide.html","id":"parasite-densities","dir":"Articles","previous_headings":"","what":"Parasite Densities","title":"Memory and Malaria","text":"\\(\\mu(\\alpha)\\) - probability density function mean, logged parasite densities given mean \\(\\beta'(\\mu)\\) - probability density function parasite densities, given mean \\(\\mu(\\sigma)\\) - variance function mean Parasite densities distribution parasite cohorts infecting cohort humans given age. Parasite densities cohort humans given age.","code":""},{"path":"https://dd-harp.github.io/pf.memory/articles/Guide.html","id":"table","dir":"Articles","previous_headings":"Parasite Densities","what":"Table","title":"Memory and Malaria","text":"\\[\\begin{equation*} \\begin{array}{cc|c|cccccccc} \\log_{10} \\mbox{Parasite Density}&& \\xi & 0 < \\xi < \\hat b() \\\\ & (\\mbox{} \\alpha) &    && P \\sim f_P(\\xi; ,\\tau) & F_P & \\left<P\\right>\\\\ & (\\mbox{} ) &    & & B \\sim f_B(\\xi; ,\\tau) & F_B & \\left<B\\right>\\\\ \\end{array} \\end{equation*}\\]","code":""},{"path":"https://dd-harp.github.io/pf.memory/articles/Guide.html","id":"detection","dir":"Articles","previous_headings":"","what":"Detection","title":"Memory and Malaria","text":"\\[\\begin{equation*} \\begin{array}{cc|c|cccccccc} \\mbox{Detection} & &\\hat p  & 0 \\leq \\hat p \\leq 1 &D \\sim f_C(0,\\xi)& \\hat p& \\\\  \\hline \\log_{10} \\mbox{Parasite Counts} & &\\hat \\xi & 0 < \\hat \\xi < \\xi &C \\sim f_C (\\hat \\xi; \\xi)&F_C& \\left<C\\right>\\\\  \\hline & \\mbox{Est PR}   & p &  0 \\leq p \\leq 1  &&& p_\\tau()\\\\ &\\mbox{MoI}  &\\zeta  & \\zeta \\{0,1,2,\\ldots} & M_\\tau() \\sim f_M(\\zeta; , \\tau) & & m_\\tau() \\\\   &\\mbox{Est MoI}  &\\hat \\zeta  & \\hat \\zeta \\{0,1,2,\\ldots, \\zeta} & \\hat M_\\tau() \\sim f_{\\hat M}(\\zeta; , \\tau) & & \\hat m_\\tau() \\\\  \\hline \\end{array} \\end{equation*}\\]","code":""},{"path":"https://dd-harp.github.io/pf.memory/articles/Hybrid.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Hybrid Models","text":"following, review hybrid models MoI, make brief observation prevalence, derive hybrid variables mean higher order moments AoI.","code":""},{"path":"https://dd-harp.github.io/pf.memory/articles/Hybrid.html","id":"moi","dir":"Articles","previous_headings":"","what":"MoI","title":"Hybrid Models","text":"random variable \\(M\\) describes distribution MoI population, follows Poisson. , provide numerical demonstration novel computational approach equivalent queuing model \\(M/M/\\infty\\), also equivalent hybrid models multiplicity infection (Nåsell, . 1985)1:","code":""},{"path":"https://dd-harp.github.io/pf.memory/articles/Hybrid.html","id":"mminfty","dir":"Articles","previous_headings":"MoI","what":"\\(M/M/\\infty\\)","title":"Hybrid Models","text":"Elsewhere, dynamics MoI described using queuing model \\(M/M/\\infty\\). MoI increases FoI, parasite can clear rate, \\(r\\). following diagram changes fraction population MoI \\(=\\), denoted \\(\\zeta_i\\), change host cohort force infection \\(h_\\tau(),\\) clearance. \\[\\begin{equation} \\begin{array}{ccccccccc} \\zeta_0 &  {h\\atop \\longrightarrow} \\atop {\\longleftarrow \\atop r} & \\zeta_1 & {h\\atop \\longrightarrow} \\atop {\\longleftarrow \\atop {2r}} & \\zeta_2 & {h \\atop \\longrightarrow} \\atop {\\longleftarrow \\atop {3r}} & \\zeta_3 & {h \\atop \\longrightarrow} \\atop {\\longleftarrow \\atop {4r}}& \\ldots \\end{array} \\end{equation}\\] master equations \\(M/M/\\infty\\) :\\[\\begin{equation} \\begin{array}{rl} \\frac{d\\zeta_0}{da} &= -h_\\tau() \\zeta_0 + r \\zeta_1   \\\\ \\frac{d\\zeta_i}{da} &= -\\left( h_\\tau\\left(\\right) + r \\right) \\zeta_i + h_\\tau\\left(\\right) \\zeta_{-1} + r\\left(+1\\right) \\zeta_{+1}   \\\\ \\end{array} \\end{equation}\\] master equations describe infinite set equations, find numerical solutions, must solve finite set equations. need compute maximum MoI vanishingly small portion distribution. constant \\(h\\), steady state distribution \\(\\zeta\\) Poisson mean \\(h/r.\\) set \\(N = \\max(4h/r,24),\\) tail negligible. , set range \\(1 \\pm 10^{-7}\\) plot portion distribution covered.  must define trace FoI function.  verify works, compute MoI day first three years life. peek distribution MoI = \\(1, \\ldots, 5\\) day 500:","code":"m = seq(0.1, 24) N = pmax(24, 4*m) plot(m, ppois(N,m), type = \"l\", ylim = c(1-1e-07,1+1e-07)) solveMMinfty(3/365, foiP3) -> out"},{"path":"https://dd-harp.github.io/pf.memory/articles/Hybrid.html","id":"nåsells-hybrid-model","dir":"Articles","previous_headings":"MoI","what":"Nåsell’s Hybrid Model","title":"Hybrid Models","text":"can also solve hybrid equation get mean MoI (Nåsell, . 1985)\\(^1\\): \\[\\frac{dm}{da} = h - rm\\] unction dmda computes derivative, can solve hybrid equation using solve_dm plot output:","code":"solve_dm(3/365, foiP3) -> mt  plot(mt$time, mt$m, type = \"l\",       xlab = \"Age (in Days)\", ylab = expression(m[tau](a)))"},{"path":"https://dd-harp.github.io/pf.memory/articles/Hybrid.html","id":"numerical-verification","dir":"Articles","previous_headings":"MoI","what":"Numerical Verification","title":"Hybrid Models","text":"presented three ways computing mean MoI using cohort ages arbitrary function \\(h_\\tau()\\): Using meanMoI integrates zda: \\[\\int_0^z_\\tau(\\alpha, ) d\\alpha\\] solving queuing model \\(M/M/\\infty\\), compartmental model tracks full distribution MoI, competing mean: solving hybrid model tracking mean MoI. following plots three graph using different colors different widths, colors, patterns:  maximum errors order \\(1e-07\\) developed hybrid model can use compute mean higher order moments age infection (AoI). related vignette (AoI), define AoI random variable develop functions compute moments. , develop notation moments:","code":"aa = 0:1825 v1 = meanMoI(aa, foiP3, hhat=5/365) v2 = solveMMinfty(5/365, foiP3, Amax=1825)$m v3 = solve_dm(5/365, foiP3, Amax=1825)[,2] par(mfrow = c(2,2))  plot(aa, v1, type = \"l\", col = \"red\", lwd=4,       xlab = \"Age (in Days)\",       ylab = expression(m[tau](a)),       main = \"meanMoI\")  plot(aa, v2, type = \"l\", lwd=2,       xlab = \"Age (in Days)\",       ylab = expression(m[tau](a)),       main = \"solveMMinfty\") lines(aa, v2, type = \"l\", col = \"yellow\", lwd=2, lty=2)  plot(aa, v3, type = \"l\", col = \"darkblue\", lwd=1,       xlab = \"Age (in Days)\",       ylab = expression(m[tau](a)),       main = \"solve_dm\")  plot(aa, v1, type = \"l\", col = \"red\", lwd=4,       xlab = \"Age (in Days)\",       ylab = expression(m[tau](a)),       main = \"All Three\") lines(aa, v2, type = \"l\", col = \"yellow\", lwd = 2) lines(aa, v3, type = \"l\", col = \"darkblue\", lwd = 2, lty =2) c(max(abs(v1-v2)), max(abs(v2-v3)), max(abs(v1-v3))) ## [1] 2.511903e-09 1.785516e-13 2.511903e-09"},{"path":"https://dd-harp.github.io/pf.memory/articles/Hybrid.html","id":"prevalence","dir":"Articles","previous_headings":"","what":"Prevalence","title":"Hybrid Models","text":"George Maccdonald published model superinfection 19502. presenting model, Macdonald trying solve problem: super-infection possible, long take person clear parasites become uninfected ? Macdonald proposed solution, problem mathematical formulation (essay Paul Fine, 1975, recommended reading)3: model Macdonald described didn’t match function used. model formulated part Garki project (Dietz K, et al., 1974)4, model allowed superinfection proposed useful approximating model. One solution came taking hybrid modeling approach (Nåsell , 1985)5, just discussed. Nåsell showed distribution MoI converge Poisson distribution: \\[M(t) \\sim f_M(\\zeta; m) = \\mbox{Pois}(m(t))\\] Since \\(m\\) mean Poisson, prevalence infection complement zero term: \\[p(t) = 1-\\mbox{Pois}(\\zeta =0; m(t)) = 1 - e^{-m(t)}\\] , nevertheless, sometimes useful know clearance rate, transition MoI = 1 MoI=0. Clearance infected class can occur person infected MoI one, infection clears: \\[ R(m) = r \\frac{\\mbox{Pr}(\\zeta=1; m(t))}{\\mbox{Pr}(\\zeta>0; m(t))} = r \\frac{m}{e^m - 1} \\] change prevalence thus described equation: \\[ \\frac{dp}{dt} = h(1-p)-R(m)p \\] interesting, solves problem modeling clearance superinfection, equation depends \\(m\\). Since can compute \\(p(t)\\) directly \\(m(t)\\), equation redundant. Code exists pf.memory compute prevalence three ways: Using function truePRa Using hybrid equations solve_dpda hybrid model solve_dm \\(p(t)= 1 - exp(-m(t))\\)","code":""},{"path":"https://dd-harp.github.io/pf.memory/articles/Hybrid.html","id":"aoi---hybrid-variables","dir":"Articles","previous_headings":"","what":"AoI - Hybrid Variables","title":"Hybrid Models","text":"Let \\(x = \\left< \\right>;\\) x first moment AoI cohort age \\(\\), conditioned history exposure, given function \\(h\\). longer form: \\[x_\\tau(; h) = \\left< A_\\tau(; h) \\right> = \\int_0^\\infty \\alpha \\frac{z_\\tau(\\alpha, ; h_\\tau())} {m_\\tau(;h_\\tau())}\\] , show : \\[ \\frac{\\textstyle{dx}}{\\textstyle{da}} = 1- \\frac{\\textstyle{h}}{\\textstyle{m}} x   \\] Similarly, let \\(x_{[n]} = \\left< ^n \\right>\\) denote higher order moments random variable \\(\\). longer form: \\[x_{n}(, \\tau; h) = \\int_0^\\infty \\alpha^n \\frac{z_\\tau(\\alpha, ; h_\\tau())} {m_\\tau(;h_\\tau())}\\] show higher order moments can computed recursively: \\[ \\frac{\\textstyle{dx_{[n]}}}{\\textstyle{da}} = nx_{[n-1]} -     \\frac{\\textstyle{h}}{\\textstyle{m}} x_{[n]} \\] following, first demonstrate hybrid equations give answers direct computation moments.","code":""},{"path":"https://dd-harp.github.io/pf.memory/articles/Hybrid.html","id":"solving","dir":"Articles","previous_headings":"AoI - Hybrid Variables","what":"Solving","title":"Hybrid Models","text":"function solve_dAoI computes first three moments AoI default. plot \\(n^{th}\\) root first three moments.","code":"par(mar = c(7, 4, 2, 2)) solve_dAoI(5/365, foiP3) -> mt  plot(mt$time, mt$xn1, type = \"l\", xlab = \"Age (in Days)\", ylab = expression(list(x, sqrt(x[paste(\"[2]\")]), sqrt(x[paste(\"[3]\")], 3))), ylim = range(mt$xn3^(1/3)))  lines(mt$time, mt$xn2^(1/2), col = \"purple\") lines(mt$time, mt$xn3^(1/3), col = \"darkgreen\")"},{"path":"https://dd-harp.github.io/pf.memory/articles/Hybrid.html","id":"numerical-verification-1","dir":"Articles","previous_headings":"AoI - Hybrid Variables","what":"Numerical Verification","title":"Hybrid Models","text":"solving hybrid model variables track moments, using equations derived :","code":"aa = seq(5, 5*365, by = 5)  moment1 = momentAoI(aa, foiP3) moment2 = momentAoI(aa, foiP3, n=2) moment3 = momentAoI(aa, foiP3, n=3) solve_dAoI(5/365, foiP3, Amax = 5*365, dt=5) -> mt par(mfrow = c(2,2), mar = c(7, 4, 2, 2)) # Top Left plot(mt$time, mt$xn1, type = \"l\", xlab = \"Age (in Days)\", ylab = expression(x), lwd=3)  lines(aa, moment1, col = \"yellow\", lwd=2, lty=2)  # Top Right  plot(mt$time, mt$xn2, type = \"l\", xlab = \"Age (in Days)\", ylab = expression(x[paste(\"[2]\")]), lwd=3, col = \"purple\")  lines(aa, moment2, col = \"yellow\", lwd=2, lty=2) plot(mt$time, mt$xn3, type = \"l\", lwd=3, col = \"darkgreen\",      xlab = \"Age (in Days)\", ylab = expression(x[paste(\"[3]\")])) lines(aa, moment3, col = \"yellow\", lwd=2, lty=2) par(mar = c(7, 4, 2, 2)) solve_dAoI(5/365, foiP3) -> mt  plot(mt$time, mt$xn1, type = \"l\", xlab = \"Age (in Days)\", ylab = expression(list(x, sqrt(x[paste(\"[2]\")]), sqrt(x[paste(\"[3]\")], 3))), lwd=3, ylim = range(mt$xn3^(1/3)))  lines(mt$time, mt$xn2^(1/2), col = \"purple\", lwd=3) lines(mt$time, mt$xn3^(1/3), col = \"darkgreen\", lwd=3)  lines(aa, moment1, col = \"yellow\", lwd=2, lty=2) lines(aa, moment2^(1/2), col = \"yellow\", lwd=2, lty=2) lines(aa, moment3^(1/3), col = \"yellow\", lwd=2, lty=2)"},{"path":"https://dd-harp.github.io/pf.memory/articles/Hybrid.html","id":"aoy---hybrid-variables","dir":"Articles","previous_headings":"","what":"AoY - Hybrid Variables","title":"Hybrid Models","text":"Let \\(y\\) denote first moment AoY. \\[ y_\\tau() = \\int_0^\\alpha \\; f_Y(\\alpha, , \\tau) \\; d\\alpha \\] differential equation \\(y_\\tau()\\) : \\[ \\frac{dy}{da} = 1 - \\frac{h}{p} y + F(r,m) \\frac{x}{p} \\] verify, can compute moment directly. function solve_dAoYda gives solutions: moments can computed directly using momentAoY following plots first moment computed ways:  errors minor. 5 years, difference two methods less two days.","code":"solve_dAoYda(5/365, foiP3, Amax=5*365, dt=5, n=5) -> mt moment1y = momentAoY(aa, foiP3, hhat=5/365)"},{"path":"https://dd-harp.github.io/pf.memory/articles/MoI.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Multiplicity of Infection","text":"random variable \\(M\\) describes distribution MoI population, follows Poisson. , provide numerical demonstration novel computational approach equivalent queuing model \\(M/M/\\infty\\), also equivalent hybrid models multiplicity infection (Nåsell, . 1985)1:","code":""},{"path":"https://dd-harp.github.io/pf.memory/articles/MoI.html","id":"mminfty","dir":"Articles","previous_headings":"","what":"\\(M/M/\\infty\\)","title":"Multiplicity of Infection","text":"Elsewhere, dynamics MoI described using queuing model \\(M/M/\\infty\\). MoI increases FoI, parasite can clear rate, \\(r\\). following diagram changes fraction population MoI \\(=\\), denoted \\(\\zeta_i\\), change host cohort force infection \\(h_\\tau(),\\) clearance. \\[\\begin{equation} \\begin{array}{ccccccccc} \\zeta_0 &  {h\\atop \\longrightarrow} \\atop {\\longleftarrow \\atop r} & \\zeta_1 & {h\\atop \\longrightarrow} \\atop {\\longleftarrow \\atop {2r}} & \\zeta_2 & {h \\atop \\longrightarrow} \\atop {\\longleftarrow \\atop {3r}} & \\zeta_3 & {h \\atop \\longrightarrow} \\atop {\\longleftarrow \\atop {4r}}& \\ldots \\end{array} \\end{equation}\\] master equations \\(M/M/\\infty\\) :\\[\\begin{equation} \\begin{array}{rl} \\frac{d\\zeta_0}{da} &= -h_\\tau() \\zeta_0 + r \\zeta_1   \\\\ \\frac{d\\zeta_i}{da} &= -\\left( h_\\tau\\left(\\right) + r \\right) \\zeta_i + h_\\tau\\left(\\right) \\zeta_{-1} + r\\left(+1\\right) \\zeta_{+1}   \\\\ \\end{array} \\end{equation}\\] master equations describe infinite set equations, find numerical solutions, must solve finite set equations. need compute maximum MoI vanishingly small portion distribution. constant \\(h\\), steady state distribution \\(\\zeta\\) Poisson mean \\(h/r.\\) set \\(N = \\max(4h/r,24),\\) tail negligible. , set range \\(1 \\pm 10^{-7}\\) plot portion distribution covered.  must define trace FoI function.  verify works, compute MoI day first three years life. peek distribution MoI = \\(1, \\ldots, 5\\) day 500:","code":"m = seq(0.1, 24) N = pmax(24, 4*m) plot(m, ppois(N,m), type = \"l\", ylim = c(1-1e-07,1+1e-07)) solveMMinfty(3/365, foiP3) -> out"},{"path":"https://dd-harp.github.io/pf.memory/articles/MoI.html","id":"hybrid-model","dir":"Articles","previous_headings":"","what":"Hybrid Model","title":"Multiplicity of Infection","text":"can also solve hybrid equation get mean MoI (Nåsell, . 1985)\\(^1\\): \\[\\frac{dm}{da} = h - rm\\] unction dmda computes derivative, can solve hybrid equation using solve_dm plot output:","code":"solve_dm(3/365, foiP3) -> mt  plot(mt$time, mt$m, type = \"l\",       xlab = \"Age (in Days)\", ylab = expression(m[tau](a)))"},{"path":"https://dd-harp.github.io/pf.memory/articles/MoI.html","id":"verification","dir":"Articles","previous_headings":"","what":"Verification","title":"Multiplicity of Infection","text":"presented three ways computing mean MoI using cohort ages arbitrary function \\(h_\\tau()\\): Using meanMoI integrates zda: \\[\\int_0^z_\\tau(\\alpha, ) d\\alpha\\] solving queuing model \\(M/M/\\infty\\), compartmental model tracks full distribution MoI, competing mean: solving hybrid model tracking mean MoI. following plots three graph using different colors different widths, colors, patterns:  maximum errors order \\(1e-07\\)","code":"aa = 0:1825 v1 = meanMoI(aa, foiP3, hhat=5/365) v2 = solveMMinfty(5/365, foiP3, Tmax=1825)$m v3 = solve_dm(5/365, foiP3, Tmax=1825)[,2] par(mfrow = c(2,2))  plot(aa, v1, type = \"l\", col = \"red\", lwd=4,       xlab = \"Age (in Days)\",       ylab = expression(m[tau](a)),       main = \"meanMoI\")  plot(aa, v2, type = \"l\", lwd=2,       xlab = \"Age (in Days)\",       ylab = expression(m[tau](a)),       main = \"solveMMinfty\") lines(aa, v2, type = \"l\", col = \"yellow\", lwd=2, lty=2)  plot(aa, v3, type = \"l\", col = \"darkblue\", lwd=1,       xlab = \"Age (in Days)\",       ylab = expression(m[tau](a)),       main = \"solve_dm\")  plot(aa, v1, type = \"l\", col = \"red\", lwd=4,       xlab = \"Age (in Days)\",       ylab = expression(m[tau](a)),       main = \"All Three\") lines(aa, v2, type = \"l\", col = \"yellow\", lwd = 2) lines(aa, v3, type = \"l\", col = \"darkblue\", lwd = 2, lty =2) c(max(abs(v1-v2)), max(abs(v2-v3)), max(abs(v1-v3))) ## [1] 1.833689e-07 9.797276e-08 1.833689e-07"},{"path":"https://dd-harp.github.io/pf.memory/articles/Parasite_Densities.html","id":"expected-logged-densities","dir":"Articles","previous_headings":"","what":"Expected Logged Densities","title":"Parasite Density Distributions","text":"pf.memory, S3 function family developed model relationship age infection (AoI) parasite infection, \\(\\alpha\\), mean, \\(\\mu(\\alpha).\\)","code":""},{"path":"https://dd-harp.github.io/pf.memory/articles/Parasite_Densities.html","id":"alpha2mu-base","dir":"Articles","previous_headings":"Expected Logged Densities","what":"alpha2mu.base","title":"Parasite Density Distributions","text":"function alpha2mu.base following form: \\[\\begin{equation} F_\\mu(\\alpha) = \\begin{cases}     \\text{NA} \\ & \\mbox{} 0 \\leq \\alpha < 7 \\\\[10pt]       l + (b - l)  \\frac{{\\textstyle \\alpha}}{{\\delta}}   & \\mbox{} 7 \\leq \\alpha \\leq \\delta  \\\\[10pt]      l + (b - l) e^{-s_\\alpha (\\alpha-\\delta)}   & \\mbox{} \\alpha \\geq \\delta\\\\   \\end{cases} \\label{mualpha} \\end{equation}\\]","code":""},{"path":"https://dd-harp.github.io/pf.memory/articles/Parasite_Densities.html","id":"the-function-alpha2mu-chronic-has-the-following-form","dir":"Articles","previous_headings":"Expected Logged Densities","what":"The function alpha2mu.chronic has the following form:","title":"Parasite Density Distributions","text":"\\[\\begin{equation} F_\\mu(\\alpha) = l + (b - l) e^{-s_\\alpha (\\alpha-\\delta)}    \\end{equation}\\] pf.memory, functions set parameters case, -writable defaults: plot two functions : default parameters (black), parameters (dark blue): ## Parasite Density Distributions developed function family compute parasite densities function mean logged parasite densities, \\(\\mu\\)","code":"base_pars = par_Fmu_base() base_pars1 = par_Fmu_base(tildeb=11, Sa=0.0045) chronic_pars = par_Fmu_chronic() aalpha = 7:366 mu_alpha =  alpha2mu(aalpha, 0, base_pars) mu_alpha1 =  alpha2mu(aalpha, 0, base_pars1) mu_alpha2 =  alpha2mu(aalpha, 0, chronic_pars) parD = par_mu2dens_beta()  d_mu2density(9, 9, parD) ## [1] 0.4593359 par(mfrow = c(2,2)) xx = seq(0, 13, by=0.1) plot(xx, d_mu2density(xx, 9, parD), type = \"l\",       xlab = expression(xi), ylab = \"d_mu2density\", main = \"d_mu2density\") lines(xx, d_mu2density(xx, 7,  parD), col = \"darkred\") pp = seq(0,13, by = 0.01) plot(pp, p_mu2density(pp, 9,  parD), type = \"l\",       xlab = expression(xi), ylab = \"p_mu2density\", main = \"p_mu2density\") lines(xx, p_mu2density(xx, 7, parD), col = \"darkred\") hist(r_mu2density(1000, 9, parD), xlab = expression(xi),       main = \"r_mu2density\", xlim = c(0,13)) qq = seq(0.01,.99, length.out=100) plot(qq, q_mu2density(qq, 9,  parD), type = \"l\",       xlab = expression(xi), ylab = \"q_mu2density\", main = \"q_mu2density\")"},{"path":"https://dd-harp.github.io/pf.memory/articles/Parasite_Densities.html","id":"simple-infections","dir":"Articles","previous_headings":"","what":"Simple Infections","title":"Parasite Density Distributions","text":"first look density parasites simple infections – MoI = 1. compute anything, need function model exposure, FoI function age, \\(h_\\tau()\\). Notably, function accepts birth date, \\(\\tau\\) argument, can used look cohorts different birth dates. , show FoI function age two cohorts born six months apart.  one cohorts (black line), plotted density parasite cohorts. Notably, age cohorts representing infections occurred \\(\\alpha\\) days ago, \\(x-\\)axis looking past:  Now want understand parasite densities cohort humans. compute full probability distribution function cohort 5-year olds, use bits information: Mean logged parasite densities parasite infection age, \\(\\mu(\\alpha)\\) density cohorts age, \\(A_\\tau()\\)  parasite age, can plot probability density function. , show probability density function parasite infection age \\(60\\) days:  Now, parasite densities simple infections given distribution mean logged parasite densities. compute full distribution, create mesh \\(\\xi\\): every age infection, \\(\\alpha\\) compute expected parasite densities \\(\\mu(\\alpha)\\) compute full parasite density distribution, multiplied density parasites age \\(\\alpha\\): \\[\\phi(\\alpha) = P(\\mu(\\alpha))\\; f_A(\\alpha, )\\] add \\(\\phi(\\alpha)\\) appropriate bin, defined mesh \\(\\xi\\). function dPdensity computes parasite distributions function host age, given function describing history exposure.  can check ensure distribution function integrates 1:","code":"mu_alpha =  alpha2mu(a5years, 0, base_pars) dAoI(a5years, 5*365, foiP3) -> dalpha alpha = 60 fA = dAoI(alpha, 5*365, foiP3) Pmu = fA*d_alpha2density(xx, alpha, 5*365) Pa = d_Pdensity(xx, 5*365, foiP3) integrate(d_Pdensity, 0, 13, a=5*365, FoIpar=foiP3)$value ## [1] 1.000014"},{"path":[]},{"path":"https://dd-harp.github.io/pf.memory/articles/Simple_Infections.html","id":"mean-logged-parasite-densities-mualpha","dir":"Articles","previous_headings":"","what":"Mean, logged parasite densities, \\(\\mu(\\alpha)\\)","title":"Parasite Densities in Simple Infections","text":"pf.memory, S3 function family developed model relationship age infection (AoI) parasite infection, \\(\\alpha\\), mean, \\(\\mu(\\alpha).\\) function alpha2mu.base following form: \\[\\begin{equation} \\mu(\\alpha) = \\begin{cases}     \\text{NA} \\ & \\mbox{} 0 \\leq \\alpha < 7 \\\\[10pt] %      l +  (b - l)  \\frac{{\\textstyle \\alpha}}{{\\textstyle D}}   & \\mbox{} 7 \\leq \\alpha \\leq D  \\\\[10pt]       l + (b - l)  \\frac{{\\textstyle \\alpha}}{{\\textstyle \\delta}}   & \\mbox{} 7 \\leq \\alpha \\leq \\delta  \\\\[10pt]      l + (b - l) e^{-s_\\alpha (\\alpha-\\delta)}   & \\mbox{} \\alpha \\geq \\delta\\\\   \\end{cases} \\label{mualpha} \\end{equation}\\] pf.memory, functions set parameters case, -writable defaults: plot two functions : default parameters (black), parameters (dark blue):","code":"base_pars = par_alpha2mu_base() base_pars1 = par_alpha2mu_base(tildeb=11, Sa=0.0045) aalpha = 7:366 mu_alpha =  alpha2mu(aalpha, 0, base_pars) mu_alpha1 =  alpha2mu(aalpha, 0, base_pars1)"},{"path":"https://dd-harp.github.io/pf.memory/articles/Simple_Infections.html","id":"p_mu","dir":"Articles","previous_headings":"","what":"\\(P_\\mu\\)","title":"Parasite Densities in Simple Infections","text":"developed function family compute parasite densities function mean logged parasite densities, \\(\\mu\\)","code":"par(mfrow = c(2,2)) xx = seq(0, 13, by=0.1) plot(xx, dDensityPmu(xx,9), type = \"l\", xlab = expression(x), ylab = \"dDensityPmu\", main = \"dDensityPmu\") lines(xx, dDensityPmu(xx, 7), col = \"darkred\") pp = seq(0,13, by = 0.01) plot(pp, pDensityPmu(pp,9), type = \"l\", xlab = expression(x), ylab = \"pDensityPmu\", main = \"pDensityPmu\") lines(xx, pDensityPmu(xx, 7), col = \"darkred\") hist(rDensityPmu(1000, 9), main = \"rDensityPmu\", xlim = c(0,13)) qq = seq(0.01,.99, length.out=100) plot(qq, qDensityPmu(qq,9), type = \"l\", xlab = expression(x), ylab = \"qDensityPmu\", main = \"qDensityPmu\")"},{"path":"https://dd-harp.github.io/pf.memory/articles/Simple_Infections.html","id":"pxi-alpha","dir":"Articles","previous_headings":"","what":"\\(P(\\xi, \\alpha)\\)","title":"Parasite Densities in Simple Infections","text":"must specify function model exposure:  age five, distribution age infection looks like :  compute parasite density distributions, need construct mesh \\(\\xi.\\) function dDensityPa computes parasite distributions function host age, given function describing history exposure. Now, parasite densities simple infections given distribution mean logged parasite densities.","code":"meshX= seq(0, 13, by=.1) Pmu = dDensityPa(meshX,5*365, foiP3)"},{"path":"https://dd-harp.github.io/pf.memory/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"David L. Smith. Author, maintainer. John M. Henry. Author.","code":""},{"path":"https://dd-harp.github.io/pf.memory/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Smith D, Henry J (2024). pf.memory: Probabilistic Approaches Malaria Parasite Infections. R package version 0.1.0, https://dd-harp.github.io/pf.memory/.","code":"@Manual{,   title = {pf.memory: Probabilistic Approaches to Malaria Parasite Infections},   author = {David L. Smith and John M. Henry},   year = {2024},   note = {R package version 0.1.0},   url = {https://dd-harp.github.io/pf.memory/}, }"},{"path":"https://dd-harp.github.io/pf.memory/index.html","id":"pfmemory----the-age-of-infection-immunity--malaria-epidemiology","dir":"","previous_headings":"","what":"Probabilistic Approaches to Malaria Parasite Infections","title":"Probabilistic Approaches to Malaria Parasite Infections","text":"software set computational algorithms implements synthetic approach malaria epidemiology, defined narrowly include exposure bites infective mosquitoes, dynamics infection (including superinfection). epidemiology Plasmodium falciparum malaria presents unique set challenges due complex dynamics infection, immunity, disease infectiousness well treatment chemo-protection, diagnostics detection. Malaria can measured dozen different ways, difficult present simple synthesis malaria infection disease terms metrics commonly used research clinical surveillance. important metric Plasmodium falciparum parasite rate, PfPR, defined average prevalence malaria taken cross-sectional survey. Another metric, often measured covariate research studies, parasite count, number parasites blood slide field counted light microscopist. old data set, collected malariotherapy, parasite counts fluctuated substantially time course infection, strongly statistically correlated age infection AoI (Henry JM, et al., 2022)1. malaria, PfPR several old studies characterstic shape plotted age. patterns also differ diagnostic method, season, sex, location. Parasite densities used correlate disease. many interacting factors, challenge develop model deal everything. One approach studying malaria infection develop mechanistic models dynamics malaria infection within single host. prominent models type OpenMalaria eMod, several others. computational models made possible develope comprehensive individual-based simulation models, IBMs, malaria policy. approaches able replicate patterns, outputs models usually just complex data collected field studies. synthesis malaria epidemiology proven elusive. present computational algorithms support probabilistic approach malaria epidemiology. start semi-Markovian model malaria exposure infection, whose states represented random variables describe multiplicity infection (MoI) host age infection (AoI). Assuming parasite densities , least statistically, predicted AoI, can compute probability distribution functions describing parasite densities, parasite counts, detection individual chosen random population. , present model parasite detection parasite counts. approach extended predict disease, immunity, treatment anti-malarial drugs, brief period chemo-protection. probabilistic approach highly realistic descriptive, goal synthesis. synthesis involves steps: derive variables can track mean MoI, mean AoI moments, probability detection. Hybrid models MoI already exist, show approach can extended systems differential equations track mean higher order moments distribution AoI. new random variable describing age youngest infection (AoY). show variable serves basis computing parasite density distributions complex infections. derive hybrid model variable approximates mean AoY. demonstrate simple system ordinary differential equations can used place probabilistic models compute values research metrics. put another way, can reduce behavior highly complex probabilistic systems simple system equations high degree accuracy. computational conceptual simplicity hybrid models simplicity compartmental models stochastic individual-based models, supporting probabilistic framework, provide sound basis synthesis observational malaria epidemiology.","code":""},{"path":[]},{"path":"https://dd-harp.github.io/pf.memory/reference/Bda.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute \\(B_\\tau(a | h)\\) — Bda","title":"Compute \\(B_\\tau(a | h)\\) — Bda","text":"$$f_B(\\xi; , \\tau |h) = \\log_{10} \\left( \\sum_{M_\\tau(|h)>0} 10^{P_\\tau(|h)}\\right)$$","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/Bda.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute \\(B_\\tau(a | h)\\) — Bda","text":"","code":"Bda(   meshX,   a,   FoIpar,   tau = 0,   hhat = 1,   r = 1/200,   par_RBC = par_lRBC_static(),   Fmu_par = Fmu_par_base(),   mu_par = mu_par_beta(),   pWda = par_Wda_none() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/Bda.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute \\(B_\\tau(a | h)\\) — Bda","text":"meshX mesh parasite densities host cohort age FoIpar parameters define FoI function tau cohort birthday hhat local scaling parameter FoI r clearance rate simple infection par_RBC parameters compute log10RBC Fmu_par parameters compute alpha2mu mu_par parameters compute d_mu2density pWda parameters dispatch Wda","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/Bda.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute \\(B_\\tau(a | h)\\) — Bda","text":"numeric vector length meshX","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/Bdensity.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute \\(B_\\tau(a | h)\\) — Bdensity","title":"Compute \\(B_\\tau(a | h)\\) — Bdensity","text":"function first computes PDF simple infections, d_Pdensity, computes CDF full distribution, summed MoI = 1 large number using convolutions.","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/Bdensity.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute \\(B_\\tau(a | h)\\) — Bdensity","text":"","code":"Bdensity(   meshX,   a,   FoIpar,   tau = 0,   hhat = 1,   r = 1/200,   RBC_par = par_lRBC_static(),   Fmu_par = par_Fmu_base(),   mu_par = par_mu2dens_beta(),   pWda = par_Wda_none() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/Bdensity.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute \\(B_\\tau(a | h)\\) — Bdensity","text":"meshX mesh parasite densities host cohort age FoIpar parameters define FoI function tau cohort birthday hhat local scaling parameter FoI r clearance rate simple infection RBC_par parameters compute log10RBC Fmu_par parameters compute alpha2mu mu_par parameters compute d_mu2density pWda parameters dispatch Wda","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/Bdensity.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute \\(B_\\tau(a | h)\\) — Bdensity","text":"numeric vector length meshX","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/Detect.html","id":null,"dir":"Reference","previous_headings":"","what":"Detection of infection given parasitemia — Detect","title":"Detection of infection given parasitemia — Detect","text":"Detection infection given parasitemia","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/Detect.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Detection of infection given parasitemia — Detect","text":"","code":"Detect(xi, a = 0, Cpar = par_nbCounts())"},{"path":"https://dd-harp.github.io/pf.memory/reference/Detect.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Detection of infection given parasitemia — Detect","text":"xi mean \\(\\log_{10}\\) parasite densities host cohort age Cpar parameters define detection function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/Detect.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Detection of infection given parasitemia — Detect","text":"binary detection result","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/Detect.nb.html","id":null,"dir":"Reference","previous_headings":"","what":"Detection of infection given parasitemia — Detect.nb","title":"Detection of infection given parasitemia — Detect.nb","text":"Detection infection given parasitemia","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/Detect.nb.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Detection of infection given parasitemia — Detect.nb","text":"","code":"# S3 method for nb Detect(xi, a = 0, Cpar = par_nbCounts())"},{"path":"https://dd-harp.github.io/pf.memory/reference/Detect.nb.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Detection of infection given parasitemia — Detect.nb","text":"xi mean log10 parasite densities host cohort age Cpar parameters define detection function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/Detect.nb.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Detection of infection given parasitemia — Detect.nb","text":"binary detection result","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/Detect.pois.html","id":null,"dir":"Reference","previous_headings":"","what":"Detection of infection given parasitemia — Detect.pois","title":"Detection of infection given parasitemia — Detect.pois","text":"Detection infection given parasitemia","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/Detect.pois.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Detection of infection given parasitemia — Detect.pois","text":"","code":"# S3 method for pois Detect(xi, a = 0, Cpar = par_poisCounts())"},{"path":"https://dd-harp.github.io/pf.memory/reference/Detect.pois.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Detection of infection given parasitemia — Detect.pois","text":"xi mean log10 parasite densities host cohort age Cpar parameters define detection function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/Detect.pois.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Detection of infection given parasitemia — Detect.pois","text":"binary detection result","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/DetectBda.html","id":null,"dir":"Reference","previous_headings":"","what":"Detection of infection given parasitemia — DetectBda","title":"Detection of infection given parasitemia — DetectBda","text":"Detection infection given parasitemia","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/DetectBda.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Detection of infection given parasitemia — DetectBda","text":"","code":"DetectBda(   a,   FoIpar,   dx = 0.1,   tau = 0,   hhat = 1,   r = 1/200,   par_RBC = par_lRBC_static(),   Fmu_par = par_Fmu_base(),   par_mu2dens = par_mu2dens_beta(),   pWda = par_Wda_none(),   pC = par_nbCounts() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/DetectBda.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Detection of infection given parasitemia — DetectBda","text":"host cohort age FoIpar parameters define FoI function dx width mesh tau cohort birthday hhat local scaling parameter FoI r clearance rate simple infection par_RBC parameters compute log10RBC Fmu_par parameters compute alpha2mu par_mu2dens parameters compute d_mu2density pWda parameters dispatch Wda pC parameters define detection function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/DetectBda.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Detection of infection given parasitemia — DetectBda","text":"binary detection result","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/DetectPM.html","id":null,"dir":"Reference","previous_headings":"","what":"Detection of infection given parasitemia — DetectPM","title":"Detection of infection given parasitemia — DetectPM","text":"Detection infection given parasitemia","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/DetectPM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Detection of infection given parasitemia — DetectPM","text":"","code":"DetectPM(   a,   FoIpar,   tau = 0,   hhat = 1,   r = 1/200,   par_RBC = par_lRBC_static(),   Fmu_par = par_Fmu_base(),   par_mu2dens = par_mu2dens_beta(),   pWda = par_Wda_none(),   pC = par_nbCounts() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/DetectPM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Detection of infection given parasitemia — DetectPM","text":"host cohort age FoIpar parameters define FoI function tau cohort birthday hhat local scaling parameter FoI r clearance rate simple infection par_RBC parameters compute log10RBC Fmu_par parameters compute alpha2mu par_mu2dens parameters compute d_mu2density pWda parameters dispatch Wda pC parameters define detection function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/DetectPM.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Detection of infection given parasitemia — DetectPM","text":"binary detection result","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/DetectPa.html","id":null,"dir":"Reference","previous_headings":"","what":"Detection of infection given parasitemia — DetectPa","title":"Detection of infection given parasitemia — DetectPa","text":"Detection infection given parasitemia","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/DetectPa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Detection of infection given parasitemia — DetectPa","text":"","code":"DetectPa(   a,   FoIpar,   tau = 0,   hhat = 1,   r = 1/200,   par_RBC = par_lRBC_static(),   Fmu_par = par_Fmu_base(),   par_mu2dens = par_mu2dens_beta(),   pWda = par_Wda_none(),   pC = par_nbCounts() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/DetectPa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Detection of infection given parasitemia — DetectPa","text":"host cohort age FoIpar parameters define FoI function tau cohort birthday hhat local scaling parameter FoI r clearance rate simple infection par_RBC parameters compute log10RBC Fmu_par parameters compute alpha2mu par_mu2dens parameters compute d_mu2density pWda parameters dispatch Wda pC parameters define detection function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/DetectPa.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Detection of infection given parasitemia — DetectPa","text":"numeric vector length()","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/FoI.html","id":null,"dir":"Reference","previous_headings":"","what":"Force of Infection, \\(h_\\tau(a)\\) — FoI","title":"Force of Infection, \\(h_\\tau(a)\\) — FoI","text":"Given birth day, \\(\\tau,\\) age related time formula \\(t = +\\tau\\). FoI computed $$\\bar h \\; \\omega() S(+\\tau) T(+\\tau)$$","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/FoI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Force of Infection, \\(h_\\tau(a)\\) — FoI","text":"","code":"FoI(a, FoIpar, tau = 0)"},{"path":"https://dd-harp.github.io/pf.memory/reference/FoI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Force of Infection, \\(h_\\tau(a)\\) — FoI","text":"host age FoIpar compound list compute \\(h_\\tau()\\) tau host cohort's birthday","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/FoI.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Force of Infection, \\(h_\\tau(a)\\) — FoI","text":"numeric","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/MoIDistPlot.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot the output of solveMMinfty — MoIDistPlot","title":"Plot the output of solveMMinfty — MoIDistPlot","text":"Plot output solveMMinfty","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/MoIDistPlot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot the output of solveMMinfty — MoIDistPlot","text":"","code":"MoIDistPlot(moi, t, clr1 = \"red\")"},{"path":"https://dd-harp.github.io/pf.memory/reference/MoIDistPlot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot the output of solveMMinfty — MoIDistPlot","text":"moi mean moi t time clr1 color","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/MoIPM.html","id":null,"dir":"Reference","previous_headings":"","what":"Detection of infection given parasitemia — MoIPM","title":"Detection of infection given parasitemia — MoIPM","text":"Detection infection given parasitemia","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/MoIPM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Detection of infection given parasitemia — MoIPM","text":"","code":"MoIPM(   a,   FoIpar,   tau = 0,   hhat = 1,   r = 1/200,   par_RBC = par_lRBC_static(),   Fmu_par = par_Fmu_base(),   par_mu2dens = par_mu2dens_beta(),   pWda = par_Wda_none(),   pC = par_nbCounts() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/MoIPM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Detection of infection given parasitemia — MoIPM","text":"host cohort age FoIpar parameters define FoI function tau cohort birthday hhat local scaling parameter FoI r clearance rate simple infection par_RBC parameters compute log10RBC Fmu_par parameters compute alpha2mu par_mu2dens parameters compute d_mu2density pWda parameters dispatch Wda pC parameters define detection function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/MoIPM.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Detection of infection given parasitemia — MoIPM","text":"detection probability","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/Wda.0.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute immune tracking variables as a function of host age and exposure — Wda.0","title":"Compute immune tracking variables as a function of host age and exposure — Wda.0","text":"Compute immune tracking variables function host age exposure","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/Wda.0.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute immune tracking variables as a function of host age and exposure — Wda.0","text":"","code":"# S3 method for `0` Wda(a, FoIpar, hhat = NULL, tau = 0, par = par_Wda.0())"},{"path":"https://dd-harp.github.io/pf.memory/reference/Wda.0.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute immune tracking variables as a function of host age and exposure — Wda.0","text":"age host cohort FoIpar parameters define FoI function hhat overrides value hbar par tau cohort birthday par parameters list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/Wda.0.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute immune tracking variables as a function of host age and exposure — Wda.0","text":"numeric vector 0's length()","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/Wda.delta.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute immune tracking variables as a function of host age and exposure — Wda.delta","title":"Compute immune tracking variables as a function of host age and exposure — Wda.delta","text":"Compute immune tracking variables function host age exposure","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/Wda.delta.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute immune tracking variables as a function of host age and exposure — Wda.delta","text":"","code":"# S3 method for delta Wda(a, FoIpar, tau = 0, hhat = 1, par = par_Wda_delta())"},{"path":"https://dd-harp.github.io/pf.memory/reference/Wda.delta.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute immune tracking variables as a function of host age and exposure — Wda.delta","text":"age host cohort FoIpar parameters define FoI function tau cohort birthday hhat overrides value hbar par par parameters list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/Wda.delta.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute immune tracking variables as a function of host age and exposure — Wda.delta","text":"numeric vector length()","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/Wda.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute immune tracking variables as a function of host age and exposure — Wda","title":"Compute immune tracking variables as a function of host age and exposure — Wda","text":"function dispatches class(par)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/Wda.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute immune tracking variables as a function of host age and exposure — Wda","text":"","code":"Wda(a, FoIpar, tau = 0, hhat = 1, par = par_Wda_none())"},{"path":"https://dd-harp.github.io/pf.memory/reference/Wda.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute immune tracking variables as a function of host age and exposure — Wda","text":"age host cohort FoIpar parameters define FoI function tau cohort birthday hhat overrides value hbar par par parameters list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/Wda.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute immune tracking variables as a function of host age and exposure — Wda","text":"numeric vector length()","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/Wda.none.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute immune tracking variables as a function of host age and exposure — Wda.none","title":"Compute immune tracking variables as a function of host age and exposure — Wda.none","text":"Compute immune tracking variables function host age exposure","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/Wda.none.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute immune tracking variables as a function of host age and exposure — Wda.none","text":"","code":"# S3 method for none Wda(a, FoIpar, tau = 0, hhat = 1, par = par_Wda_none())"},{"path":"https://dd-harp.github.io/pf.memory/reference/Wda.none.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute immune tracking variables as a function of host age and exposure — Wda.none","text":"age host cohort FoIpar parameters define FoI function tau cohort birthday hhat overrides value hbar par par parameters list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/Wda.none.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute immune tracking variables as a function of host age and exposure — Wda.none","text":"numeric vector 0's length()","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/ageFoI.flat.html","id":null,"dir":"Reference","previous_headings":"","what":"A function that does not modify the FoI by age — ageFoI.flat","title":"A function that does not modify the FoI by age — ageFoI.flat","text":"function modify FoI age","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/ageFoI.flat.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A function that does not modify the FoI by age — ageFoI.flat","text":"","code":"# S3 method for flat ageFoI(a, par)"},{"path":"https://dd-harp.github.io/pf.memory/reference/ageFoI.flat.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A function that does not modify the FoI by age — ageFoI.flat","text":"host age par list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/ageFoI.flat.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"A function that does not modify the FoI by age — ageFoI.flat","text":"numeric","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/ageFoI.html","id":null,"dir":"Reference","previous_headings":"","what":"Functions to modify the FoI by age — ageFoI","title":"Functions to modify the FoI by age — ageFoI","text":"method dispatches par.","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/ageFoI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Functions to modify the FoI by age — ageFoI","text":"","code":"ageFoI(a, par)"},{"path":"https://dd-harp.github.io/pf.memory/reference/ageFoI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Functions to modify the FoI by age — ageFoI","text":"host age par list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/ageFoI.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Functions to modify the FoI by age — ageFoI","text":"numeric","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/ageFoI.type2.html","id":null,"dir":"Reference","previous_headings":"","what":"A function that does not modify the FoI by age — ageFoI.type2","title":"A function that does not modify the FoI by age — ageFoI.type2","text":"function modify FoI age","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/ageFoI.type2.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A function that does not modify the FoI by age — ageFoI.type2","text":"","code":"# S3 method for type2 ageFoI(a, par)"},{"path":"https://dd-harp.github.io/pf.memory/reference/ageFoI.type2.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A function that does not modify the FoI by age — ageFoI.type2","text":"host age par list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/ageFoI.type2.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"A function that does not modify the FoI by age — ageFoI.type2","text":"numeric","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/alpha2mu.0.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute expected log10 parasite densities, mu, as a function of the age of infection alpha — alpha2mu.0","title":"Compute expected log10 parasite densities, mu, as a function of the age of infection alpha — alpha2mu.0","text":"Compute mean log10 parasites model immunity","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/alpha2mu.0.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute expected log10 parasite densities, mu, as a function of the age of infection alpha — alpha2mu.0","text":"","code":"# S3 method for `0` alpha2mu(alpha, W, par)"},{"path":"https://dd-harp.github.io/pf.memory/reference/alpha2mu.0.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute expected log10 parasite densities, mu, as a function of the age of infection alpha — alpha2mu.0","text":"alpha age parasite infection W immune tracking variables par list defines model","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/alpha2mu.0.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute expected log10 parasite densities, mu, as a function of the age of infection alpha — alpha2mu.0","text":"mean log10 parasite densities","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/alpha2mu.W.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute expected log10 parasite densities, mu, as a function of the age of infection alpha — alpha2mu.W","title":"Compute expected log10 parasite densities, mu, as a function of the age of infection alpha — alpha2mu.W","text":"Compute mean log10 parasites model immunity","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/alpha2mu.W.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute expected log10 parasite densities, mu, as a function of the age of infection alpha — alpha2mu.W","text":"","code":"# S3 method for W alpha2mu(alpha, W, par_Fmu)"},{"path":"https://dd-harp.github.io/pf.memory/reference/alpha2mu.W.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute expected log10 parasite densities, mu, as a function of the age of infection alpha — alpha2mu.W","text":"alpha age parasite infection W immune tracking variables par_Fmu list defines model","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/alpha2mu.W.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute expected log10 parasite densities, mu, as a function of the age of infection alpha — alpha2mu.W","text":"mean log10 parasite densities","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/alpha2mu.base.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute expected log10 parasite densities, mu, as a function of the age of infection alpha — alpha2mu.base","title":"Compute expected log10 parasite densities, mu, as a function of the age of infection alpha — alpha2mu.base","text":"Compute mean log10 parasites model immunity","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/alpha2mu.base.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute expected log10 parasite densities, mu, as a function of the age of infection alpha — alpha2mu.base","text":"","code":"# S3 method for base alpha2mu(alpha, W, par_Fmu)"},{"path":"https://dd-harp.github.io/pf.memory/reference/alpha2mu.base.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute expected log10 parasite densities, mu, as a function of the age of infection alpha — alpha2mu.base","text":"alpha age parasite infection W immune tracking variables par_Fmu list defines model","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/alpha2mu.base.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute expected log10 parasite densities, mu, as a function of the age of infection alpha — alpha2mu.base","text":"mean log10 parasite densities","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/alpha2mu.chronic.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute expected log10 parasite densities, mu, as a function of the age of infection alpha — alpha2mu.chronic","title":"Compute expected log10 parasite densities, mu, as a function of the age of infection alpha — alpha2mu.chronic","text":"Compute mean log10 parasites model immunity","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/alpha2mu.chronic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute expected log10 parasite densities, mu, as a function of the age of infection alpha — alpha2mu.chronic","text":"","code":"# S3 method for chronic alpha2mu(alpha, W, par_Fmu)"},{"path":"https://dd-harp.github.io/pf.memory/reference/alpha2mu.chronic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute expected log10 parasite densities, mu, as a function of the age of infection alpha — alpha2mu.chronic","text":"alpha age parasite infection W immune tracking variables par_Fmu list defines model","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/alpha2mu.chronic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute expected log10 parasite densities, mu, as a function of the age of infection alpha — alpha2mu.chronic","text":"mean log10 parasite densities","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/alpha2mu.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute mean, expected parasite densities mu as a function of the age of infection alpha — alpha2mu","title":"Compute mean, expected parasite densities mu as a function of the age of infection alpha — alpha2mu","text":"Compute mean, expected parasite densities mu function age infection alpha","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/alpha2mu.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute mean, expected parasite densities mu as a function of the age of infection alpha — alpha2mu","text":"","code":"alpha2mu(alpha, W, par_Fmu)"},{"path":"https://dd-harp.github.io/pf.memory/reference/alpha2mu.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute mean, expected parasite densities mu as a function of the age of infection alpha — alpha2mu","text":"alpha age parasite infection W immune tracking variables par_Fmu list defines model","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/alpha2mu.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute mean, expected parasite densities mu as a function of the age of infection alpha — alpha2mu","text":"mean log10 parasite densities, numeric vector length(alpha)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/binnedCounts.html","id":null,"dir":"Reference","previous_headings":"","what":"Detection of infection given parasitemia — binnedCounts","title":"Detection of infection given parasitemia — binnedCounts","text":"Detection infection given parasitemia","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/binnedCounts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Detection of infection given parasitemia — binnedCounts","text":"","code":"binnedCounts(xi, a, bins, Cpar = par_nbCounts())"},{"path":"https://dd-harp.github.io/pf.memory/reference/binnedCounts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Detection of infection given parasitemia — binnedCounts","text":"xi mean log10 parasite densities host cohort age bins breakpoints summarizing outputs Cpar parameters define detection function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/binnedCounts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Detection of infection given parasitemia — binnedCounts","text":"binary detection result","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/binnedCounts.nb.html","id":null,"dir":"Reference","previous_headings":"","what":"Detection of infection given parasitemia — binnedCounts.nb","title":"Detection of infection given parasitemia — binnedCounts.nb","text":"Detection infection given parasitemia","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/binnedCounts.nb.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Detection of infection given parasitemia — binnedCounts.nb","text":"","code":"# S3 method for nb binnedCounts(xi, a, bins, Cpar = par_nbCounts())"},{"path":"https://dd-harp.github.io/pf.memory/reference/binnedCounts.nb.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Detection of infection given parasitemia — binnedCounts.nb","text":"xi mean log10 parasite densities host cohort age bins break points binning counts data Cpar parameters define detection function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/binnedCounts.nb.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Detection of infection given parasitemia — binnedCounts.nb","text":"binary detection result","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/binnedCounts.pois.html","id":null,"dir":"Reference","previous_headings":"","what":"Detection of infection given parasitemia — binnedCounts.pois","title":"Detection of infection given parasitemia — binnedCounts.pois","text":"Detection infection given parasitemia","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/binnedCounts.pois.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Detection of infection given parasitemia — binnedCounts.pois","text":"","code":"# S3 method for pois binnedCounts(xi, a, bins, Cpar = par_poisCounts())"},{"path":"https://dd-harp.github.io/pf.memory/reference/binnedCounts.pois.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Detection of infection given parasitemia — binnedCounts.pois","text":"xi mean log10 parasite densities host cohort age bins breakpoints binning data Cpar parameters define detection function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/binnedCounts.pois.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Detection of infection given parasitemia — binnedCounts.pois","text":"binary detection result","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/cdfConvolve2.html","id":null,"dir":"Reference","previous_headings":"","what":"The density function for the sum of two infections — cdfConvolve2","title":"The density function for the sum of two infections — cdfConvolve2","text":"density function sum two infections","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/cdfConvolve2.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The density function for the sum of two infections — cdfConvolve2","text":"","code":"cdfConvolve2(meshX, CDF1, CDF2)"},{"path":"https://dd-harp.github.io/pf.memory/reference/cdfConvolve2.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The density function for the sum of two infections — cdfConvolve2","text":"meshX mesh host cohort ages CDF1 CDF complex distribution CDF2 CDF complex distribution","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/cdfConvolve2.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The density function for the sum of two infections — cdfConvolve2","text":"numeric vector length(meshX)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/cdfConvolve2a.html","id":null,"dir":"Reference","previous_headings":"","what":"The density function for the sum of two infections, method b — cdfConvolve2a","title":"The density function for the sum of two infections, method b — cdfConvolve2a","text":"density function sum two infections, method b","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/cdfConvolve2a.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The density function for the sum of two infections, method b — cdfConvolve2a","text":"","code":"cdfConvolve2a(meshX, CDF1, CDF2)"},{"path":"https://dd-harp.github.io/pf.memory/reference/cdfConvolve2a.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The density function for the sum of two infections, method b — cdfConvolve2a","text":"meshX mesh host cohort ages CDF1 CDF complex distribution CDF2 CDF complex distribution","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/cdfConvolve2a.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The density function for the sum of two infections, method b — cdfConvolve2a","text":"numeric vector length(meshX)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/cdfConvolve2b.html","id":null,"dir":"Reference","previous_headings":"","what":"The density function for the sum of two infections, method a — cdfConvolve2b","title":"The density function for the sum of two infections, method a — cdfConvolve2b","text":"density function sum two infections, method ","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/cdfConvolve2b.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The density function for the sum of two infections, method a — cdfConvolve2b","text":"","code":"cdfConvolve2b(meshX, CDF1, CDF2)"},{"path":"https://dd-harp.github.io/pf.memory/reference/cdfConvolve2b.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The density function for the sum of two infections, method a — cdfConvolve2b","text":"meshX mesh host cohort ages CDF1 CDF complex distribution CDF2 CDF complex distribution","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/cdfConvolve2b.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The density function for the sum of two infections, method a — cdfConvolve2b","text":"numeric vector length(meshX)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dAoI.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the density function for AoI — dAoI","title":"Compute the density function for AoI — dAoI","text":"density AoI given $$f_A(\\alpha | , \\tau, h) = \\frac{\\int_0^z(\\alpha, )}{m_\\tau()}$$","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dAoI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the density function for AoI — dAoI","text":"","code":"dAoI(alpha, a, FoIpar, tau = 0, hhat = 1, r = 1/200)"},{"path":"https://dd-harp.github.io/pf.memory/reference/dAoI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the density function for AoI — dAoI","text":"alpha age infection, \\(\\alpha\\) host age FoIpar compound list compute \\(h_\\tau()\\) tau host cohort's birthday hhat scaling parameter FoI r clearance rate simple infection","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dAoI.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the density function for AoI — dAoI","text":"numeric vector length(alpha)","code":""},{"path":[]},{"path":"https://dd-harp.github.io/pf.memory/reference/dAoIda.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the derivatives of the AoI moments dynamically — dAoIda","text":"","code":"dAoIda(a, M, p, FoIpar)"},{"path":"https://dd-harp.github.io/pf.memory/reference/dAoIda.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the derivatives of the AoI moments dynamically — dAoIda","text":"host age M state variables p parameters FoIpar parameters define FoI function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dAoIda.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the derivatives of the AoI moments dynamically — dAoIda","text":"derivatives MoI AoI list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dAoY.html","id":null,"dir":"Reference","previous_headings":"","what":"The density function for the age of the youngest infection (AoY) — dAoY","title":"The density function for the age of the youngest infection (AoY) — dAoY","text":"density function age youngest infection (AoY)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dAoY.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The density function for the age of the youngest infection (AoY) — dAoY","text":"","code":"dAoY(alpha, a, FoIpar, tau = 0, hhat = 1, r = 1/200)"},{"path":"https://dd-harp.github.io/pf.memory/reference/dAoY.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The density function for the age of the youngest infection (AoY) — dAoY","text":"alpha age infection, \\(\\alpha\\) host age FoIpar compound list compute \\(h_\\tau()\\) tau host cohort's birthday hhat scaling parameter FoI r clearance rate simple infection","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dAoY.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The density function for the age of the youngest infection (AoY) — dAoY","text":"numeric vector length(alpha)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dAoYN.html","id":null,"dir":"Reference","previous_headings":"","what":"The youngest of N infections, density function — dAoYN","title":"The youngest of N infections, density function — dAoYN","text":"youngest N infections, density function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dAoYN.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The youngest of N infections, density function — dAoYN","text":"","code":"dAoYN(N, a, FoIpar, hhat = NULL, tau = 0, r = 1/200)"},{"path":"https://dd-harp.github.io/pf.memory/reference/dAoYN.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The youngest of N infections, density function — dAoYN","text":"N number infections age cohort FoIpar parameters define FoI function hhat local scaling parameter FoI tau cohort birthday r clearance rate simple infection","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dAoYN.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The youngest of N infections, density function — dAoYN","text":"numeric vector length + 1","code":""},{"path":[]},{"path":"https://dd-harp.github.io/pf.memory/reference/dAoYda.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the derivatives of the approximate moments of the AoY dynamically — dAoYda","text":"","code":"dAoYda(a, vars, pars, FoIpar)"},{"path":"https://dd-harp.github.io/pf.memory/reference/dAoYda.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the derivatives of the approximate moments of the AoY dynamically — dAoYda","text":"host age vars state variables pars parameters FoIpar parameters define FoI function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dAoYda.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the derivatives of the approximate moments of the AoY dynamically — dAoYda","text":"derivatives MoI AoI list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dBda.html","id":null,"dir":"Reference","previous_headings":"","what":"The density function for parasite densities in a host cohort — dBda","title":"The density function for parasite densities in a host cohort — dBda","text":"density function parasite densities host cohort","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dBda.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The density function for parasite densities in a host cohort — dBda","text":"","code":"dBda(   meshX,   a,   FoIpar,   hhat = NULL,   tau = 0,   r = 1/200,   pMu = par_alpha2mu_base(),   pPDens = par_mu2density_beta(),   pWda = par_Wda_none() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/dBda.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The density function for parasite densities in a host cohort — dBda","text":"meshX mesh parasite densities host cohort age FoIpar parameters define FoI function hhat local scaling parameter FoI tau cohort birthday r clearance rate simple infection pMu parameters compute alpha2mu pPDens parameters defining parasite densities function mu pWda parameters dispatch Wda","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dBda.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The density function for parasite densities in a host cohort — dBda","text":"numeric vector length meshX","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dCounts.html","id":null,"dir":"Reference","previous_headings":"","what":"density function of counts — dCounts","title":"density function of counts — dCounts","text":"density function counts","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dCounts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"density function of counts — dCounts","text":"","code":"dCounts(hatxi, xi, a = 0, Cpar = par_nbCounts())"},{"path":"https://dd-harp.github.io/pf.memory/reference/dCounts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"density function of counts — dCounts","text":"hatxi mean \\(\\log_{10}\\) parasite counts xi mean \\(\\log_{10}\\) parasite densities host cohort age Cpar parameters define detection function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dCounts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"density function of counts — dCounts","text":"binary detection result","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dCounts.nb.html","id":null,"dir":"Reference","previous_headings":"","what":"Detection of infection given parasitemia — dCounts.nb","title":"Detection of infection given parasitemia — dCounts.nb","text":"Detection infection given parasitemia","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dCounts.nb.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Detection of infection given parasitemia — dCounts.nb","text":"","code":"# S3 method for nb dCounts(hatxi, xi, a = 0, Cpar = par_nbCounts())"},{"path":"https://dd-harp.github.io/pf.memory/reference/dCounts.nb.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Detection of infection given parasitemia — dCounts.nb","text":"hatxi mean log10 parasite counts xi mean log10 parasite densities host cohort age Cpar parameters define detection function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dCounts.nb.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Detection of infection given parasitemia — dCounts.nb","text":"binary detection result","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dCounts.pois.html","id":null,"dir":"Reference","previous_headings":"","what":"Detection of infection given parasitemia — dCounts.pois","title":"Detection of infection given parasitemia — dCounts.pois","text":"Detection infection given parasitemia","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dCounts.pois.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Detection of infection given parasitemia — dCounts.pois","text":"","code":"# S3 method for pois dCounts(hatxi, xi, a = 0, Cpar = par_poisCounts())"},{"path":"https://dd-harp.github.io/pf.memory/reference/dCounts.pois.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Detection of infection given parasitemia — dCounts.pois","text":"hatxi mean log10 parasite densities xi mean log10 parasite densities host cohort age Cpar parameters define detection function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dCounts.pois.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Detection of infection given parasitemia — dCounts.pois","text":"binary detection result","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dCountsBa.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the density of parasite counts in complex infections — dCountsBa","title":"Compute the density of parasite counts in complex infections — dCountsBa","text":"Compute density parasite counts complex infections","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dCountsBa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the density of parasite counts in complex infections — dCountsBa","text":"","code":"dCountsBa(   a,   FoIpar,   bins = 1,   dx = 0.1,   hhat = 1,   tau = 0,   r = 1/200,   RBC_par = par_lRBC_static(),   Fmu_par = par_Fmu_base(),   mu_par = par_mu2dens_beta(),   pWda = par_Wda_none(),   Cpar = par_nbCounts() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/dCountsBa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the density of parasite counts in complex infections — dCountsBa","text":"host cohort age FoIpar parameters define FoI function bins set break points computing counts dx width mesh computing CDF parasite densities hhat local scaling parameter FoI tau cohort birthday r clearance rate simple infection RBC_par parameters compute log10RBC Fmu_par parameters compute alpha2mu mu_par parameters defining parasite densities function mu pWda parameters dispatch Wda Cpar parameters define detection function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dCountsBa.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the density of parasite counts in complex infections — dCountsBa","text":"list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dCountsPa.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the density of parasite counts for simple infections — dCountsPa","title":"Compute the density of parasite counts for simple infections — dCountsPa","text":"Compute density parasite counts simple infections","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dCountsPa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the density of parasite counts for simple infections — dCountsPa","text":"","code":"dCountsPa(   a,   FoIpar,   bins = 1,   dx = 0.1,   hhat = 1,   tau = 0,   r = 1/200,   RBC_par = par_lRBC_static(),   Fmu_par = par_Fmu_base(),   mu_par = par_mu2dens_beta(),   pWda = par_Wda_none(),   Cpar = par_nbCounts() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/dCountsPa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the density of parasite counts for simple infections — dCountsPa","text":"host cohort age FoIpar parameters define FoI function bins set break points computing counts dx width mesh computing CDF parasite densities hhat local scaling parameter FoI tau cohort birthday r clearance rate simple infection RBC_par parameters compute log10RBC Fmu_par parameters compute alpha2mu mu_par parameters defining parasite densities function mu pWda parameters dispatch Wda Cpar parameters define detection function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dCountsPa.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the density of parasite counts for simple infections — dCountsPa","text":"list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dDensityPa.html","id":null,"dir":"Reference","previous_headings":"","what":"The density function for parasite densities from a host cohort population of age a — dDensityPa","title":"The density function for parasite densities from a host cohort population of age a — dDensityPa","text":"density function parasite densities host cohort population age ","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dDensityPa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The density function for parasite densities from a host cohort population of age a — dDensityPa","text":"","code":"dDensityPa(   x,   a,   FoIpar,   hhat = NULL,   tau = 0,   r = 1/200,   pMu = par_alpha2mu_base(),   pPDens = par_mu2density_beta(),   pWda = par_Wda_none() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/dDensityPa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The density function for parasite densities from a host cohort population of age a — dDensityPa","text":"x host cohort age host cohort age FoIpar parameters define FoI function hhat local scaling parameter FoI tau cohort birthday r clearance rate simple infection pMu parameters compute alpha2mu pPDens parameters defining parasite densities function mu pWda parameters dispatch Wda","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dDensityPa.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The density function for parasite densities from a host cohort population of age a — dDensityPa","text":"numeric vector length(x)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dDensityPaConvolve2.html","id":null,"dir":"Reference","previous_headings":"","what":"The density function for the sum of two infections — dDensityPaConvolve2","title":"The density function for the sum of two infections — dDensityPaConvolve2","text":"density function sum two infections","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dDensityPaConvolve2.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The density function for the sum of two infections — dDensityPaConvolve2","text":"","code":"dDensityPaConvolve2(   x,   a,   FoIpar,   hhat = NULL,   tau = 0,   r = 1/200,   par_RBC = par_lRBC_static(),   par_Fmu = par_Fmu_base(),   par_mu2dens = par_mu2dens_beta(),   pWda = par_Wda_none() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/dDensityPaConvolve2.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The density function for the sum of two infections — dDensityPaConvolve2","text":"x host cohort age host cohort age FoIpar parameters define FoI function hhat local scaling parameter FoI tau cohort birthday r clearance rate simple infection par_RBC parameters compute log10RBC par_Fmu parameters compute alpha2mu par_mu2dens parameters compute d_mu2density pWda parameters dispatch Wda","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dDensityPaConvolve2.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The density function for the sum of two infections — dDensityPaConvolve2","text":"numeric value","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dDensityPalpha.html","id":null,"dir":"Reference","previous_headings":"","what":"The density function for parasite densities in a simple malaria infection of age alpha — dDensityPalpha","title":"The density function for parasite densities in a simple malaria infection of age alpha — dDensityPalpha","text":"density function parasite densities simple malaria infection age alpha","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dDensityPalpha.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The density function for parasite densities in a simple malaria infection of age alpha — dDensityPalpha","text":"","code":"dDensityPalpha(   x,   alpha,   W = 0,   a = 0,   pMu = par_alpha2mu_base(),   pRBC = par_lRBC_static(),   pSig = par_sigma_abc() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/dDensityPalpha.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The density function for parasite densities in a simple malaria infection of age alpha — dDensityPalpha","text":"x vector quantiles alpha age parasite infection W immune tracking variables host cohort age pMu parameters compute alpha2mu pRBC parameters compute log10RBC pSig parameters dispatch sigma_mu","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dDensityPalpha.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The density function for parasite densities in a simple malaria infection of age alpha — dDensityPalpha","text":"numeric vector length(x)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dDensityPmu.html","id":null,"dir":"Reference","previous_headings":"","what":"The density function for parasite densities in a simple malaria infection — dDensityPmu","title":"The density function for parasite densities in a simple malaria infection — dDensityPmu","text":"density function parasite densities simple malaria infection","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dDensityPmu.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The density function for parasite densities in a simple malaria infection — dDensityPmu","text":"","code":"dDensityPmu(xi, mu, a = 0, pRBC = par_lRBC_static(), pSig = par_sigma_abc())"},{"path":"https://dd-harp.github.io/pf.memory/reference/dDensityPmu.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The density function for parasite densities in a simple malaria infection — dDensityPmu","text":"xi vector quantiles mu expected value log10 parasite densities host cohort age pRBC parameters compute log10RBC pSig parameters dispatch sigma_mu","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dDensityPmu.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The density function for parasite densities in a simple malaria infection — dDensityPmu","text":"numeric vector length(xi)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dMoIda.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivatives for the queuing model \\(M/M/\\infty\\) — dMoIda","title":"Derivatives for the queuing model \\(M/M/\\infty\\) — dMoIda","text":"queuing model \\(M/M/\\infty\\) tracks MoI cohort humans ages. assumes time- age-dependent hazard rate infection, called force infection (FoI, \\(h_\\tau()\\)). Infections affect , one clears independently rate \\(r\\). Let \\(\\zeta_i\\) fraction population MoI = , $$\\frac{d\\zeta_0}{da}= -h_\\tau() \\zeta_0 + r \\zeta_1$$ \\(\\geq 1\\) $$\\frac{d\\zeta_i}{da}= h_\\tau() \\left( \\zeta_{-1} - \\zeta_i \\right)  - ri \\zeta_i + r(+1)\\zeta_{+1}$$ function computes derivatives form can used deSolve::ode.","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dMoIda.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivatives for the queuing model \\(M/M/\\infty\\) — dMoIda","text":"","code":"dMoIda(a, M, pars, FoIpar)"},{"path":"https://dd-harp.github.io/pf.memory/reference/dMoIda.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivatives for the queuing model \\(M/M/\\infty\\) — dMoIda","text":"host age M state variables pars parameters FoIpar \\(h_\\tau()\\), list formatted compute FoI","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dMoIda.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivatives for the queuing model \\(M/M/\\infty\\) — dMoIda","text":"derivatives list","code":""},{"path":[]},{"path":"https://dd-harp.github.io/pf.memory/reference/d_Bdensity.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the distribution function for \\(B_\\tau(a)\\) — d_Bdensity","title":"Compute the distribution function for \\(B_\\tau(a)\\) — d_Bdensity","text":"Call Bdensity return PDF: $$f_B(\\xi; , \\tau |h) = \\log_{10} \\left( \\sum_{M_\\tau(|h)>0} 10^{P_\\tau(|h)}\\right)$$","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/d_Bdensity.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the distribution function for \\(B_\\tau(a)\\) — d_Bdensity","text":"","code":"d_Bdensity(   meshX,   a,   FoIpar,   tau = 0,   hhat = 1,   r = 1/200,   RBC_par = par_lRBC_static(),   Fmu_par = par_Fmu_base(),   mu_par = par_mu2dens_beta(),   pWda = par_Wda_none() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/d_Bdensity.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the distribution function for \\(B_\\tau(a)\\) — d_Bdensity","text":"meshX mesh parasite densities host cohort age FoIpar parameters define FoI function tau cohort birthday hhat local scaling parameter FoI r clearance rate simple infection RBC_par parameters compute log10RBC Fmu_par parameters compute alpha2mu mu_par parameters compute d_mu2density pWda parameters dispatch Wda","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/d_Bdensity.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the distribution function for \\(B_\\tau(a)\\) — d_Bdensity","text":"numeric vector length meshX","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/d_Pdensity.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute \\(P_\\tau(a |h)\\) — d_Pdensity","title":"Compute \\(P_\\tau(a |h)\\) — d_Pdensity","text":"Compute $$P_\\tau(| h) \\sim f_P(\\xi; , \\tau |h ) = \\int_0^\\Omega(\\xi|F_\\mu(\\alpha)) \\; f_A(\\alpha; , \\tau | h) d\\alpha$$ Compute $$P_\\tau(| h) \\sim f_P(\\xi; , \\tau |h ) = \\int_0^\\Omega(\\xi|F_\\mu(\\alpha)) \\; f_A(\\alpha; , \\tau | h) d\\alpha$$","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/d_Pdensity.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute \\(P_\\tau(a |h)\\) — d_Pdensity","text":"","code":"d_Pdensity(   xi,   a,   FoIpar,   tau = 0,   hhat = 1,   r = 1/200,   par_RBC = par_lRBC_static(),   par_Fmu = par_Fmu_base(),   par_mu2dens = par_mu2dens_beta(),   pWda = par_Wda_none() )  d_Pdensity(   xi,   a,   FoIpar,   tau = 0,   hhat = 1,   r = 1/200,   par_RBC = par_lRBC_static(),   par_Fmu = par_Fmu_base(),   par_mu2dens = par_mu2dens_beta(),   pWda = par_Wda_none() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/d_Pdensity.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute \\(P_\\tau(a |h)\\) — d_Pdensity","text":"xi log10 host cohort age FoIpar parameters define FoI function tau cohort birthday hhat local scaling parameter FoI r clearance rate simple infection par_RBC parameters compute log10RBC par_Fmu parameters compute alpha2mu par_mu2dens parameters compute d_mu2density pWda parameters dispatch Wda","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/d_Pdensity.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute \\(P_\\tau(a |h)\\) — d_Pdensity","text":"numeric vector length(x) numeric vector length(x)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/d_alpha2density.html","id":null,"dir":"Reference","previous_headings":"","what":"The density function for parasite densities in a simple malaria infection of age alpha — d_alpha2density","title":"The density function for parasite densities in a simple malaria infection of age alpha — d_alpha2density","text":"density function parasite densities simple malaria infection age alpha","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/d_alpha2density.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The density function for parasite densities in a simple malaria infection of age alpha — d_alpha2density","text":"","code":"d_alpha2density(   xi,   alpha,   W = 0,   a = 0,   par_RBC = par_lRBC_static(),   par_Fmu = par_Fmu_base(),   par_mu2dens = par_mu2dens_beta() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/d_alpha2density.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The density function for parasite densities in a simple malaria infection of age alpha — d_alpha2density","text":"xi vector quantiles alpha age parasite infection W immune tracking variables host cohort age par_RBC parameters compute log10RBC par_Fmu parameters compute alpha2mu par_mu2dens parameters compute d_mu2density","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/d_alpha2density.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The density function for parasite densities in a simple malaria infection of age alpha — d_alpha2density","text":"numeric vector length(x)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/d_mu2density.beta.html","id":null,"dir":"Reference","previous_headings":"","what":"Modified beta distribution, density function — d_mu2density.beta","title":"Modified beta distribution, density function — d_mu2density.beta","text":"beta distribution, parameterized mean variance, modified return number 0 bvm (number red blood cells)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/d_mu2density.beta.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Modified beta distribution, density function — d_mu2density.beta","text":"","code":"# S3 method for beta d_mu2density(xi, mu, par_mu2dens = par_mu2dens_beta(), bvm = 13)"},{"path":"https://dd-harp.github.io/pf.memory/reference/d_mu2density.beta.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Modified beta distribution, density function — d_mu2density.beta","text":"xi vector quantiles \\(log_{10}\\) parasite densities mu expected value \\(log_{10}\\) parasite densities par_mu2dens parameters compute parasite densities function mu bvm blood volume \\(log_{10}\\) red blood cells","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/d_mu2density.beta.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Modified beta distribution, density function — d_mu2density.beta","text":"numeric vector length(xi)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/d_mu2density.html","id":null,"dir":"Reference","previous_headings":"","what":"The density function for parasite densities in a simple malaria infection — d_mu2density","title":"The density function for parasite densities in a simple malaria infection — d_mu2density","text":"density function parasite densities simple malaria infection","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/d_mu2density.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The density function for parasite densities in a simple malaria infection — d_mu2density","text":"","code":"d_mu2density(xi, mu, par_mu2dens = par_mu2dens_beta(), bvm = 13)"},{"path":"https://dd-harp.github.io/pf.memory/reference/d_mu2density.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The density function for parasite densities in a simple malaria infection — d_mu2density","text":"xi vector quantiles \\(log_{10}\\) parasite densities mu expected value \\(log_{10}\\) parasite densities par_mu2dens parameters compute parasite densities function mu bvm blood volume \\(log_{10}\\) red blood cells","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/d_mu2density.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The density function for parasite densities in a simple malaria infection — d_mu2density","text":"numeric vector length(xi)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dbeta1.html","id":null,"dir":"Reference","previous_headings":"","what":"Density function for the beta distribution, an alternative parameterization — dbeta1","title":"Density function for the beta distribution, an alternative parameterization — dbeta1","text":"beta distribution parameterized using mean function sigma_mu computes variance function mean","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dbeta1.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Density function for the beta distribution, an alternative parameterization — dbeta1","text":"","code":"dbeta1(x, mu, pSig = par_sigma_abc())"},{"path":"https://dd-harp.github.io/pf.memory/reference/dbeta1.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Density function for the beta distribution, an alternative parameterization — dbeta1","text":"x vector quantiles mu mean value distribution (0 <= mu <= 1) pSig parameters dispatch S3 function sigma_mu","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dbeta1.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Density function for the beta distribution, an alternative parameterization — dbeta1","text":"numeric vector length(x)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dmda.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the derivatives for MoI using a hybrid model — dmda","title":"Compute the derivatives for MoI using a hybrid model — dmda","text":"Compute derivatives MoI using hybrid model","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dmda.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the derivatives for MoI using a hybrid model — dmda","text":"","code":"dmda(a, M, p, FoIpar)"},{"path":"https://dd-harp.github.io/pf.memory/reference/dmda.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the derivatives for MoI using a hybrid model — dmda","text":"host age M state variables p parameters FoIpar parameters define FoI function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dmda.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the derivatives for MoI using a hybrid model — dmda","text":"derivatives list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dpda.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the derivatives for MoI and true PR — dpda","title":"Compute the derivatives for MoI and true PR — dpda","text":"Compute derivatives MoI true PR","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dpda.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the derivatives for MoI and true PR — dpda","text":"","code":"dpda(a, M, par, FoIpar)"},{"path":"https://dd-harp.github.io/pf.memory/reference/dpda.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the derivatives for MoI and true PR — dpda","text":"host age M state variables par model parameters FoIpar parameters define FoI function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dpda.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the derivatives for MoI and true PR — dpda","text":"derivatives, list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/log10RBC.0.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute log10 of the red blood cell population — log10RBC.0","title":"Compute log10 of the red blood cell population — log10RBC.0","text":"static model","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/log10RBC.0.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute log10 of the red blood cell population — log10RBC.0","text":"","code":"# S3 method for `0` log10RBC(a, par)"},{"path":"https://dd-harp.github.io/pf.memory/reference/log10RBC.0.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute log10 of the red blood cell population — log10RBC.0","text":"age host cohort par list parameters","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/log10RBC.0.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute log10 of the red blood cell population — log10RBC.0","text":"numeric vector length()","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/log10RBC.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute log10 of the red blood cell population — log10RBC","title":"Compute log10 of the red blood cell population — log10RBC","text":"Compute log10 red blood cell population","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/log10RBC.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute log10 of the red blood cell population — log10RBC","text":"","code":"log10RBC(a, par)"},{"path":"https://dd-harp.github.io/pf.memory/reference/log10RBC.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute log10 of the red blood cell population — log10RBC","text":"age host cohort par list parameters","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/log10RBC.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute log10 of the red blood cell population — log10RBC","text":"numeric vector length()","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/log10RBC.static.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute log10 of the red blood cell population — log10RBC.static","title":"Compute log10 of the red blood cell population — log10RBC.static","text":"static model","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/log10RBC.static.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute log10 of the red blood cell population — log10RBC.static","text":"","code":"# S3 method for static log10RBC(a, par)"},{"path":"https://dd-harp.github.io/pf.memory/reference/log10RBC.static.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute log10 of the red blood cell population — log10RBC.static","text":"age host cohort par list parameters","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/log10RBC.static.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute log10 of the red blood cell population — log10RBC.static","text":"numeric vector length()","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/make_FoI.html","id":null,"dir":"Reference","previous_headings":"","what":"Trace Function - Force of Infection — make_FoI","title":"Trace Function - Force of Infection — make_FoI","text":"Trace Function - Force Infection","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/make_FoI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Trace Function - Force of Infection — make_FoI","text":"","code":"make_FoI(par, maxAge = 50)"},{"path":"https://dd-harp.github.io/pf.memory/reference/make_FoI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Trace Function - Force of Infection — make_FoI","text":"par formatted list maxAge age years normalize ","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/make_FoI.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Trace Function - Force of Infection — make_FoI","text":"numeric","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/meanCountsBa.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the mean parasite counts in complex infections — meanCountsBa","title":"Compute the mean parasite counts in complex infections — meanCountsBa","text":"Compute mean parasite counts complex infections","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/meanCountsBa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the mean parasite counts in complex infections — meanCountsBa","text":"","code":"meanCountsBa(   a,   FoIpar,   dx = 0.1,   hhat = 1,   tau = 0,   r = 1/200,   Fmu_par = par_Fmu_base(),   mu_par = par_mu2dens_beta(),   pWda = par_Wda_none(),   Cpar = par_nbCounts() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/meanCountsBa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the mean parasite counts in complex infections — meanCountsBa","text":"host cohort age FoIpar parameters define FoI function dx width mesh computing CDF parasite densities hhat local scaling parameter FoI tau cohort birthday r clearance rate simple infection Fmu_par parameters compute alpha2mu mu_par parameters defining parasite densities function mu pWda parameters dispatch Wda Cpar parameters define detection function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/meanCountsBa.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the mean parasite counts in complex infections — meanCountsBa","text":"list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/meanCountsPa.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the mean parasite counts in simple infections — meanCountsPa","title":"Compute the mean parasite counts in simple infections — meanCountsPa","text":"Compute mean parasite counts simple infections","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/meanCountsPa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the mean parasite counts in simple infections — meanCountsPa","text":"","code":"meanCountsPa(   a,   FoIpar,   dx = 0.1,   hhat = 1,   tau = 0,   r = 1/200,   Fmu_par = par_Fmu_base(),   mu_par = par_mu2dens_beta(),   pWda = par_Wda_none(),   Cpar = par_nbCounts() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/meanCountsPa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the mean parasite counts in simple infections — meanCountsPa","text":"host cohort age FoIpar parameters define FoI function dx width mesh computing CDF parasite densities hhat local scaling parameter FoI tau cohort birthday r clearance rate simple infection Fmu_par parameters compute alpha2mu mu_par parameters defining parasite densities function mu pWda parameters dispatch Wda Cpar parameters define detection function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/meanCountsPa.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the mean parasite counts in simple infections — meanCountsPa","text":"list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/meanMoI.html","id":null,"dir":"Reference","previous_headings":"","what":"The mean MoI in a host cohort of age \\(a\\) — meanMoI","title":"The mean MoI in a host cohort of age \\(a\\) — meanMoI","text":"mean multiplicity infection (MoI) $$m_\\tau() = \\int_0^z_\\tau(\\alpha, ) d \\alpha$$","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/meanMoI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The mean MoI in a host cohort of age \\(a\\) — meanMoI","text":"","code":"meanMoI(a, FoIpar, tau = 0, hhat = 1, r = 1/200)"},{"path":"https://dd-harp.github.io/pf.memory/reference/meanMoI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The mean MoI in a host cohort of age \\(a\\) — meanMoI","text":"host age FoIpar compound list compute \\(h_\\tau()\\) tau host cohort's birthday hhat local scaling parameter FoI r clearance rate simple infection","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/meanMoI.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The mean MoI in a host cohort of age \\(a\\) — meanMoI","text":"numeric vector length()","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/momentAoI.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the moments for the AoI density function for a cohort of age a — momentAoI","title":"Compute the moments for the AoI density function for a cohort of age a — momentAoI","text":"Compute moments AoI density function cohort age ","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/momentAoI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the moments for the AoI density function for a cohort of age a — momentAoI","text":"","code":"momentAoI(a, FoIpar, tau = 0, hhat = 1, r = 1/200, n = 1)"},{"path":"https://dd-harp.github.io/pf.memory/reference/momentAoI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the moments for the AoI density function for a cohort of age a — momentAoI","text":"host age FoIpar compound list compute \\(h_\\tau()\\) tau host cohort's birthday hhat local scaling parameter FoI r clearance rate simple infection n moment desired","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/momentAoI.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the moments for the AoI density function for a cohort of age a — momentAoI","text":"numeric vector length()","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/momentAoY.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the moments for the AoY density function for a cohort of age a — momentAoY","title":"Compute the moments for the AoY density function for a cohort of age a — momentAoY","text":"Compute moments AoY density function cohort age ","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/momentAoY.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the moments for the AoY density function for a cohort of age a — momentAoY","text":"","code":"momentAoY(a, FoIpar, tau = 0, hhat = 1, r = 1/200, n = 1)"},{"path":"https://dd-harp.github.io/pf.memory/reference/momentAoY.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the moments for the AoY density function for a cohort of age a — momentAoY","text":"host age FoIpar compound list compute \\(h_\\tau()\\) tau host cohort's birthday hhat local scaling parameter FoI r clearance rate simple infection n moment desired","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/momentAoY.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the moments for the AoY density function for a cohort of age a — momentAoY","text":"numeric vector length()","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/nzPois.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute N non-zero values from a Poisson distribution with a given MoI — nzPois","title":"Compute N non-zero values from a Poisson distribution with a given MoI — nzPois","text":"Compute N non-zero values Poisson distribution given MoI","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/nzPois.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute N non-zero values from a Poisson distribution with a given MoI — nzPois","text":"","code":"nzPois(N, moi)"},{"path":"https://dd-harp.github.io/pf.memory/reference/nzPois.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute N non-zero values from a Poisson distribution with a given MoI — nzPois","text":"N number random variates return moi mean moi","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/nzPois.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute N non-zero values from a Poisson distribution with a given MoI — nzPois","text":"numeric vector length N","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pAoI.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the distribution function for AoI — pAoI","title":"Compute the distribution function for AoI — pAoI","text":"Compute distribution function AoI","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pAoI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the distribution function for AoI — pAoI","text":"","code":"pAoI(alpha, a, FoIpar, tau = 0, hhat = 1, r = 1/200)"},{"path":"https://dd-harp.github.io/pf.memory/reference/pAoI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the distribution function for AoI — pAoI","text":"alpha age infection, \\(\\alpha\\) host age FoIpar compound list compute \\(h_\\tau()\\) tau host cohort's birthday hhat scaling parameter FoI r clearance rate simple infection","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pAoI.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the distribution function for AoI — pAoI","text":"numeric vector length(alpha)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pAoY.html","id":null,"dir":"Reference","previous_headings":"","what":"The distribution function for the age of the youngest infection (AoY) — pAoY","title":"The distribution function for the age of the youngest infection (AoY) — pAoY","text":"distribution function age youngest infection (AoY)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pAoY.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The distribution function for the age of the youngest infection (AoY) — pAoY","text":"","code":"pAoY(alpha, a, FoIpar, tau = 0, hhat = 1, r = 1/200)"},{"path":"https://dd-harp.github.io/pf.memory/reference/pAoY.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The distribution function for the age of the youngest infection (AoY) — pAoY","text":"alpha age infection, \\(\\alpha\\) host age FoIpar compound list compute \\(h_\\tau()\\) tau host cohort's birthday hhat scaling parameter FoI r clearance rate simple infection","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pAoY.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The distribution function for the age of the youngest infection (AoY) — pAoY","text":"numeric vector length(alpha)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pAoYN.html","id":null,"dir":"Reference","previous_headings":"","what":"The youngest of N infections, distribution function — pAoYN","title":"The youngest of N infections, distribution function — pAoYN","text":"youngest N infections, distribution function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pAoYN.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The youngest of N infections, distribution function — pAoYN","text":"","code":"pAoYN(N, a, FoIpar, hhat = NULL, tau = 0, r = 1/200)"},{"path":"https://dd-harp.github.io/pf.memory/reference/pAoYN.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The youngest of N infections, distribution function — pAoYN","text":"N MoI age cohort FoIpar parameters define FoI function hhat local scaling parameter FoI tau cohort birthday r clearance rate simple infection","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pAoYN.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The youngest of N infections, distribution function — pAoYN","text":"numeric vector length + 1","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pAoY_long.html","id":null,"dir":"Reference","previous_headings":"","what":"Alternative method for computing the distribution function for the age of the youngest infection (AoY) — pAoY_long","title":"Alternative method for computing the distribution function for the age of the youngest infection (AoY) — pAoY_long","text":"method computes distribution function AoY summing AoI distributions","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pAoY_long.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Alternative method for computing the distribution function for the age of the youngest infection (AoY) — pAoY_long","text":"","code":"pAoY_long(alpha, a, FoIpar, tau = 0, hhat = 1, r = 1/200)"},{"path":"https://dd-harp.github.io/pf.memory/reference/pAoY_long.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Alternative method for computing the distribution function for the age of the youngest infection (AoY) — pAoY_long","text":"alpha age infection, \\(\\alpha\\) host age FoIpar compound list compute \\(h_\\tau()\\) tau host cohort's birthday hhat scaling parameter FoI r clearance rate simple infection","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pAoY_long.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Alternative method for computing the distribution function for the age of the youngest infection (AoY) — pAoY_long","text":"numeric vector length(alpha)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pBda.html","id":null,"dir":"Reference","previous_headings":"","what":"The distribution function for parasite densities in a host cohort — pBda","title":"The distribution function for parasite densities in a host cohort — pBda","text":"distribution function parasite densities host cohort","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pBda.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The distribution function for parasite densities in a host cohort — pBda","text":"","code":"pBda(   meshX,   a,   FoIpar,   hhat = NULL,   tau = 0,   r = 1/200,   pMu = par_alpha2mu_base(),   pPDens = par_mu2density_beta(),   pWda = par_Wda_none() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/pBda.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The distribution function for parasite densities in a host cohort — pBda","text":"meshX mesh parasite densities host cohort age FoIpar parameters define FoI function hhat local scaling parameter FoI tau cohort birthday r clearance rate simple infection pMu parameters compute alpha2mu pPDens parameters defining parasite densities function mu pWda parameters dispatch Wda","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pBda.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The distribution function for parasite densities in a host cohort — pBda","text":"numeric vector length meshX","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pCounts.html","id":null,"dir":"Reference","previous_headings":"","what":"cumulative density function of counts — pCounts","title":"cumulative density function of counts — pCounts","text":"cumulative density function counts","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pCounts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"cumulative density function of counts — pCounts","text":"","code":"pCounts(hatxi, xi, a = 0, Cpar = par_nbCounts())"},{"path":"https://dd-harp.github.io/pf.memory/reference/pCounts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"cumulative density function of counts — pCounts","text":"hatxi mean log10 parasite densities xi mean \\(\\log_{10}\\) parasite densities host cohort age Cpar parameters define detection function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pCounts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"cumulative density function of counts — pCounts","text":"binary detection result","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pCounts.nb.html","id":null,"dir":"Reference","previous_headings":"","what":"Detection of infection given parasitemia — pCounts.nb","title":"Detection of infection given parasitemia — pCounts.nb","text":"Detection infection given parasitemia","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pCounts.nb.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Detection of infection given parasitemia — pCounts.nb","text":"","code":"# S3 method for nb pCounts(hatxi, xi, a = 0, Cpar = par_nbCounts())"},{"path":"https://dd-harp.github.io/pf.memory/reference/pCounts.nb.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Detection of infection given parasitemia — pCounts.nb","text":"hatxi mean log10 parasite counts xi mean log10 parasite densities host cohort age Cpar parameters define detection function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pCounts.nb.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Detection of infection given parasitemia — pCounts.nb","text":"binary detection result","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pCounts.pois.html","id":null,"dir":"Reference","previous_headings":"","what":"Detection of infection given parasitemia — pCounts.pois","title":"Detection of infection given parasitemia — pCounts.pois","text":"Detection infection given parasitemia","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pCounts.pois.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Detection of infection given parasitemia — pCounts.pois","text":"","code":"# S3 method for pois pCounts(hatxi, xi, a = 0, Cpar = par_poisCounts())"},{"path":"https://dd-harp.github.io/pf.memory/reference/pCounts.pois.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Detection of infection given parasitemia — pCounts.pois","text":"hatxi mean log10 parasite counts xi mean log10 parasite densities host cohort age Cpar parameters define detection function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pCounts.pois.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Detection of infection given parasitemia — pCounts.pois","text":"binary detection result","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pCountsBa.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the distribution of parasite counts in complex infections — pCountsBa","title":"Compute the distribution of parasite counts in complex infections — pCountsBa","text":"Compute distribution parasite counts complex infections","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pCountsBa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the distribution of parasite counts in complex infections — pCountsBa","text":"","code":"pCountsBa(   a,   FoIpar,   bins = 1,   dx = 0.1,   hhat = 1,   tau = 0,   r = 1/200,   RBC_par = par_lRBC_static(),   Fmu_par = par_Fmu_base(),   mu_par = par_mu2dens_beta(),   pWda = par_Wda_none(),   Cpar = par_nbCounts() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/pCountsBa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the distribution of parasite counts in complex infections — pCountsBa","text":"host cohort age FoIpar parameters define FoI function bins set break points computing counts dx width mesh computing CDF parasite densities hhat local scaling parameter FoI tau cohort birthday r clearance rate simple infection RBC_par parameters compute log10RBC Fmu_par parameters compute alpha2mu mu_par parameters defining parasite densities function mu pWda parameters dispatch Wda Cpar parameters define detection function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pCountsBa.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the distribution of parasite counts in complex infections — pCountsBa","text":"list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pCountsPa.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the distribution of parasite counts for simple infections — pCountsPa","title":"Compute the distribution of parasite counts for simple infections — pCountsPa","text":"Compute distribution parasite counts simple infections","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pCountsPa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the distribution of parasite counts for simple infections — pCountsPa","text":"","code":"pCountsPa(   a,   FoIpar,   bins = c(1:5, 13),   dx = 0.1,   hhat = 1,   tau = 0,   r = 1/200,   RBC_par = par_lRBC_static(),   Fmu_par = par_Fmu_base(),   mu_par = par_mu2dens_beta(),   pWda = par_Wda_none(),   Cpar = par_nbCounts() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/pCountsPa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the distribution of parasite counts for simple infections — pCountsPa","text":"host cohort age FoIpar parameters define FoI function bins set break points computing counts dx width mesh computing CDF parasite densities hhat local scaling parameter FoI tau cohort birthday r clearance rate simple infection RBC_par parameters compute log10RBC Fmu_par parameters compute alpha2mu mu_par parameters defining parasite densities function mu pWda parameters dispatch Wda Cpar parameters define detection function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pCountsPa.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the distribution of parasite counts for simple infections — pCountsPa","text":"list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pDensityPalpha.html","id":null,"dir":"Reference","previous_headings":"","what":"The distribution function for parasite densities in a simple malaria infection of age alpha — pDensityPalpha","title":"The distribution function for parasite densities in a simple malaria infection of age alpha — pDensityPalpha","text":"distribution function parasite densities simple malaria infection age alpha","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pDensityPalpha.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The distribution function for parasite densities in a simple malaria infection of age alpha — pDensityPalpha","text":"","code":"pDensityPalpha(   x,   alpha,   W = 0,   a = 0,   pMu = par_alpha2mu_base(),   pRBC = par_lRBC_static(),   pSig = par_sigma_abc() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/pDensityPalpha.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The distribution function for parasite densities in a simple malaria infection of age alpha — pDensityPalpha","text":"x vector probabilities alpha age parasite infection W immune tracking variables host cohort age pMu parameters compute alpha2mu pRBC parameters compute log10RBC pSig parameters dispatch sigma_mu","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pDensityPalpha.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The distribution function for parasite densities in a simple malaria infection of age alpha — pDensityPalpha","text":"numeric vector length(x)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pDensityPmu.html","id":null,"dir":"Reference","previous_headings":"","what":"The density function for parasite densities as a function of the mean — pDensityPmu","title":"The density function for parasite densities as a function of the mean — pDensityPmu","text":"density function parasite densities function mean","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pDensityPmu.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The density function for parasite densities as a function of the mean — pDensityPmu","text":"","code":"pDensityPmu(xi, mu, a = 0, pRBC = par_lRBC_static(), pSig = par_sigma_abc())"},{"path":"https://dd-harp.github.io/pf.memory/reference/pDensityPmu.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The density function for parasite densities as a function of the mean — pDensityPmu","text":"xi vector probabilities mu expected value log10 parasite densities host cohort age pRBC parameters compute log10RBC pSig parameters dispatch sigma_mu","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pDensityPmu.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The density function for parasite densities as a function of the mean — pDensityPmu","text":"numeric vector length(xi)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/p_Bdensity.html","id":null,"dir":"Reference","previous_headings":"","what":"Call Bdensity and return the density vector — p_Bdensity","title":"Call Bdensity and return the density vector — p_Bdensity","text":"Call Bdensity return density vector","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/p_Bdensity.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Call Bdensity and return the density vector — p_Bdensity","text":"","code":"p_Bdensity(   meshX,   a,   FoIpar,   tau = 0,   hhat = 1,   r = 1/200,   RBC_par = par_lRBC_static(),   Fmu_par = par_Fmu_base(),   mu_par = par_mu2dens_beta(),   pWda = par_Wda_none() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/p_Bdensity.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Call Bdensity and return the density vector — p_Bdensity","text":"meshX mesh parasite densities host cohort age FoIpar parameters define FoI function tau cohort birthday hhat local scaling parameter FoI r clearance rate simple infection RBC_par parameters compute log10RBC Fmu_par parameters compute alpha2mu mu_par parameters compute d_mu2density pWda parameters dispatch Wda","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/p_Bdensity.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Call Bdensity and return the density vector — p_Bdensity","text":"numeric vector length meshX","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/p_alpha2density.html","id":null,"dir":"Reference","previous_headings":"","what":"The distribution function for parasite densities in a simple malaria infection of age alpha — p_alpha2density","title":"The distribution function for parasite densities in a simple malaria infection of age alpha — p_alpha2density","text":"distribution function parasite densities simple malaria infection age alpha","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/p_alpha2density.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The distribution function for parasite densities in a simple malaria infection of age alpha — p_alpha2density","text":"","code":"p_alpha2density(   x,   alpha,   W = 0,   a = 0,   par_RBC = par_lRBC_static(),   par_Fmu = par_Fmu_base(),   par_mu2dens = par_mu2dens_beta() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/p_alpha2density.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The distribution function for parasite densities in a simple malaria infection of age alpha — p_alpha2density","text":"x vector probabilities alpha age parasite infection W immune tracking variables host cohort age par_RBC parameters compute log10RBC par_Fmu parameters compute alpha2mu par_mu2dens parameters compute p_mu2density","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/p_alpha2density.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The distribution function for parasite densities in a simple malaria infection of age alpha — p_alpha2density","text":"numeric vector length(x)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/p_mu2density.beta.html","id":null,"dir":"Reference","previous_headings":"","what":"Modified beta distribution, distribution function — p_mu2density.beta","title":"Modified beta distribution, distribution function — p_mu2density.beta","text":"Modified beta distribution, distribution function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/p_mu2density.beta.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Modified beta distribution, distribution function — p_mu2density.beta","text":"","code":"# S3 method for beta p_mu2density(xi, mu, par_mu2dens = par_mu2dens_beta(), bvm = 13)"},{"path":"https://dd-harp.github.io/pf.memory/reference/p_mu2density.beta.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Modified beta distribution, distribution function — p_mu2density.beta","text":"xi vector probabilities \\(log_{10}\\) parasite densities mu expected value \\(log_{10}\\) parasite densities par_mu2dens parameters defining parasite densities function mu bvm blood volume \\(log_{10}\\) red blood cells","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/p_mu2density.beta.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Modified beta distribution, distribution function — p_mu2density.beta","text":"numeric vector length(xi)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/p_mu2density.html","id":null,"dir":"Reference","previous_headings":"","what":"The density function for parasite densities as a function of the mean — p_mu2density","title":"The density function for parasite densities as a function of the mean — p_mu2density","text":"density function parasite densities function mean","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/p_mu2density.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The density function for parasite densities as a function of the mean — p_mu2density","text":"","code":"p_mu2density(xi, mu, par_mu2dens = par_mu2dens_beta(), bvm = 13)"},{"path":"https://dd-harp.github.io/pf.memory/reference/p_mu2density.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The density function for parasite densities as a function of the mean — p_mu2density","text":"xi vector probabilities \\(log_{10}\\) parasite densities mu expected value \\(log_{10}\\) parasite densities par_mu2dens parameters defining parasite densities function mu bvm blood volume \\(log_{10}\\) red blood cells","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/p_mu2density.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The density function for parasite densities as a function of the mean — p_mu2density","text":"numeric vector length(xi)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_Fmu_W.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up parameters for alpha2mu.W — par_Fmu_W","title":"Set up parameters for alpha2mu.W — par_Fmu_W","text":"Set parameters alpha2mu.W","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_Fmu_W.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up parameters for alpha2mu.W — par_Fmu_W","text":"","code":"par_Fmu_W(   peak = 20,   liver = 7,   tildeb = 10.3,   tildel = 2,   Sa = 0.0033,   Sw = 0.001 )"},{"path":"https://dd-harp.github.io/pf.memory/reference/par_Fmu_W.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up parameters for alpha2mu.W — par_Fmu_W","text":"peak age infection (days) parasite densities peak liver age infection (days) parasites emerge liver tildeb maximum expected log10 parasite densities tildel minimum expected log10 parasite densities Sa decline mu respect alpha Sw decline mu respect immunity","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_Fmu_W.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up parameters for alpha2mu.W — par_Fmu_W","text":"mean log10 parasite densities","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_Fmu_base.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up parameters for alpha2mu.base — par_Fmu_base","title":"Set up parameters for alpha2mu.base — par_Fmu_base","text":"Set parameters alpha2mu.base","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_Fmu_base.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up parameters for alpha2mu.base — par_Fmu_base","text":"","code":"par_Fmu_base(peak = 20, liver = 7, tildeb = 10.3, tildel = 2, Sa = 0.0033)"},{"path":"https://dd-harp.github.io/pf.memory/reference/par_Fmu_base.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up parameters for alpha2mu.base — par_Fmu_base","text":"peak age infection (days) parasite densities peak liver age infection (days) parasites emerge liver tildeb maximum expected log10 parasite densities tildel minimum expected log10 parasite densities Sa decline mu respect alpha","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_Fmu_base.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up parameters for alpha2mu.base — par_Fmu_base","text":"list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_Fmu_chronic.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up parameters for alpha2mu.chronic — par_Fmu_chronic","title":"Set up parameters for alpha2mu.chronic — par_Fmu_chronic","text":"Set parameters alpha2mu.chronic","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_Fmu_chronic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up parameters for alpha2mu.chronic — par_Fmu_chronic","text":"","code":"par_Fmu_chronic(tildeb = 10.3, tildel = 2, Sa = 0.0033)"},{"path":"https://dd-harp.github.io/pf.memory/reference/par_Fmu_chronic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up parameters for alpha2mu.chronic — par_Fmu_chronic","text":"tildeb maximum expected log10 parasite densities tildel minimum expected log10 parasite densities Sa decline mu respect alpha","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_Fmu_chronic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up parameters for alpha2mu.chronic — par_Fmu_chronic","text":"list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_Wda.0.html","id":null,"dir":"Reference","previous_headings":"","what":"Make a parameter set for Wda.0 — par_Wda.0","title":"Make a parameter set for Wda.0 — par_Wda.0","text":"Make parameter set Wda.0","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_Wda.0.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make a parameter set for Wda.0 — par_Wda.0","text":"","code":"par_Wda.0()"},{"path":"https://dd-harp.github.io/pf.memory/reference/par_Wda.0.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make a parameter set for Wda.0 — par_Wda.0","text":"list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_Wda.delta.html","id":null,"dir":"Reference","previous_headings":"","what":"Make a parameter set for Wda.delta — par_Wda.delta","title":"Make a parameter set for Wda.delta — par_Wda.delta","text":"Make parameter set Wda.delta","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_Wda.delta.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make a parameter set for Wda.delta — par_Wda.delta","text":"","code":"par_Wda.delta(delta = 0.001)"},{"path":"https://dd-harp.github.io/pf.memory/reference/par_Wda.delta.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make a parameter set for Wda.delta — par_Wda.delta","text":"delta decay rate","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_Wda.delta.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make a parameter set for Wda.delta — par_Wda.delta","text":"list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_Wda_delta.html","id":null,"dir":"Reference","previous_headings":"","what":"Make a parameter set for Wda.none — par_Wda_delta","title":"Make a parameter set for Wda.none — par_Wda_delta","text":"Make parameter set Wda.none","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_Wda_delta.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make a parameter set for Wda.none — par_Wda_delta","text":"","code":"par_Wda_delta(delta = 0.001)"},{"path":"https://dd-harp.github.io/pf.memory/reference/par_Wda_delta.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make a parameter set for Wda.none — par_Wda_delta","text":"delta decay rate","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_Wda_delta.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make a parameter set for Wda.none — par_Wda_delta","text":"list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_Wda_none.html","id":null,"dir":"Reference","previous_headings":"","what":"Make a parameter set for Wda.none — par_Wda_none","title":"Make a parameter set for Wda.none — par_Wda_none","text":"Make parameter set Wda.none","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_Wda_none.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make a parameter set for Wda.none — par_Wda_none","text":"","code":"par_Wda_none()"},{"path":"https://dd-harp.github.io/pf.memory/reference/par_Wda_none.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make a parameter set for Wda.none — par_Wda_none","text":"list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_alpha2mu.0.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up parameters for alpha2mu.0 — par_alpha2mu.0","title":"Set up parameters for alpha2mu.0 — par_alpha2mu.0","text":"Set parameters alpha2mu.0","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_alpha2mu.0.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up parameters for alpha2mu.0 — par_alpha2mu.0","text":"","code":"par_alpha2mu.0(D = 20, liver = 7, tildeb = 10.3, tildel = 2, Sa = 0.0033)"},{"path":"https://dd-harp.github.io/pf.memory/reference/par_alpha2mu.0.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up parameters for alpha2mu.0 — par_alpha2mu.0","text":"D age infection (days) parasite densities peak liver age infection (days) parasites emerge liver tildeb maximum expected log10 parasite densities tildel minimum expected log10 parasite densities Sa decline mu respect alpha","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_alpha2mu.0.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up parameters for alpha2mu.0 — par_alpha2mu.0","text":"list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_alpha2mu.W.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up parameters for alpha2mu.W — par_alpha2mu.W","title":"Set up parameters for alpha2mu.W — par_alpha2mu.W","text":"Set parameters alpha2mu.W","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_alpha2mu.W.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up parameters for alpha2mu.W — par_alpha2mu.W","text":"","code":"par_alpha2mu.W(   peak = 20,   liver = 7,   tildeb = 10.3,   tildel = 2,   Sa = 0.0033,   Sw = 0.001 )"},{"path":"https://dd-harp.github.io/pf.memory/reference/par_alpha2mu.W.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up parameters for alpha2mu.W — par_alpha2mu.W","text":"peak age infection (days) parasite densities peak liver age infection (days) parasites emerge liver tildeb maximum expected log10 parasite densities tildel minimum expected log10 parasite densities Sa decline mu respect alpha Sw decline mu respect immunity","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_alpha2mu.W.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up parameters for alpha2mu.W — par_alpha2mu.W","text":"mean log10 parasite densities","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_alpha2mu_base.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up parameters for alpha2mu.base — par_alpha2mu_base","title":"Set up parameters for alpha2mu.base — par_alpha2mu_base","text":"Set parameters alpha2mu.base","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_alpha2mu_base.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up parameters for alpha2mu.base — par_alpha2mu_base","text":"","code":"par_alpha2mu_base(peak = 20, liver = 7, 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par_alpha2mu_chronic","text":"list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_expSeason.html","id":null,"dir":"Reference","previous_headings":"","what":"Return a list to dispatch seasonalFoI.exp — par_expSeason","title":"Return a list to dispatch seasonalFoI.exp — par_expSeason","text":"Return list dispatch seasonalFoI.exp","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_expSeason.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return a list to dispatch seasonalFoI.exp — par_expSeason","text":"","code":"par_expSeason(phase = 0, pwr = 1, lift = 0, shift = 0)"},{"path":"https://dd-harp.github.io/pf.memory/reference/par_expSeason.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return a list to dispatch seasonalFoI.exp — par_expSeason","text":"phase shift phase / time year pwr raise seasonal pattern power lift amplitude shift shift everything 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for parasite densities in a simple malaria infection — par_mu2density_beta","text":"","code":"par_mu2density_beta(par_lRBC = par_lRBC_static(), par_sigma = par_sigma_abc())"},{"path":"https://dd-harp.github.io/pf.memory/reference/par_mu2density_beta.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The quantile function for parasite densities in a simple malaria infection — par_mu2density_beta","text":"par_lRBC parameters compute log10 RBC density par_sigma parameters compute sigma_mu","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_mu2density_beta.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The quantile function for parasite densities in a simple malaria infection — par_mu2density_beta","text":"compound list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_nbCounts.html","id":null,"dir":"Reference","previous_headings":"","what":"Detection of infection given 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par_nbCounts","text":"binary detection result","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_poisCounts.html","id":null,"dir":"Reference","previous_headings":"","what":"Detection of infection given parasitemia — par_poisCounts","title":"Detection of infection given parasitemia — par_poisCounts","text":"Detection infection given parasitemia","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_poisCounts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Detection of infection given parasitemia — par_poisCounts","text":"","code":"par_poisCounts(q = 6, bvm = par_lRBC_static())"},{"path":"https://dd-harp.github.io/pf.memory/reference/par_poisCounts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Detection of infection given parasitemia — par_poisCounts","text":"q fraction blood volume sampled bvm blood volume log10 red blood 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sigma.0 — par_sigma.0","text":"aa shape parameter bb shape parameter cc shape parameter","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_sigma.0.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parameters to configure sigma.0 — par_sigma.0","text":"list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_sigma_abc.html","id":null,"dir":"Reference","previous_headings":"","what":"Parameters to configure sigma_mu.abc — par_sigma_abc","title":"Parameters to configure sigma_mu.abc — par_sigma_abc","text":"Parameters configure sigma_mu.abc","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_sigma_abc.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parameters to configure sigma_mu.abc — par_sigma_abc","text":"","code":"par_sigma_abc(aa = 3.11, bb = 2.14, cc = 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sigma_mu","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/qDensityPalpha.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The quantile function for parasite densities in a simple malaria infection of age alpha — qDensityPalpha","text":"numeric vector length(x)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/qDensityPmu.html","id":null,"dir":"Reference","previous_headings":"","what":"The quantile function for parasite densities in a simple malaria infection — qDensityPmu","title":"The quantile function for parasite densities in a simple malaria infection — qDensityPmu","text":"quantile function parasite densities simple malaria infection","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/qDensityPmu.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The quantile function for parasite densities in a simple malaria infection — 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age parasite infection W immune tracking variables host cohort age par_RBC parameters compute log10RBC par_Fmu parameters compute alpha2mu par_mu2dens parameters compute q_mu2density","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/q_alpha2density.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The quantile function for parasite densities in a simple malaria infection of age alpha — q_alpha2density","text":"numeric vector length(x)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/q_mu2density.beta.html","id":null,"dir":"Reference","previous_headings":"","what":"Modified beta distribution, distribution function — q_mu2density.beta","title":"Modified beta distribution, distribution function — q_mu2density.beta","text":"Modified beta distribution, distribution function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/q_mu2density.beta.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Modified beta distribution, distribution function — q_mu2density.beta","text":"","code":"# S3 method for beta q_mu2density(xi, mu, par_mu2dens = par_mu2dens_beta(), bvm = 13)"},{"path":"https://dd-harp.github.io/pf.memory/reference/q_mu2density.beta.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Modified beta distribution, distribution function — q_mu2density.beta","text":"xi vector quantiles mu expected value \\(log_{10}\\) parasite densities par_mu2dens parameters defining parasite densities function mu bvm blood volume \\(log_{10}\\) red blood cells","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/q_mu2density.beta.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Modified beta distribution, distribution function — q_mu2density.beta","text":"numeric vector length(xi)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/q_mu2density.html","id":null,"dir":"Reference","previous_headings":"","what":"The quantile function for parasite densities in a simple malaria infection — q_mu2density","title":"The quantile function for parasite densities in a simple malaria infection — q_mu2density","text":"quantile function parasite densities simple malaria infection","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/q_mu2density.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The quantile function for parasite densities in a simple malaria infection — q_mu2density","text":"","code":"q_mu2density(xi, mu, par_mu2dens = par_mu2dens_beta(), bvm = 13)"},{"path":"https://dd-harp.github.io/pf.memory/reference/q_mu2density.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The quantile function for parasite densities in a simple malaria infection — q_mu2density","text":"xi vector quantiles mu expected value \\(log_{10}\\) parasite densities par_mu2dens parameters defining parasite densities function mu bvm blood volume \\(log_{10}\\) red blood cells","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/q_mu2density.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The quantile function for parasite densities in a simple malaria infection — q_mu2density","text":"numeric vector length(xi)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/qbeta1.html","id":null,"dir":"Reference","previous_headings":"","what":"The quantile function for the beta distribution, an alternative parameterization — qbeta1","title":"The quantile function for the beta distribution, an alternative parameterization — qbeta1","text":"quantile function beta distribution, alternative parameterization","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/qbeta1.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The quantile function for the beta distribution, an alternative parameterization — qbeta1","text":"","code":"qbeta1(x, mu, pSig = par_sigma_abc())"},{"path":"https://dd-harp.github.io/pf.memory/reference/qbeta1.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The quantile function for the beta distribution, an alternative parameterization — qbeta1","text":"x vector quantiles mu mean value distribution (0 <= mu <= 1) pSig parameters dispatch S3 function sigma_mu","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/qbeta1.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The quantile function for the beta distribution, an alternative parameterization — qbeta1","text":"numeric vector length(x)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/rAoI.html","id":null,"dir":"Reference","previous_headings":"","what":"Random numbers for the AoI — rAoI","title":"Random numbers for the AoI — rAoI","text":"Random numbers AoI","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/rAoI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Random numbers for the AoI — rAoI","text":"","code":"rAoI(N, a, FoIpar, tau = 0, hhat = 1, r = 1/200, alphamin = 0)"},{"path":"https://dd-harp.github.io/pf.memory/reference/rAoI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Random numbers for the AoI — rAoI","text":"N number observations host age FoIpar compound list compute \\(h_\\tau()\\) tau host cohort's birthday hhat local scaling parameter FoI r clearance rate simple infection alphamin minimum value AoI return","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/rAoI.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Random numbers for the AoI — rAoI","text":"numeric vector length(alpha)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/rAoY.html","id":null,"dir":"Reference","previous_headings":"","what":"The random generation function for the age of the youngest infection (AoY) — rAoY","title":"The random generation function for the age of the youngest infection (AoY) — rAoY","text":"random generation function age youngest infection (AoY)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/rAoY.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The random generation function for the age of the youngest infection (AoY) — rAoY","text":"","code":"rAoY(N, a, FoIpar, tau = 0, hhat = 1, r = 1/200, alphamin = 0)"},{"path":"https://dd-harp.github.io/pf.memory/reference/rAoY.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The random generation function for the age of the youngest infection (AoY) — rAoY","text":"N number observations host age FoIpar compound list compute \\(h_\\tau()\\) tau host cohort's birthday hhat local scaling parameter FoI r clearance rate simple infection alphamin minimum value AoI return","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/rAoY.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The random generation function for the age of the youngest infection (AoY) — rAoY","text":"numeric vector length(N)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/rAoYN.html","id":null,"dir":"Reference","previous_headings":"","what":"The youngest of N infections, random numbers — rAoYN","title":"The youngest of N infections, random numbers — rAoYN","text":"youngest N infections, random numbers","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/rAoYN.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The youngest of N infections, random numbers — rAoYN","text":"","code":"rAoYN(R, N, a, FoIpar, hhat = NULL, tau = 0, r = 1/200, alphamin = 0)"},{"path":"https://dd-harp.github.io/pf.memory/reference/rAoYN.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The youngest of N infections, random numbers — rAoYN","text":"R number observations N number infections per person host cohort age FoIpar parameters define FoI function hhat local scaling parameter FoI tau cohort birthday r clearance rate simple infection alphamin minimum value AoI return","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/rAoYN.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The youngest of N infections, random numbers — rAoYN","text":"numeric vector length R","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/rBda.html","id":null,"dir":"Reference","previous_headings":"","what":"Random generation for parasite densities in a host cohort — rBda","title":"Random generation for parasite densities in a host cohort — rBda","text":"Random generation parasite densities host cohort","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/rBda.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Random generation for parasite densities in a host cohort — rBda","text":"","code":"rBda(   N,   a,   FoIpar,   hhat = NULL,   r = 1/200,   tau = 0,   alphamin = 7,   pMu = par_alpha2mu_base(),   pPDens = par_mu2density_beta(),   pWda = par_Wda_none() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/rBda.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Random generation for parasite densities in a host cohort — rBda","text":"N number observations host cohort age FoIpar parameters define FoI function hhat local scaling parameter FoI r clearance rate simple infection tau cohort birthday alphamin minimum value alpha allowed pMu parameters compute alpha2mu pPDens parameters defining parasite densities function mu pWda parameters dispatch Wda","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/rBda.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Random generation for parasite densities in a host cohort — rBda","text":"numeric vector length N","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/rDensityPalpha.html","id":null,"dir":"Reference","previous_headings":"","what":"The distribution function for parasite densities in a simple malaria infection of age alpha — rDensityPalpha","title":"The distribution function for parasite densities in a simple malaria infection of age alpha — rDensityPalpha","text":"distribution function parasite densities simple malaria infection age alpha","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/rDensityPalpha.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The distribution function for parasite densities in a simple malaria infection of age alpha — rDensityPalpha","text":"","code":"rDensityPalpha(   n,   alpha,   W = 0,   a = 0,   pMu = par_alpha2mu_base(),   pRBC = par_lRBC_static(),   pSig = par_sigma_abc() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/rDensityPalpha.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The distribution function for parasite densities in a simple malaria infection of age alpha — rDensityPalpha","text":"n number observations alpha age parasite infection W immune tracking variables host cohort age pMu parameters compute alpha2mu pRBC parameters compute log10RBC pSig parameters compute sigma_mu","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/rDensityPalpha.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The distribution function for parasite densities in a simple malaria infection of age alpha — rDensityPalpha","text":"numeric vector length(n)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/rDensityPmu.html","id":null,"dir":"Reference","previous_headings":"","what":"Random generation of parasite densities from a simple malaria infection — rDensityPmu","title":"Random generation of parasite densities from a simple malaria infection — rDensityPmu","text":"Random generation parasite densities simple malaria infection","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/rDensityPmu.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Random generation of parasite densities from a simple malaria infection — rDensityPmu","text":"","code":"rDensityPmu(n, mu, a = 0, pRBC = par_lRBC_static(), pSig = par_sigma_abc())"},{"path":"https://dd-harp.github.io/pf.memory/reference/rDensityPmu.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Random generation of parasite densities from a simple malaria infection — rDensityPmu","text":"n number observations mu expected value log10 parasite densities host cohort age pRBC parameters compute log10RBC pSig parameters dispatch sigma_mu","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/rDensityPmu.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Random generation of parasite densities from a simple malaria infection — rDensityPmu","text":"numeric vector length(n)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/rRda.html","id":null,"dir":"Reference","previous_headings":"","what":"Random generation for M parasite densities in a host cohort with MoI — rRda","title":"Random generation for M parasite densities in a host cohort with MoI — rRda","text":"Random generation M parasite densities host cohort MoI","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/rRda.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Random generation for M parasite densities in a host cohort with MoI — rRda","text":"","code":"rRda(   M,   R,   a,   FoIpar,   tau = 0,   hhat = 1,   r = 1/200,   alphamin = 7,   RBC_par = par_lRBC_static(),   Fmu_par = par_Fmu_base(),   mu_par = par_mu2dens_beta(),   pWda = par_Wda_none() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/rRda.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Random generation for M parasite densities in a host cohort with MoI — rRda","text":"M MoI R number observations host cohort age FoIpar parameters define FoI function tau cohort birthday hhat local scaling parameter FoI r clearance rate simple infection alphamin minimum value alpha allowed RBC_par parameters compute log10RBC Fmu_par parameters compute alpha2mu mu_par parameters defining parasite densities function mu pWda parameters dispatch Wda","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/rRda.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Random generation for M parasite densities in a host cohort with MoI — rRda","text":"R M matrix","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/r_Bdensity.html","id":null,"dir":"Reference","previous_headings":"","what":"Random generation for parasite densities in a host cohort — r_Bdensity","title":"Random generation for parasite densities in a host cohort — r_Bdensity","text":"Random generation parasite densities host cohort","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/r_Bdensity.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Random generation for parasite densities in a host cohort — r_Bdensity","text":"","code":"r_Bdensity(   N,   a,   FoIpar,   tau = 0,   hhat = 1,   r = 1/200,   alphamin = 7,   RBC_par = par_lRBC_static(),   Fmu_par = par_Fmu_base(),   mu_par = par_mu2dens_beta(),   pWda = par_Wda_none() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/r_Bdensity.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Random generation for parasite densities in a host cohort — r_Bdensity","text":"N number observations host cohort age FoIpar parameters define FoI function tau cohort birthday hhat local scaling parameter FoI r clearance rate simple infection alphamin minimum value alpha allowed RBC_par parameters compute log10RBC Fmu_par parameters compute alpha2mu mu_par parameters compute d_mu2density pWda parameters dispatch Wda","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/r_Bdensity.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Random generation for parasite densities in a host cohort — r_Bdensity","text":"numeric vector length N","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/r_alpha2density.html","id":null,"dir":"Reference","previous_headings":"","what":"The distribution function for parasite densities in a simple malaria infection of age alpha — r_alpha2density","title":"The distribution function for parasite densities in a simple malaria infection of age alpha — r_alpha2density","text":"distribution function parasite densities simple malaria infection age alpha","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/r_alpha2density.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The distribution function for parasite densities in a simple malaria infection of age alpha — r_alpha2density","text":"","code":"r_alpha2density(   n,   alpha,   W = 0,   a = 0,   par_RBC = par_lRBC_static(),   par_Fmu = par_Fmu_base(),   par_mu2dens = par_mu2dens_beta() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/r_alpha2density.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The distribution function for parasite densities in a simple malaria infection of age alpha — r_alpha2density","text":"n number observations alpha age parasite infection W immune tracking variables host cohort age par_RBC parameters compute log10RBC par_Fmu parameters compute alpha2mu par_mu2dens parameters compute r_mu2density","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/r_alpha2density.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The distribution function for parasite densities in a simple malaria infection of age alpha — r_alpha2density","text":"numeric vector length(n)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/r_mu2density.beta.html","id":null,"dir":"Reference","previous_headings":"","what":"Modified beta distribution, random numbers — r_mu2density.beta","title":"Modified beta distribution, random numbers — r_mu2density.beta","text":"beta distribution, parameterized mean variance, modified return number 0 bvm (number red blood cells)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/r_mu2density.beta.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Modified beta distribution, random numbers — r_mu2density.beta","text":"","code":"# S3 method for beta r_mu2density(n, mu, par_mu2dens = par_mu2dens_beta(), bvm = 13)"},{"path":"https://dd-harp.github.io/pf.memory/reference/r_mu2density.beta.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Modified beta distribution, random numbers — r_mu2density.beta","text":"n number observations mu expected value \\(log_{10}\\) parasite densities par_mu2dens parameters defining parasite densities function mu bvm blood volume \\(log_{10}\\) red blood cells","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/r_mu2density.beta.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Modified beta distribution, random numbers — r_mu2density.beta","text":"numeric vector length(xi)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/r_mu2density.html","id":null,"dir":"Reference","previous_headings":"","what":"Random generation of parasite densities from a simple malaria infection — r_mu2density","title":"Random generation of parasite densities from a simple malaria infection — r_mu2density","text":"Random generation parasite densities simple malaria infection","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/r_mu2density.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Random generation of parasite densities from a simple malaria infection — r_mu2density","text":"","code":"r_mu2density(n, mu, par_mu2dens = par_mu2dens_beta(), bvm = 13)"},{"path":"https://dd-harp.github.io/pf.memory/reference/r_mu2density.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Random generation of parasite densities from a simple malaria infection — r_mu2density","text":"n number observations mu expected value \\(log_{10}\\) parasite densities par_mu2dens parameters defining parasite densities function mu bvm blood volume \\(log_{10}\\) red blood cells","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/r_mu2density.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Random generation of parasite densities from a simple malaria infection — r_mu2density","text":"numeric vector length(n)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/rbeta1.html","id":null,"dir":"Reference","previous_headings":"","what":"The random generation function for the beta distribution, an alternative parameterization\nTitle — rbeta1","title":"The random generation function for the beta distribution, an alternative parameterization\nTitle — rbeta1","text":"random generation function beta distribution, alternative parameterization Title","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/rbeta1.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The random generation function for the beta distribution, an alternative parameterization\nTitle — rbeta1","text":"","code":"rbeta1(n, mu, pSig = par_sigma_abc())"},{"path":"https://dd-harp.github.io/pf.memory/reference/rbeta1.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The random generation function for the beta distribution, an alternative parameterization\nTitle — rbeta1","text":"n number observations mu mean value distribution (0 <= mu <= 1) pSig parameters dispatch S3 function sigma_mu","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/rbeta1.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The random generation function for the beta distribution, an alternative parameterization\nTitle — rbeta1","text":"numeric vector length n","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/salpha2mu.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute mean, expected parasite densities mu for multiple values of the age of infection alpha — salpha2mu","title":"Compute mean, expected parasite densities mu for multiple values of the age of infection alpha — salpha2mu","text":"Compute mean, expected parasite densities mu multiple values age infection alpha","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/salpha2mu.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute mean, expected parasite densities mu for multiple values of the age of infection alpha — salpha2mu","text":"","code":"salpha2mu(alpha, W, par_Fmu)"},{"path":"https://dd-harp.github.io/pf.memory/reference/salpha2mu.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute mean, expected parasite densities mu for multiple values of the age of infection alpha — salpha2mu","text":"alpha parasite's age infection W immune tracking variables par_Fmu list defines model","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/salpha2mu.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute mean, expected parasite densities mu for multiple values of the age of infection alpha — salpha2mu","text":"mean log10 parasite densities, numeric vector length(alpha)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/seasonalFoI.exp.html","id":null,"dir":"Reference","previous_headings":"","what":"A generalized sinusoidal seasonal pattern, exponentiated — seasonalFoI.exp","title":"A generalized sinusoidal seasonal pattern, exponentiated — seasonalFoI.exp","text":"generalized sinusoidal seasonal pattern, exponentiated","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/seasonalFoI.exp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A generalized sinusoidal seasonal pattern, exponentiated — seasonalFoI.exp","text":"","code":"# S3 method for exp seasonalFoI(t, par = par_expSeason())"},{"path":"https://dd-harp.github.io/pf.memory/reference/seasonalFoI.exp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A generalized sinusoidal seasonal pattern, exponentiated — seasonalFoI.exp","text":"t time par list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/seasonalFoI.exp.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"A generalized sinusoidal seasonal pattern, exponentiated — seasonalFoI.exp","text":"numeric","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/seasonalFoI.flat.html","id":null,"dir":"Reference","previous_headings":"","what":"The ","title":"The ","text":"\"seasonality\" function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/seasonalFoI.flat.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The ","text":"","code":"# S3 method for flat seasonalFoI(t, par)"},{"path":"https://dd-harp.github.io/pf.memory/reference/seasonalFoI.flat.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The ","text":"t time par list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/seasonalFoI.flat.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The ","text":"numeric","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/seasonalFoI.html","id":null,"dir":"Reference","previous_headings":"","what":"Add a seasonal pattern to the FoI trace function — seasonalFoI","title":"Add a seasonal pattern to the FoI trace function — seasonalFoI","text":"Add seasonal pattern FoI trace function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/seasonalFoI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add a seasonal pattern to the FoI trace function — seasonalFoI","text":"","code":"seasonalFoI(t, par)"},{"path":"https://dd-harp.github.io/pf.memory/reference/seasonalFoI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add a seasonal pattern to the FoI trace function — seasonalFoI","text":"t time par list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/seasonalFoI.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add a seasonal pattern to the FoI trace function — seasonalFoI","text":"numeric","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/seasonalFoI.sin.html","id":null,"dir":"Reference","previous_headings":"","what":"A generalized sinusoidal seasonal pattern — seasonalFoI.sin","title":"A generalized sinusoidal seasonal pattern — seasonalFoI.sin","text":"generalized sinusoidal seasonal pattern","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/seasonalFoI.sin.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A generalized sinusoidal seasonal pattern — seasonalFoI.sin","text":"","code":"# S3 method for sin seasonalFoI(t, par = par_sinSeason())"},{"path":"https://dd-harp.github.io/pf.memory/reference/seasonalFoI.sin.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A generalized sinusoidal seasonal pattern — seasonalFoI.sin","text":"t time par list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/seasonalFoI.sin.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"A generalized sinusoidal seasonal pattern — seasonalFoI.sin","text":"numeric","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/sigma.0.html","id":null,"dir":"Reference","previous_headings":"","what":"A function that returns constrained values of the variance for the beta distrution as a function of the mean. — sigma.0","title":"A function that returns constrained values of the variance for the beta distrution as a function of the mean. — sigma.0","text":"function returns constrained values variance beta distrution function mean.","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/sigma.0.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A function that returns constrained values of the variance for the beta distrution as a function of the mean. — sigma.0","text":"","code":"# S3 method for `0` sigma(mu, par)"},{"path":"https://dd-harp.github.io/pf.memory/reference/sigma.0.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A function that returns constrained values of the variance for the beta distrution as a function of the mean. — sigma.0","text":"mu mean value distribution (0 <= mu <= 1) par parameters dispatch configure instances","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/sigma.0.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"A function that returns constrained values of the variance for the beta distrution as a function of the mean. — sigma.0","text":"numeric vector length(mu)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/sigma.abc.html","id":null,"dir":"Reference","previous_headings":"","what":"A function that returns constrained values of the variance for the beta distrution as a function of the mean. — sigma.abc","title":"A function that returns constrained values of the variance for the beta distrution as a function of the mean. — sigma.abc","text":"function returns constrained values variance beta distrution function mean.","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/sigma.abc.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A function that returns constrained values of the variance for the beta distrution as a function of the mean. — sigma.abc","text":"","code":"# S3 method for abc sigma(mu, par)"},{"path":"https://dd-harp.github.io/pf.memory/reference/sigma.abc.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A function that returns constrained values of the variance for the beta distrution as a function of the mean. — sigma.abc","text":"mu mean value distribution (0 <= mu <= 1) par parameters dispatch configure instances","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/sigma.abc.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"A function that returns constrained values of the variance for the beta distrution as a function of the mean. — sigma.abc","text":"numeric vector length(mu)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/sigma.html","id":null,"dir":"Reference","previous_headings":"","what":"A function to compute the variance of the beta distrution as a function of the mean. — sigma","title":"A function to compute the variance of the beta distrution as a function of the mean. — sigma","text":"function compute variance beta distrution function mean.","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/sigma.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A function to compute the variance of the beta distrution as a function of the mean. — sigma","text":"","code":"sigma(mu, par)"},{"path":"https://dd-harp.github.io/pf.memory/reference/sigma.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A function to compute the variance of the beta distrution as a function of the mean. — sigma","text":"mu mean value distribution (0 <= mu <= 1) par parameters dispatch configure instances","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/sigma.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"A function to compute the variance of the beta distrution as a function of the mean. — sigma","text":"numeric vector length(mu)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/sigma_mu.abc.html","id":null,"dir":"Reference","previous_headings":"","what":"A function that returns constrained values of the variance for the beta distrution as a function of the mean. — sigma_mu.abc","title":"A function that returns constrained values of the variance for the beta distrution as a function of the mean. — sigma_mu.abc","text":"function returns constrained values variance beta distrution function mean.","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/sigma_mu.abc.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A function that returns constrained values of the variance for the beta distrution as a function of the mean. — sigma_mu.abc","text":"","code":"# S3 method for abc sigma_mu(mu, par)"},{"path":"https://dd-harp.github.io/pf.memory/reference/sigma_mu.abc.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A function that returns constrained values of the variance for the beta distrution as a function of the mean. — sigma_mu.abc","text":"mu mean value distribution (0 <= mu <= 1) par parameters dispatch configure instances","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/sigma_mu.abc.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"A function that returns constrained values of the variance for the beta distrution as a function of the mean. — sigma_mu.abc","text":"numeric vector length(mu)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/sigma_mu.html","id":null,"dir":"Reference","previous_headings":"","what":"A function to compute the variance of the beta distrution as a function of the mean. — sigma_mu","title":"A function to compute the variance of the beta distrution as a function of the mean. — sigma_mu","text":"function compute variance beta distrution function mean.","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/sigma_mu.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A function to compute the variance of the beta distrution as a function of the mean. — sigma_mu","text":"","code":"sigma_mu(mu, par)"},{"path":"https://dd-harp.github.io/pf.memory/reference/sigma_mu.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A function to compute the variance of the beta distrution as a function of the mean. — sigma_mu","text":"mu mean value distribution (0 <= mu <= 1) par parameters dispatch configure instances","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/sigma_mu.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"A function to compute the variance of the beta distrution as a function of the mean. — sigma_mu","text":"numeric vector length(mu)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/solveMMinfty.html","id":null,"dir":"Reference","previous_headings":"","what":"Solve the queuing model \\(M/M/\\infty\\) — solveMMinfty","title":"Solve the queuing model \\(M/M/\\infty\\) — solveMMinfty","text":"wrapper solve queuing model \\(M/M/\\infty\\) (see dMoIda). function automatically sets maximum MoI computed, sets initial conditions. equations solved using deSolve::ode returned regular intervals dt age 0 Amax (days).","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/solveMMinfty.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Solve the queuing model \\(M/M/\\infty\\) — solveMMinfty","text":"","code":"solveMMinfty(h, FoIpar, r = 1/200, tau = 0, Amax = 730, dt = 1)"},{"path":"https://dd-harp.github.io/pf.memory/reference/solveMMinfty.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Solve the queuing model \\(M/M/\\infty\\) — solveMMinfty","text":"h force infection FoIpar \\(h_\\tau()\\), list formatted compute FoI r clearance rate simple infection tau cohort birthday Amax maximum runtime (days) dt output frequency (days)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/solveMMinfty.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Solve the queuing model \\(M/M/\\infty\\) — solveMMinfty","text":"list orbits name","code":""},{"path":[]},{"path":"https://dd-harp.github.io/pf.memory/reference/solve_dAoI.html","id":null,"dir":"Reference","previous_headings":"","what":"Solve the system of differential equations to compute the moments of the AoI over time. — solve_dAoI","title":"Solve the system of differential equations to compute the moments of the AoI over time. — solve_dAoI","text":"Solve system differential equations compute moments AoI time.","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/solve_dAoI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Solve the system of differential equations to compute the moments of the AoI over time. — solve_dAoI","text":"","code":"solve_dAoI(h, FoIpar, r = 1/200, tau = 0, Amax = 730, dt = 1, N = 3)"},{"path":"https://dd-harp.github.io/pf.memory/reference/solve_dAoI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Solve the system of differential equations to compute the moments of the AoI over time. — solve_dAoI","text":"h force infection FoIpar FoI trace function r clearance rate simple infection tau cohort birthday Amax maximum runtime (days) dt output frequency (days) N total number moments compute","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/solve_dAoI.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Solve the system of differential equations to compute the moments of the AoI over time. — solve_dAoI","text":"data.frame orbits","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/solve_dAoYda.html","id":null,"dir":"Reference","previous_headings":"","what":"Solve the system of differential equations to compute the approximate moments of the AoY over time. — solve_dAoYda","title":"Solve the system of differential equations to compute the approximate moments of the AoY over time. — solve_dAoYda","text":"Solve system differential equations compute approximate moments AoY time.","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/solve_dAoYda.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Solve the system of differential equations to compute the approximate moments of the AoY over time. — solve_dAoYda","text":"","code":"solve_dAoYda(h, FoIpar, r = 1/200, tau = 0, Amax = 730, dt = 1, n = 8)"},{"path":"https://dd-harp.github.io/pf.memory/reference/solve_dAoYda.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Solve the system of differential equations to compute the approximate moments of the AoY over time. — solve_dAoYda","text":"h force infection FoIpar FoI trace function r clearance rate simple infection tau cohort birthday Amax maximum runtime (days) dt output frequency (days) n number terms use \\(\\phi(r,m)\\)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/solve_dAoYda.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Solve the system of differential equations to compute the approximate moments of the AoY over time. — solve_dAoYda","text":"data.frame describing orbits","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/solve_dm.html","id":null,"dir":"Reference","previous_headings":"","what":"Solve the hybrid model for the MoI — solve_dm","title":"Solve the hybrid model for the MoI — solve_dm","text":"Solve hybrid model MoI","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/solve_dm.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Solve the hybrid model for the MoI — solve_dm","text":"","code":"solve_dm(h, FoIpar, r = 1/200, tau = 0, Amax = 730, dt = 1)"},{"path":"https://dd-harp.github.io/pf.memory/reference/solve_dm.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Solve the hybrid model for the MoI — solve_dm","text":"h average, annual force infection FoIpar FoI trace function r clearance rate simple infection tau cohort birthday Amax maximum runtime (days) dt output frequency (days)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/solve_dm.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Solve the hybrid model for the MoI — solve_dm","text":"matrix orbits","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/solve_dpda.html","id":null,"dir":"Reference","previous_headings":"","what":"Solve a system of differential equations to compute the true PR and the MoI — solve_dpda","title":"Solve a system of differential equations to compute the true PR and the MoI — solve_dpda","text":"Solve system differential equations compute true PR MoI","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/solve_dpda.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Solve a system of differential equations to compute the true PR and the MoI — solve_dpda","text":"","code":"solve_dpda(h, FoIpar, r = 1/200, tau = 0, Amax = 730, dt = 1)"},{"path":"https://dd-harp.github.io/pf.memory/reference/solve_dpda.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Solve a system of differential equations to compute the true PR and the MoI — solve_dpda","text":"h scaling factor FoI FoIpar parameters define FoI function r clearance rate simple infection tau cohort birthday Amax maximum runtime (days) dt output frequency (days)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/solve_dpda.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Solve a system of differential equations to compute the true PR and the MoI — solve_dpda","text":"data.frame orbits","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/trendFoI.flat.html","id":null,"dir":"Reference","previous_headings":"","what":"The ","title":"The ","text":"\"trend\" function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/trendFoI.flat.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The ","text":"","code":"# S3 method for flat trendFoI(t, par)"},{"path":"https://dd-harp.github.io/pf.memory/reference/trendFoI.flat.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The ","text":"t time par list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/trendFoI.flat.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The ","text":"numeric","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/trendFoI.html","id":null,"dir":"Reference","previous_headings":"","what":"Add a trend to the FoI trace function — trendFoI","title":"Add a trend to the FoI trace function — trendFoI","text":"Add trend FoI trace function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/trendFoI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add a trend to the FoI trace function — trendFoI","text":"","code":"trendFoI(t, par)"},{"path":"https://dd-harp.github.io/pf.memory/reference/trendFoI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add a trend to the FoI trace function — trendFoI","text":"t time par list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/trendFoI.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add a trend to the FoI trace function — trendFoI","text":"numeric","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/truePRa.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the true PR in a cohort as a function of age and exposure — truePRa","title":"Compute the true PR in a cohort as a function of age and exposure — truePRa","text":"Compute true PR cohort function age exposure","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/truePRa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the true PR in a cohort as a function of age and exposure — truePRa","text":"","code":"truePRa(a, FoIpar, tau = 0, hhat = 1, r = 1/200)"},{"path":"https://dd-harp.github.io/pf.memory/reference/truePRa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the true PR in a cohort as a function of age and exposure — truePRa","text":"host cohort age FoIpar parameters define FoI function tau cohort birthday hhat local scaling parameter FoI r clearance rate simple infection","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/truePRa.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the true PR in a cohort as a function of age and exposure — truePRa","text":"numeric vector length()","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/zda.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute infection density in a cohort of humans, \\(z_\\tau(\\alpha, a)\\) — zda","title":"Compute infection density in a cohort of humans, \\(z_\\tau(\\alpha, a)\\) — zda","text":"Given function describing FoI (\\(h_\\tau()\\)), parameter describing clearance rate infections (\\(r\\)), density parasites age \\(\\alpha\\) cohort humans age \\(\\) $$z_\\tau(\\alpha, ) = e^{-r \\alpha} h_\\tau(-\\alpha)$$","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/zda.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute infection density in a cohort of humans, \\(z_\\tau(\\alpha, a)\\) — zda","text":"","code":"zda(alpha, a, FoIpar, tau = 0, hhat = 1, r = 1/200)"},{"path":"https://dd-harp.github.io/pf.memory/reference/zda.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute infection density in a cohort of humans, \\(z_\\tau(\\alpha, a)\\) — zda","text":"alpha age infection, \\(\\alpha\\) host age FoIpar compound list compute \\(h_\\tau()\\) tau host cohort's birthday hhat scaling parameter FoI r clearance rate simple infection","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/zda.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute infection density in a cohort of humans, \\(z_\\tau(\\alpha, a)\\) — zda","text":"numeric vector length(alpha)","code":""},{"path":[]}]
+[{"path":"https://dd-harp.github.io/pf.memory/articles/AoI-Hybrid.html","id":"hybrid-model","dir":"Articles","previous_headings":"","what":"Hybrid Model","title":"Hybrid Model for the Age of Infection","text":"function solve_dAoI computes first three moments AoI default. plot \\(n^{th}\\) root first three moments. ## Numerical Verification solving hybrid model variables track moments, using equations derived :","code":"aa = seq(5, 3*365, by = 5)  moment1y = momentAoY(aa, foiP3) par(mar = c(7, 4, 2, 2)) solve_dAoI(5/365, foiP3) -> mt  plot(mt$time, mt$xn1, type = \"l\", xlab = \"Age (in Days)\", ylab = expression(list(x, sqrt(x[paste(\"[2]\")]), sqrt(x[paste(\"[3]\")], 3))), ylim = range(mt$xn3^(1/3)))  lines(mt$time, mt$xn2^(1/2), col = \"purple\") lines(mt$time, mt$xn3^(1/3), col = \"darkgreen\") aa = seq(1, 5*365, by = 5)  moment1 = momentAoI(aa, foiP3) moment2 = momentAoI(aa, foiP3, n=2) moment3 = momentAoI(aa, foiP3, n=3) solve_dAoI(5/365, foiP3, Tmax = 5*365, dt=5) -> mt par(mfrow = c(2,2), mar = c(7, 4, 2, 2)) # Top Left plot(mt$time, mt$xn1, type = \"l\", xlab = \"Age (in Days)\", ylab = expression(x), lwd=3)  lines(aa, moment1, col = \"yellow\", lwd=2, lty=2)  # Top Right  plot(mt$time, mt$xn2, type = \"l\", xlab = \"Age (in Days)\", ylab = expression(x[paste(\"[2]\")]), lwd=3, col = \"purple\")  lines(aa, moment2, col = \"yellow\", lwd=2, lty=2) plot(mt$time, mt$xn3, type = \"l\", lwd=3, col = \"darkgreen\",      xlab = \"Age (in Days)\", ylab = expression(x[paste(\"[3]\")])) lines(aa, moment3, col = \"yellow\", lwd=2, lty=2) par(mar = c(7, 4, 2, 2)) solve_dAoI(5/365, foiP3) -> mt  plot(mt$time, mt$xn1, type = \"l\", xlab = \"Age (in Days)\", ylab = expression(list(x, sqrt(x[paste(\"[2]\")]), sqrt(x[paste(\"[3]\")], 3))), lwd=3, ylim = range(mt$xn3^(1/3)))  lines(mt$time, mt$xn2^(1/2), col = \"purple\", lwd=3) lines(mt$time, mt$xn3^(1/3), col = \"darkgreen\", lwd=3)  lines(aa, moment1, col = \"yellow\", lwd=2, lty=2) lines(aa, moment2^(1/2), col = \"yellow\", lwd=2, lty=2) lines(aa, moment3^(1/3), col = \"yellow\", lwd=2, lty=2)"},{"path":"https://dd-harp.github.io/pf.memory/articles/AoI.html","id":"the-density-function","dir":"Articles","previous_headings":"","what":"The Density Function","title":"Age of Infection","text":"following shows distribution AoI looks like cohort age 2.  , plot distributions 12 cohorts age 2, born one month apart.","code":"plot(a2years, dAoI(a2years, max(a2years), foiP3), type =\"l\", xlab = \"Parasite Age\", ylab = expression(F[A](alpha, a, tau)), ylim = c(0,0.009)) plot(a2years, dAoI(a2years, max(a2years), foiP3), type = \"n\", xlab = \"Parasite Age\", ylab = expression(F[A](alpha, a, tau)), ylim = c(0,0.013)) for(i in 1:12)   lines(a2years, dAoI(a2years,max(a2years),foiP3, tau=30*i), col = clrs[i])"},{"path":"https://dd-harp.github.io/pf.memory/articles/AoI.html","id":"the-distribution-function","dir":"Articles","previous_headings":"","what":"The Distribution Function","title":"Age of Infection","text":"","code":"plot(a2years, cumsum(dAoI(a2years, max(a2years), foiP3)), type = \"l\", xlab = \"Parasite Cohort Age\", ylab = expression(1-F[X](alpha, a, tau)), lwd=2) lines(a2years, pAoI(a2years, max(a2years), foiP3), col = \"red\", lwd=2, lty =2) par(mar = c(5,4,1,2))  plot(a2years, pAoI(a2years, max(a2years), foiP3), type = \"n\", xlab =  expression(list(alpha, \" Parasite Age\")), ylab = expression(F[X](alpha, a, tau)))  for(i in 1:12)   lines(a2years, pAoI(a2years,max(a2years), foiP3, tau=30*i), col = clrs[i])"},{"path":"https://dd-harp.github.io/pf.memory/articles/AoI.html","id":"random-numbers","dir":"Articles","previous_headings":"","what":"Random Numbers","title":"Age of Infection","text":"","code":"par(mar = c(5,4,1,2)) a5years = 0:(5*365) rhx = rAoI(10000, 5*365, foiP3) hist(rhx, breaks = c(0:c(5*365)), right=F, probability=T, main = \"\", xlab = expression(alpha), border = grey(0.5)) cdf1 = pAoI(a5years, 5*365, foiP3) pdf1 = dAoI(a5years, 5*365, foiP3)  lines(a5years, pdf1, col=\"red\", lwd=2) par(mar = c(5,4,1,2)) plot(ecdf(rhx), xlim = c(0,1825), cex=0.2, main = \"\", xlab = expression(alpha)) lines(a5years, cdf1, col = \"red\", lty = 2, lwd=2)"},{"path":"https://dd-harp.github.io/pf.memory/articles/AoI.html","id":"moments","dir":"Articles","previous_headings":"","what":"Moments","title":"Age of Infection","text":"Let \\(x\\) denote first moment \\(A_\\tau()\\): \\[x_\\tau() = \\left< A_\\tau() \\right> = \\int_0^\\infty \\alpha \\frac{z_\\tau(\\alpha, )} {m_\\tau()}\\] Similarly, let \\(x_\\tau()[n]\\) denote higher order moments \\(A_\\tau()\\): \\[x_{n}(, \\tau) = \\int_0^\\infty \\alpha^n \\frac{z_\\tau(\\alpha, )} {m_\\tau()}\\] first three moments AoY plotted time. top plot, ’ve also plotted \\(n^{th}\\) root \\(n^{th}\\) moment.","code":"aa = seq(1, 5*365, by = 5)  moment1 = momentAoI(aa, foiP3) moment2 = momentAoI(aa, foiP3, n=2) moment3 = momentAoI(aa, foiP3, n=3) par(mfrow = c(3,1), mar = c(0.5, 4, 0.5, 2)) plot(aa, moment1, type = \"l\", xlab = \"\", ylab = expression(E(A)), lwd=2, xaxt=\"n\", ylim = range((moment3)^(1/3)) )  lines(aa, sqrt(moment2), col = \"darkgreen\") lines(aa, (moment3)^(1/3), col = \"purple\") plot(aa, moment2, type = \"l\", xlab = \"\", ylab = expression(E(A^2)), lwd=2, xaxt=\"n\", col = \"darkgreen\")  plot(aa, moment3, type = \"l\", xlab = \"\", ylab = expression(E(A^2)), lwd=2, col = \"purple\")  mtext(\"Age (in Days)\", 1, 3)"},{"path":"https://dd-harp.github.io/pf.memory/articles/AoY-Hybrid.html","id":"derivation-for-dyda","dir":"Articles","previous_headings":"","what":"Derivation for \\(dy/da\\)","title":"AoY Hybrid Model","text":"start multiplying \\(\\alpha\\) integrating respect \\(\\alpha\\): \\[ \\int_0^\\alpha \\frac{\\partial y(\\alpha, )}{\\partial } d \\alpha + \\int_0^\\alpha \\frac{\\partial y(\\alpha, )}{\\partial \\alpha} d\\alpha = - \\left(F(r,m)  + h \\right) \\int_0^\\alpha y(\\alpha, ) d\\alpha \\] \\[\\int_0^\\alpha y(\\alpha, ) d\\alpha =  \\left<Y \\right> p\\] \\[ \\frac{d \\left< Y \\right> p}{da} + \\int_0^\\alpha dy = - p \\left(F(r,m) + h \\right) \\left< Y \\right>    \\] Using chain rule: \\[ \\frac{\\partial \\left<\\right> p}{\\partial }= p \\frac{\\partial \\left<\\right>}{\\partial }  + \\left<\\right> \\frac{\\partial p}{\\partial }   \\] substituting: \\[ p \\frac{d \\left< Y \\right>}{da} + \\left<Y \\right> \\frac{dp}{da}  + \\int_0^\\alpha dy = - p \\left(F(r,m) + h \\right) \\left<Y \\right> \\] \\(dp/da = h(1-p) - R(m) p\\) \\[ p \\frac{d \\left< Y \\right>}{da} = - \\left[h (1-p) - R(m) p \\right] \\left<Y \\right>   - p \\left(F(r,m) + h \\right) \\left<Y \\right>  - \\int_0^\\alpha dy   \\] now lots things cancel, : \\[ p \\frac{d \\left< Y \\right>}{da} = - h \\left<Y \\right> -(F(r,m)-R(m)) \\left<Y \\right> - \\int_0^\\alpha dy   \\] last term, integrate parts: \\[ \\int_0^\\alpha \\partial z = \\alpha y(,\\alpha) \\big|_{\\alpha = } - \\alpha y(,\\alpha) \\big|_{\\alpha = 0} - \\int_0^y d\\alpha \\] simplifies : (first terms wrong, think wrong) \\[ \\int_0^\\alpha \\partial y =  h_d(0)e^{-ra} \\] \\[ \\frac{dy}{da} = 1 - \\frac{h}{p} y  - \\left( F(r,m) - R(m) \\right) y \\]","code":""},{"path":"https://dd-harp.github.io/pf.memory/articles/AoY-Hybrid.html","id":"frm","dir":"Articles","previous_headings":"","what":"\\(F(r,m)\\)","title":"AoY Hybrid Model","text":"intuition changes AoY worked treating MoI cases. arrived function: \\[F(r, \\zeta) = R(m) \\left( 1 + \\frac{\\zeta^{\\sqrt{2}}}{4} + \\sum_{k \\geq 3} \\frac{1}{k} \\frac{\\zeta^3}{k!} \\right). \\] \\[F(r, \\zeta) = r \\frac{\\mbox{Pr}(\\zeta=1; m(t))}{\\mbox{Pr}(\\zeta>0; m(t))} \\left( 1 + \\frac{\\zeta^{\\sqrt{2}}}{4} + \\sum_{k \\geq 3} \\frac{1}{k} \\frac{\\zeta^3}{k!} \\right). \\] Performance seem improve adding terms \\(k>5.\\) \\(\\zeta=1\\) MoI=1, term clear. cancels \\(R(m)\\) term. reasoned MoI 2 greater, change occur probability \\(1/\\zeta\\), increasing AoY something close \\(y\\). \\(\\zeta=2\\): Somehow, made mistake wrote first term, didn’t notice much later. fiddling around exponent, found \\(\\zeta^{\\sqrt{2}}\\) worked better \\(\\zeta\\) (started, mistake), curiously, better \\(\\zeta^2\\) \\(\\zeta>2\\): seemed work reasonably well. Ultimately, justification using formula seems work quite well.","code":""},{"path":"https://dd-harp.github.io/pf.memory/articles/AoY.html","id":"aoy-density","dir":"Articles","previous_headings":"","what":"AoY Density","title":"Age of the Youngest Infection (AoY)","text":"","code":"aoy = dAoY(1:1825, 5*365, foiP3) raoy = rAoY(10^5, 5*365, foiP3) hist(raoy, breaks=c(0:(5*365)), right=F, plot=F)->daoy plot(daoy$mids, daoy$density, type = \"l\") lines(1:1825, aoy, type = \"l\", col = \"red\")"},{"path":"https://dd-harp.github.io/pf.memory/articles/AoY.html","id":"moments","dir":"Articles","previous_headings":"","what":"Moments","title":"Age of the Youngest Infection (AoY)","text":"first three moments AoY plotted time. top plot, ’ve also plotted \\(n^{th}\\) root \\(n^{th}\\) moment.","code":"aa = seq(5, 5*365, by = 5)  moment1y = momentAoY(aa, foiP3) moment2y = momentAoY(aa, foiP3, n=2) moment3y = momentAoY(aa, foiP3, n=3) par(mfrow = c(4,1), mar = c(0.5, 4, 0.5, 2)) plot(aa, moment1y, type = \"l\", xlab = \"\", ylab = expression(E(Y)), lwd=2, xaxt=\"n\", ylim = range((moment3y)^(1/3)) )  lines(aa, sqrt(moment2y), col = \"darkgreen\") lines(aa, (moment3y)^(1/3), col = \"purple\") plot(aa, moment2y, type = \"l\", xlab = \"\", ylab = expression(E(Y^2)), lwd=2, xaxt=\"n\", col = \"darkgreen\")  plot(aa, moment3y, type = \"l\", xlab = \"\", ylab = expression(E(Y^2)), lwd=2, col = \"purple\")  mtext(\"Age (in Days)\", 1, 3)"},{"path":"https://dd-harp.github.io/pf.memory/articles/AoY.html","id":"derivation","dir":"Articles","previous_headings":"","what":"Derivation","title":"Age of the Youngest Infection (AoY)","text":"First, note CDF minimum \\(n\\) random values AoI cohort : \\[1-(1-F_A(\\alpha,,\\tau))^n\\] Using , can compute CDF full distribution AoY across population: \\[F_Y(\\alpha, , \\tau) = \\frac{1}{p_\\tau()} \\sum_{\\zeta>0} \\mbox{dpois}\\left(\\zeta,m_\\tau()\\right) \\left( 1-(1-F_A(\\alpha,,\\tau))^\\zeta \\right)\\] rewriting slightly: \\[F_Y(\\alpha, , \\tau)  p_\\tau() = \\sum_{\\zeta>0} \\frac{m_\\tau()^\\zeta}{\\zeta!} e^{-m_\\tau()} \\left(1- \\left(1-F_A \\left(\\alpha,, \\tau\\right)\\right)^\\zeta\\right)\\] pulling \\(e^{-m_\\tau()}\\) recombining terms, get: \\[F_Y (\\alpha, , \\tau) p_\\tau()= p_\\tau() - e^{-m_\\tau()} \\sum_{\\zeta>0} \\frac{ \\left[m_\\tau() \\left(1-F_A \\left(\\alpha,, \\tau\\right)\\right)\\right]^\\zeta}{\\zeta!}\\] sum \\(\\zeta=0\\ldots\\infty,\\) expression inside simple, sum \\(M>0\\), add term \\(M=0\\) sum, subtract outside: \\[F_Y(\\alpha, ,\\tau) p_\\tau() = p_\\tau() - e^{-m_\\tau()} \\left(-1+ \\sum_{\\zeta>=0} \\frac{ \\left[m_\\tau() \\left(1-F_A \\left(\\alpha,\\right)\\right)\\right]^\\zeta}{\\zeta!} \\right)\\] \\(e^{-m_\\tau()} = 1-p_\\tau()\\) infinite sum simply exponential, : \\[F_Y(\\alpha, , \\tau) p_\\tau() = p_\\tau() + 1-p_\\tau() - e^{-m_\\tau()} e^{m_\\tau() (1-F_A(\\alpha, , \\tau))}  \\] \\[F_Y(\\alpha, ,\\tau) p_\\tau() = 1-e^{-m_\\tau()F_a(\\alpha, )}\\] \\[F_Y(\\alpha, ,\\tau) = \\frac{1-e^{-m_\\tau()F_A(\\alpha, ,\\tau)}}{p_\\tau()}.\\] PDF AoY found taking derivative \\(F_Y\\): \\[ \\begin{array}{rcl} Y \\sim f_Y(\\alpha, , \\tau) & = & \\frac{d F_Y(\\alpha, ,\\tau)}{d\\alpha} \\\\ &=&  \\; f_A(\\alpha, ) e^{-m_\\tau() F_A(\\alpha, ,\\tau)}   \\frac{\\textstyle{m_\\tau()}}{\\textstyle{p_\\tau()}}\\\\ \\end{array} \\]","code":""},{"path":"https://dd-harp.github.io/pf.memory/articles/Dynamics.html","id":"formulas-and-computation","dir":"Articles","previous_headings":"","what":"Formulas and Computation","title":"Random Variables for Parasite Infection Dynamics","text":"Let \\(z_\\tau(\\alpha,)\\) denote density infections age \\(\\alpha\\) host cohort age \\(\\) born day \\(\\tau\\). dynamics \\(z(\\alpha,)\\) described following: \\[ \\frac{\\partial z}{\\partial } + \\frac{\\partial z}{\\partial \\alpha} = - r z \\label{dzda} \\] boundary condition: \\[ \\begin{equation} z_\\tau(0,) = h_\\tau(). \\end{equation} \\] solutions given : \\[ z_\\tau(\\alpha,) = h_\\tau(-\\alpha) e^{-r \\alpha} \\] function zda computes \\(z_\\tau(\\alpha, ).\\) mean MoI given formula: \\[ m_\\tau() = \\int_0^z_\\tau(\\alpha, ) d \\alpha \\] distribution MoI Poisson (Nåsell , 1985)2 mean \\(m_\\tau().\\) function meanMoI computes \\(m_\\tau()\\) using zda true prevalence \\[ p_\\tau() = 1 - e^{-m_\\tau()} \\] function truePRa computes true prevalence using meanMoI density function age infection (AoI) \\[ A_\\tau() \\sim f_A(\\alpha, , \\tau) = \\frac{z_\\tau(\\alpha,)}{m_\\tau()} \\] moments \\[ x_n(, \\tau | h) = \\int_0^ \\alpha^n f_A(\\alpha, , \\tau) d \\alpha \\] age youngest infection (AoY) defined : \\[ Y_\\tau() \\sim f_Y(\\alpha, , \\tau) = \\min_{\\zeta \\sim M_\\tau()} \\left\\{ \\alpha_i \\right\\}_{=1}^\\zeta,  \\alpha_i \\sim A_\\tau() \\] density function can expressed terms density distribution functions AoI MoI. \\[ f_Y(\\alpha; , \\tau) = f_A(\\alpha, ,\\tau) e^{-m_\\tau() F_A(\\alpha, ,\\tau)} \\frac{m_\\tau()}{p_\\tau()}. \\] distribution function AoY : \\[ F_Y() \\sim \\frac{1-e^{-m_\\tau()F_A(\\alpha, ,\\tau)}}{1-e^{-m_\\tau()}} = \\frac{1-e^{-m_\\tau()F_A(\\alpha, ,\\tau)}}{p_\\tau()} \\label{FY} \\] moments : \\[ y_n(, \\tau | h) = \\int_0^ \\alpha^n f_Y(\\alpha | , \\tau, h) d \\alpha \\] also developed functions compute age youngest \\(N\\) infections, called AoYN \\[ N_\\tau() \\sim \\min_{N} \\left\\{ \\alpha_i \\right\\}_{=1}^N \\mbox { }  \\alpha_i \\sim A_\\tau() \\] distribution function AoYN, \\(N_\\tau()\\), \\[F_N(\\alpha, , t) \\sim 1- (1-F_A(\\alpha, , \\tau))^N\\] following summary table functions compute MoI, AoI, AoY, moments. density function AoYN found differentiating: \\[f_N(\\alpha, , t) \\sim N (1-F_A(\\alpha, , \\tau))^{N-1}\\frac{f_A(\\alpha, , \\tau)}{m_\\tau()}\\]","code":""},{"path":"https://dd-harp.github.io/pf.memory/articles/Dynamics.html","id":"quick-reference","dir":"Articles","previous_headings":"","what":"Quick Reference","title":"Random Variables for Parasite Infection Dynamics","text":"following summary table functions compute MoI, AoI, AoY, AoYN, moments.","code":""},{"path":[]},{"path":"https://dd-harp.github.io/pf.memory/articles/Dynamics.html","id":"force-of-infection-foi","dir":"Articles","previous_headings":"Demonstration","what":"Force of Infection (FoI)","title":"Random Variables for Parasite Infection Dynamics","text":"compute anything, must first set function describe exposure (see FoI vignette). define functions plot FoI cohort ages (red), can also compute population average FoI (black). Different cohorts experience different histories exposure.","code":""},{"path":"https://dd-harp.github.io/pf.memory/articles/Dynamics.html","id":"computing-zda","dir":"Articles","previous_headings":"Demonstration","what":"Computing zda","title":"Random Variables for Parasite Infection Dynamics","text":"function pf.memory::zda(alpha, , FoIpar, ...) uses formula Eq. 1 compute density parasite infections cohort humans ages. Using zda, can compute density parasites cohort age without solving full system equations. Given function describing FoI population, \\(h(t)\\), cohort birthday, \\(\\tau.\\) following computes density infections every age cohort age 3. plot \\(z_\\tau(\\alpha, )\\), note \\(\\alpha\\) grows larger, parasite cohort gets older. plot parasite cohorts age, time going backwards x-axis.  Now, can imagine zda look like several different host cohorts age three, born different times. effect, taking snapshot cohorts age, different times. curves different hosts born different months, thus experienced different levels exposure first two years life. annual FoI 5 infections, per person, per year (\\(\\bar h = 5/365\\)):","code":"alpha = 60 a = 6*365 zda(60, 6*365, foiP3) ## [1] 0.001601196 zz = zda(a3years, max(a3years), foiP3)"},{"path":"https://dd-harp.github.io/pf.memory/articles/Dynamics.html","id":"multiplicity-of-infection-moi","dir":"Articles","previous_headings":"","what":"Multiplicity of Infection (MoI)","title":"Random Variables for Parasite Infection Dynamics","text":"define random variable \\(M\\) describing multiplicity infection (MoI). distribution MoI Poisson (see MoI vignette). \\[M_\\tau() \\sim f_M(\\zeta; , \\tau) = \\mbox{Pois}(m_\\tau())\\] Since \\(z_\\tau(\\alpha, )\\) describes density infections age \\(\\alpha\\) cohort age \\(\\), density infections must MoI. Since \\(0 \\leq \\alpha < \\), must true : \\[\\begin{equation} \\tag{2} m_\\tau() = \\int_0^z_\\tau(\\alpha, ) d \\alpha \\end{equation}\\] function computes \\(m_\\tau()\\) called meanMoI. , plot average MoI host cohort ages:","code":"mm = meanMoI(a3years, foiP3, hhat=5/365)"},{"path":"https://dd-harp.github.io/pf.memory/articles/Dynamics.html","id":"age-of-infection-aoi","dir":"Articles","previous_headings":"","what":"Age of Infection (AoI)","title":"Random Variables for Parasite Infection Dynamics","text":"define random variable \\(A_\\tau()\\) describes age infection (AoI), given formula \\[ A_\\tau() \\sim f_A(\\alpha; , \\tau) = \\frac{z_\\tau(\\alpha,)}{m_\\tau()} \\]","code":""},{"path":"https://dd-harp.github.io/pf.memory/articles/Dynamics.html","id":"the-density-function-daoi","dir":"Articles","previous_headings":"Age of Infection (AoI)","what":"The Density Function, dAoI","title":"Random Variables for Parasite Infection Dynamics","text":"can compute \\(A_\\tau()\\) using density function dAoI:  Now, plot distribution AoI cohorts age two, born different months (), notice distributions changed shapes:","code":"f_A = dAoI(a3years, max(a3years), foiP3)"},{"path":"https://dd-harp.github.io/pf.memory/articles/Dynamics.html","id":"the-distribution-function-paoi","dir":"Articles","previous_headings":"Age of Infection (AoI)","what":"The Distribution Function, pAoI","title":"Random Variables for Parasite Infection Dynamics","text":"distribution function \\(A_\\tau()\\) : \\[ F_A() \\sim \\int_0^\\alpha f_A(\\alpha; , \\tau) d\\alpha \\] functions work correctly, get approximately answer computing cumulative sum dAoI. shouldn’t expect answers exactly , close, pAoI black.","code":"F_A = pAoI(a3years, max(a3years), foiP3) F_A_alt = cumsum(f_A) par(mar = c(5,4,1,1))  plot(a3years, F_A, type = \"l\",       xlab = \"Parasite Cohort Age\",       ylab = expression(1-F[X](alpha, a, tau)), lwd=3)  lines(a3years, F_A_alt, col = \"red\", lwd=2, lty =2)"},{"path":"https://dd-harp.github.io/pf.memory/articles/Dynamics.html","id":"random-numbers-raoi","dir":"Articles","previous_headings":"Age of Infection (AoI)","what":"Random Numbers, rAoI","title":"Random Variables for Parasite Infection Dynamics","text":"function rAoI uses pAoI generate random numbers \\(F_A(\\alpha)\\) simple visual check computes empirical CDF random variates \\(F_A(\\alpha)\\) computed using pAoI  can also plot distribution functions.","code":"rhx = rAoI(10000, 3*365, foiP3) par(mar = c(5,4,1,2)) plot(stats::ecdf(rhx), xlim = c(0,1095), cex=0.2, main = \"\",       xlab = expression(list(alpha, paste(\"Parasite Age (in Days)\"))),       ylab = expression(list(F[A](alpha), paste(\"ecdf\")))) lines(a3years, F_A, col = \"red\", lty = 2, lwd=2)"},{"path":"https://dd-harp.github.io/pf.memory/articles/Dynamics.html","id":"aoi-moments","dir":"Articles","previous_headings":"Age of Infection (AoI)","what":"AoI Moments","title":"Random Variables for Parasite Infection Dynamics","text":"Let \\(x\\) denote first moment \\(A_\\tau()\\): \\[x_\\tau() = \\left< A_\\tau() \\right> = \\int_0^\\infty \\alpha \\frac{z_\\tau(\\alpha, )} {m_\\tau()}\\] Similarly, let \\(x_\\tau()[n]\\) denote higher order moments \\(A_\\tau()\\): \\[x_{[n]}(, \\tau) = \\int_0^\\infty \\alpha^n \\frac{z_\\tau(\\alpha, )} {m_\\tau()}\\] first three moments AoY plotted time. top plot, ’ve also plotted \\(n^{th}\\) root \\(n^{th}\\) moment. ## Age Youngest Infection (AoY) derived random variable \\(Y_\\tau()\\) describing age youngest infection (AoY). density function AoY : \\[Y_\\tau() \\sim f_Y(\\alpha; , \\tau) = f_A(\\alpha, ,\\tau) e^{-m_\\tau() F_A(\\alpha, ,\\tau)} \\frac{m_\\tau()}{p_\\tau()}\\] distribution function : \\[F_Y() \\sim \\frac{1-e^{-m_\\tau()F_A(\\alpha, ,\\tau)}}{1-e^{-m_\\tau()}} = \\frac{1-e^{-m_\\tau()F_A(\\alpha, ,\\tau)}}{p_\\tau()} \\] derivations found Suppplement Henry JM, et al. (2024)3 mean AoY : \\[ \\left< Y_\\tau() \\right> = \\int_0^\\alpha \\; f_Y(\\alpha, , \\tau) \\; d\\alpha \\] higher order moments AoY : \\[\\left< Y_\\tau()^n \\right> = \\int_0^n \\alpha^n \\; f_y(\\alpha, , \\tau) \\; d\\alpha \\]","code":"moment1 = momentAoI(a3years, foiP3) moment2 = momentAoI(a3years, foiP3, n=2) moment3 = momentAoI(a3years, foiP3, n=3)"},{"path":"https://dd-harp.github.io/pf.memory/articles/Dynamics.html","id":"aoy-density-daoy","dir":"Articles","previous_headings":"Age of Infection (AoI)","what":"AoY Density, dAoY","title":"Random Variables for Parasite Infection Dynamics","text":"density function computed function dAoY. can compare \\(f_Y(\\alpha)\\) (black) \\(f_A(alpha)\\) (grey).","code":"f_Y = dAoY(a3years, 3*365, foiP3)"},{"path":"https://dd-harp.github.io/pf.memory/articles/Dynamics.html","id":"random-variables-raoy","dir":"Articles","previous_headings":"Age of Infection (AoI)","what":"Random Variables, rAoY","title":"Random Variables for Parasite Infection Dynamics","text":"","code":"raoy = rAoY(10^5, 3*365, foiP3) hist(raoy, breaks=seq(0, 1095, by = 15),       right=F, probability=T, main = \"\",       xlab = expression(list(alpha, paste(\"Parasite Age (in Days)\"))),       border = grey(0.5)) -> out lines(a3years, f_Y, type = \"l\", col = \"red\")"},{"path":"https://dd-harp.github.io/pf.memory/articles/Dynamics.html","id":"aoy-moments","dir":"Articles","previous_headings":"Age of Infection (AoI)","what":"AoY Moments","title":"Random Variables for Parasite Infection Dynamics","text":"first three moments AoY plotted time. top plot, ’ve also plotted \\(n^{th}\\) root \\(n^{th}\\) moment.  Next: vignette Multiplicity Infection: Hybrid Models, Queuing Models, Verification, show mean MoI computed using formula Eq. 2 gives answer approaches.","code":"aa = seq(5, 3*365, by = 5)  moment1y = momentAoY(aa, foiP3) moment2y = momentAoY(aa, foiP3, n=2) moment3y = momentAoY(aa, foiP3, n=3)"},{"path":"https://dd-harp.github.io/pf.memory/articles/FoI-TraceFunctions.html","id":"references","dir":"Articles","previous_headings":"","what":"References","title":"FoI Trace Functions","text":"G. R. Port, P. F. L. Boreham, J. H. Bryan, relationship host size feeding mosquitoes Anopheles Gambiae Giles complex (Diptera: Culicidae). Bulletin Entomological Research 70, 133–144 (1980). P. Carnevale, J. L. Frézil, M. F. Bosseno, F. Le Pont, J. Lancien, [aggressiveness Anopheles gambiae relation age sex human subjects]. Bull. World Health Organ. 56, 147–154 (1978). K. . Liebman, et al., Determinants Heterogeneous Blood Feeding Patterns Aedes Aegypti Iquitos, Peru. PLoS Negl. Trop. Dis. 8, e2702 (2014).","code":""},{"path":"https://dd-harp.github.io/pf.memory/articles/FoI.html","id":"references","dir":"Articles","previous_headings":"","what":"References","title":"The Force of Infection (FoI)","text":"G. R. Port, P. F. L. Boreham, J. H. Bryan, relationship host size feeding mosquitoes Anopheles Gambiae Giles complex (Diptera: Culicidae). Bulletin Entomological Research 70, 133–144 (1980). P. Carnevale, J. L. Frézil, M. F. Bosseno, F. Le Pont, J. Lancien, [aggressiveness Anopheles gambiae relation age sex human subjects]. Bull. World Health Organ. 56, 147–154 (1978). K. . Liebman, et al., Determinants Heterogeneous Blood Feeding Patterns Aedes Aegypti Iquitos, Peru. PLoS Negl. Trop. Dis. 8, e2702 (2014).","code":""},{"path":"https://dd-harp.github.io/pf.memory/articles/Guide.html","id":"dynamics","dir":"Articles","previous_headings":"","what":"Dynamics","title":"Memory and Malaria","text":"derived mathematical formulas describe dynamics malaria infections random variables cohorts humans age (Henry JM, et al., 2024)1 R package computational companion.","code":""},{"path":"https://dd-harp.github.io/pf.memory/articles/Guide.html","id":"formulas","dir":"Articles","previous_headings":"Dynamics","what":"Formulas","title":"Memory and Malaria","text":"Let \\(z_\\tau(\\alpha,)\\) denote density infections age \\(\\alpha\\) host cohort age \\(\\) born day \\(\\tau\\). dynamics \\(z(\\alpha,)\\) described following: \\[ \\frac{\\partial z}{\\partial } + \\frac{\\partial z}{\\partial \\alpha} = - r z \\label{dzda} \\] boundary condition: \\[ \\begin{equation} z_\\tau(0,) = h_\\tau(). \\end{equation} \\] solutions given : \\[ z_\\tau(\\alpha,) = h_\\tau(-\\alpha) e^{-r \\alpha} \\] function zda computes \\(z_\\tau(\\alpha, ).\\) mean MoI given formula: \\[ m_\\tau() = \\int_0^z_\\tau(\\alpha, ) d \\alpha \\] distribution MoI Poisson (Nåsell , 1985)2 mean \\(m_\\tau().\\) function meanMoI computes \\(m_\\tau()\\) using zda true prevalence \\[ p_\\tau() = 1 - e^{-m_\\tau()} \\] function truePRa computes true prevalence using meanMoI. density function age infection (AoI) \\[ A_\\tau() \\sim f_A(\\alpha, , \\tau) = \\frac{z_\\tau(\\alpha,)}{m_\\tau()} \\] age youngest infection (AoY) defined : \\[ Y_\\tau() \\sim f_Y(\\alpha, , \\tau) = \\min_{\\zeta \\sim M_\\tau()} \\left\\{ \\alpha_i \\right\\}_{=1}^\\zeta,  \\alpha_i \\sim A_\\tau() \\] density function can expressed terms density distribution functions AoI MoI. \\[ f_Y(\\alpha; , \\tau) = f_A(\\alpha, ,\\tau) e^{-m_\\tau() F_A(\\alpha, ,\\tau)} \\frac{m_\\tau()}{p_\\tau()}. \\] distribution function AoY : \\[ F_Y() \\sim \\frac{1-e^{-m_\\tau()F_A(\\alpha, ,\\tau)}}{1-e^{-m_\\tau()}} = \\frac{1-e^{-m_\\tau()F_A(\\alpha, ,\\tau)}}{p_\\tau()} \\label{FY} \\] also developed functions compute age youngest \\(N\\) infections, called AoYN \\[ \\min_{N} \\left\\{ \\alpha_i \\right\\}_{=1}^N,  \\alpha_i \\sim A_\\tau() \\] distribution function AoYN \\[F_N(\\alpha, , t) \\sim 1- (1-F_A(\\alpha, , \\tau))^N\\] following summary table functions compute MoI, AoI, AoY, moments.","code":""},{"path":"https://dd-harp.github.io/pf.memory/articles/Guide.html","id":"parasite-densities","dir":"Articles","previous_headings":"","what":"Parasite Densities","title":"Memory and Malaria","text":"\\(\\mu(\\alpha)\\) - probability density function mean, logged parasite densities given mean \\(\\beta'(\\mu)\\) - probability density function parasite densities, given mean \\(\\mu(\\sigma)\\) - variance function mean Parasite densities distribution parasite cohorts infecting cohort humans given age. Parasite densities cohort humans given age.","code":""},{"path":"https://dd-harp.github.io/pf.memory/articles/Guide.html","id":"table","dir":"Articles","previous_headings":"Parasite Densities","what":"Table","title":"Memory and Malaria","text":"\\[\\begin{equation*} \\begin{array}{cc|c|cccccccc} \\log_{10} \\mbox{Parasite Density}&& \\xi & 0 < \\xi < \\hat b() \\\\ & (\\mbox{} \\alpha) &    && P \\sim f_P(\\xi; ,\\tau) & F_P & \\left<P\\right>\\\\ & (\\mbox{} ) &    & & B \\sim f_B(\\xi; ,\\tau) & F_B & \\left<B\\right>\\\\ \\end{array} \\end{equation*}\\]","code":""},{"path":"https://dd-harp.github.io/pf.memory/articles/Guide.html","id":"detection","dir":"Articles","previous_headings":"","what":"Detection","title":"Memory and Malaria","text":"\\[\\begin{equation*} \\begin{array}{cc|c|cccccccc} \\mbox{Detection} & &\\hat p  & 0 \\leq \\hat p \\leq 1 &D \\sim f_C(0,\\xi)& \\hat p& \\\\  \\hline \\log_{10} \\mbox{Parasite Counts} & &\\hat \\xi & 0 < \\hat \\xi < \\xi &C \\sim f_C (\\hat \\xi; \\xi)&F_C& \\left<C\\right>\\\\  \\hline & \\mbox{Est PR}   & p &  0 \\leq p \\leq 1  &&& p_\\tau()\\\\ &\\mbox{MoI}  &\\zeta  & \\zeta \\{0,1,2,\\ldots} & M_\\tau() \\sim f_M(\\zeta; , \\tau) & & m_\\tau() \\\\   &\\mbox{Est MoI}  &\\hat \\zeta  & \\hat \\zeta \\{0,1,2,\\ldots, \\zeta} & \\hat M_\\tau() \\sim f_{\\hat M}(\\zeta; , \\tau) & & \\hat m_\\tau() \\\\  \\hline \\end{array} \\end{equation*}\\]","code":""},{"path":"https://dd-harp.github.io/pf.memory/articles/Hybrid.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Hybrid Models","text":"following, review hybrid models MoI, make brief observation prevalence, derive hybrid variables mean higher order moments AoI.","code":""},{"path":"https://dd-harp.github.io/pf.memory/articles/Hybrid.html","id":"moi","dir":"Articles","previous_headings":"","what":"MoI","title":"Hybrid Models","text":"random variable \\(M\\) describes distribution MoI population, follows Poisson. , provide numerical demonstration novel computational approach equivalent queuing model \\(M/M/\\infty\\), also equivalent hybrid models multiplicity infection (Nåsell, . 1985)1:","code":""},{"path":"https://dd-harp.github.io/pf.memory/articles/Hybrid.html","id":"mminfty","dir":"Articles","previous_headings":"MoI","what":"\\(M/M/\\infty\\)","title":"Hybrid Models","text":"Elsewhere, dynamics MoI described using queuing model \\(M/M/\\infty\\). MoI increases FoI, parasite can clear rate, \\(r\\). following diagram changes fraction population MoI \\(=\\), denoted \\(\\zeta_i\\), change host cohort force infection \\(h_\\tau(),\\) clearance. \\[\\begin{equation} \\begin{array}{ccccccccc} \\zeta_0 &  {h\\atop \\longrightarrow} \\atop {\\longleftarrow \\atop r} & \\zeta_1 & {h\\atop \\longrightarrow} \\atop {\\longleftarrow \\atop {2r}} & \\zeta_2 & {h \\atop \\longrightarrow} \\atop {\\longleftarrow \\atop {3r}} & \\zeta_3 & {h \\atop \\longrightarrow} \\atop {\\longleftarrow \\atop {4r}}& \\ldots \\end{array} \\end{equation}\\] master equations \\(M/M/\\infty\\) :\\[\\begin{equation} \\begin{array}{rl} \\frac{d\\zeta_0}{da} &= -h_\\tau() \\zeta_0 + r \\zeta_1   \\\\ \\frac{d\\zeta_i}{da} &= -\\left( h_\\tau\\left(\\right) + r \\right) \\zeta_i + h_\\tau\\left(\\right) \\zeta_{-1} + r\\left(+1\\right) \\zeta_{+1}   \\\\ \\end{array} \\end{equation}\\] master equations describe infinite set equations, find numerical solutions, must solve finite set equations. need compute maximum MoI vanishingly small portion distribution. constant \\(h\\), steady state distribution \\(\\zeta\\) Poisson mean \\(h/r.\\) set \\(N = \\max(4h/r,24),\\) tail negligible. , set range \\(1 \\pm 10^{-7}\\) plot portion distribution covered.  must define trace FoI function.  verify works, compute MoI day first three years life. peek distribution MoI = \\(1, \\ldots, 5\\) day 500:","code":"m = seq(0.1, 24) N = pmax(24, 4*m) plot(m, ppois(N,m), type = \"l\", ylim = c(1-1e-07,1+1e-07)) solveMMinfty(3/365, foiP3) -> out"},{"path":"https://dd-harp.github.io/pf.memory/articles/Hybrid.html","id":"nåsells-hybrid-model","dir":"Articles","previous_headings":"MoI","what":"Nåsell’s Hybrid Model","title":"Hybrid Models","text":"can also solve hybrid equation get mean MoI (Nåsell, . 1985)\\(^1\\): \\[\\frac{dm}{da} = h - rm\\] unction dmda computes derivative, can solve hybrid equation using solve_dm plot output:","code":"solve_dm(3/365, foiP3) -> mt  plot(mt$time, mt$m, type = \"l\",       xlab = \"Age (in Days)\", ylab = expression(m[tau](a)))"},{"path":"https://dd-harp.github.io/pf.memory/articles/Hybrid.html","id":"numerical-verification","dir":"Articles","previous_headings":"MoI","what":"Numerical Verification","title":"Hybrid Models","text":"presented three ways computing mean MoI using cohort ages arbitrary function \\(h_\\tau()\\): Using meanMoI integrates zda: \\[\\int_0^z_\\tau(\\alpha, ) d\\alpha\\] solving queuing model \\(M/M/\\infty\\), compartmental model tracks full distribution MoI, competing mean: solving hybrid model tracking mean MoI. following plots three graph using different colors different widths, colors, patterns:  maximum errors order \\(1e-07\\) developed hybrid model can use compute mean higher order moments age infection (AoI). related vignette (AoI), define AoI random variable develop functions compute moments. , develop notation moments:","code":"aa = 0:1825 v1 = meanMoI(aa, foiP3, hhat=5/365) v2 = solveMMinfty(5/365, foiP3, Amax=1825)$m v3 = solve_dm(5/365, foiP3, Amax=1825)[,2] par(mfrow = c(2,2))  plot(aa, v1, type = \"l\", col = \"red\", lwd=4,       xlab = \"Age (in Days)\",       ylab = expression(m[tau](a)),       main = \"meanMoI\")  plot(aa, v2, type = \"l\", lwd=2,       xlab = \"Age (in Days)\",       ylab = expression(m[tau](a)),       main = \"solveMMinfty\") lines(aa, v2, type = \"l\", col = \"yellow\", lwd=2, lty=2)  plot(aa, v3, type = \"l\", col = \"darkblue\", lwd=1,       xlab = \"Age (in Days)\",       ylab = expression(m[tau](a)),       main = \"solve_dm\")  plot(aa, v1, type = \"l\", col = \"red\", lwd=4,       xlab = \"Age (in Days)\",       ylab = expression(m[tau](a)),       main = \"All Three\") lines(aa, v2, type = \"l\", col = \"yellow\", lwd = 2) lines(aa, v3, type = \"l\", col = \"darkblue\", lwd = 2, lty =2) c(max(abs(v1-v2)), max(abs(v2-v3)), max(abs(v1-v3))) ## [1] 2.511903e-09 1.785516e-13 2.511903e-09"},{"path":"https://dd-harp.github.io/pf.memory/articles/Hybrid.html","id":"prevalence","dir":"Articles","previous_headings":"","what":"Prevalence","title":"Hybrid Models","text":"George Maccdonald published model superinfection 19502. presenting model, Macdonald trying solve problem: super-infection possible, long take person clear parasites become uninfected ? Macdonald proposed solution, problem mathematical formulation (essay Paul Fine, 1975, recommended reading)3: model Macdonald described didn’t match function used. model formulated part Garki project (Dietz K, et al., 1974)4, model allowed superinfection proposed useful approximating model. One solution came taking hybrid modeling approach (Nåsell , 1985)5, just discussed. Nåsell showed distribution MoI converge Poisson distribution: \\[M(t) \\sim f_M(\\zeta; m) = \\mbox{Pois}(m(t))\\] Since \\(m\\) mean Poisson, prevalence infection complement zero term: \\[p(t) = 1-\\mbox{Pois}(\\zeta =0; m(t)) = 1 - e^{-m(t)}\\] , nevertheless, sometimes useful know clearance rate, transition MoI = 1 MoI=0. Clearance infected class can occur person infected MoI one, infection clears: \\[ R(m) = r \\frac{\\mbox{Pr}(\\zeta=1; m(t))}{\\mbox{Pr}(\\zeta>0; m(t))} = r \\frac{m}{e^m - 1} \\] change prevalence thus described equation: \\[ \\frac{dp}{dt} = h(1-p)-R(m)p \\] interesting, solves problem modeling clearance superinfection, equation depends \\(m\\). Since can compute \\(p(t)\\) directly \\(m(t)\\), equation redundant. Code exists pf.memory compute prevalence three ways: Using function truePRa Using hybrid equations solve_dpda hybrid model solve_dm \\(p(t)= 1 - exp(-m(t))\\)","code":""},{"path":"https://dd-harp.github.io/pf.memory/articles/Hybrid.html","id":"aoi---hybrid-variables","dir":"Articles","previous_headings":"","what":"AoI - Hybrid Variables","title":"Hybrid Models","text":"Let \\(x = \\left< \\right>;\\) x first moment AoI cohort age \\(\\), conditioned history exposure, given function \\(h\\). longer form: \\[x_\\tau(; h) = \\left< A_\\tau(; h) \\right> = \\int_0^\\infty \\alpha \\frac{z_\\tau(\\alpha, ; h_\\tau())} {m_\\tau(;h_\\tau())}\\] , show : \\[ \\frac{\\textstyle{dx}}{\\textstyle{da}} = 1- \\frac{\\textstyle{h}}{\\textstyle{m}} x   \\] Similarly, let \\(x_{[n]} = \\left< ^n \\right>\\) denote higher order moments random variable \\(\\). longer form: \\[x_{n}(, \\tau; h) = \\int_0^\\infty \\alpha^n \\frac{z_\\tau(\\alpha, ; h_\\tau())} {m_\\tau(;h_\\tau())}\\] show higher order moments can computed recursively: \\[ \\frac{\\textstyle{dx_{[n]}}}{\\textstyle{da}} = nx_{[n-1]} -     \\frac{\\textstyle{h}}{\\textstyle{m}} x_{[n]} \\] following, first demonstrate hybrid equations give answers direct computation moments.","code":""},{"path":"https://dd-harp.github.io/pf.memory/articles/Hybrid.html","id":"solving","dir":"Articles","previous_headings":"AoI - Hybrid Variables","what":"Solving","title":"Hybrid Models","text":"function solve_dAoI computes first three moments AoI default. plot \\(n^{th}\\) root first three moments.","code":"par(mar = c(7, 4, 2, 2)) solve_dAoI(5/365, foiP3) -> mt  plot(mt$time, mt$xn1, type = \"l\", xlab = \"Age (in Days)\", ylab = expression(list(x, sqrt(x[paste(\"[2]\")]), sqrt(x[paste(\"[3]\")], 3))), ylim = range(mt$xn3^(1/3)))  lines(mt$time, mt$xn2^(1/2), col = \"purple\") lines(mt$time, mt$xn3^(1/3), col = \"darkgreen\")"},{"path":"https://dd-harp.github.io/pf.memory/articles/Hybrid.html","id":"numerical-verification-1","dir":"Articles","previous_headings":"AoI - Hybrid Variables","what":"Numerical Verification","title":"Hybrid Models","text":"solving hybrid model variables track moments, using equations derived :","code":"aa = seq(5, 5*365, by = 5)  moment1 = momentAoI(aa, foiP3) moment2 = momentAoI(aa, foiP3, n=2) moment3 = momentAoI(aa, foiP3, n=3) solve_dAoI(5/365, foiP3, Amax = 5*365, dt=5) -> mt par(mfrow = c(2,2), mar = c(7, 4, 2, 2)) # Top Left plot(mt$time, mt$xn1, type = \"l\", xlab = \"Age (in Days)\", ylab = expression(x), lwd=3)  lines(aa, moment1, col = \"yellow\", lwd=2, lty=2)  # Top Right  plot(mt$time, mt$xn2, type = \"l\", xlab = \"Age (in Days)\", ylab = expression(x[paste(\"[2]\")]), lwd=3, col = \"purple\")  lines(aa, moment2, col = \"yellow\", lwd=2, lty=2) plot(mt$time, mt$xn3, type = \"l\", lwd=3, col = \"darkgreen\",      xlab = \"Age (in Days)\", ylab = expression(x[paste(\"[3]\")])) lines(aa, moment3, col = \"yellow\", lwd=2, lty=2) par(mar = c(7, 4, 2, 2)) solve_dAoI(5/365, foiP3) -> mt  plot(mt$time, mt$xn1, type = \"l\", xlab = \"Age (in Days)\", ylab = expression(list(x, sqrt(x[paste(\"[2]\")]), sqrt(x[paste(\"[3]\")], 3))), lwd=3, ylim = range(mt$xn3^(1/3)))  lines(mt$time, mt$xn2^(1/2), col = \"purple\", lwd=3) lines(mt$time, mt$xn3^(1/3), col = \"darkgreen\", lwd=3)  lines(aa, moment1, col = \"yellow\", lwd=2, lty=2) lines(aa, moment2^(1/2), col = \"yellow\", lwd=2, lty=2) lines(aa, moment3^(1/3), col = \"yellow\", lwd=2, lty=2)"},{"path":"https://dd-harp.github.io/pf.memory/articles/Hybrid.html","id":"aoy---hybrid-variables","dir":"Articles","previous_headings":"","what":"AoY - Hybrid Variables","title":"Hybrid Models","text":"Let \\(y\\) denote first moment AoY. \\[ y_\\tau() = \\int_0^\\alpha \\; f_Y(\\alpha, , \\tau) \\; d\\alpha \\] differential equation \\(y_\\tau()\\) : \\[ \\frac{dy}{da} = 1 - \\frac{h}{p} y + F(r,m) \\frac{x}{p} \\] verify, can compute moment directly. function solve_dAoYda gives solutions: moments can computed directly using momentAoY following plots first moment computed ways:","code":"solve_dAoYda(5/365, foiP3, Amax=5*365, dt=5, n=9) -> mt moment1y = momentAoY(aa, foiP3, hhat=5/365)"},{"path":"https://dd-harp.github.io/pf.memory/articles/MoI.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Multiplicity of Infection","text":"random variable \\(M\\) describes distribution MoI population, follows Poisson. , provide numerical demonstration novel computational approach equivalent queuing model \\(M/M/\\infty\\), also equivalent hybrid models multiplicity infection (Nåsell, . 1985)1:","code":""},{"path":"https://dd-harp.github.io/pf.memory/articles/MoI.html","id":"mminfty","dir":"Articles","previous_headings":"","what":"\\(M/M/\\infty\\)","title":"Multiplicity of Infection","text":"Elsewhere, dynamics MoI described using queuing model \\(M/M/\\infty\\). MoI increases FoI, parasite can clear rate, \\(r\\). following diagram changes fraction population MoI \\(=\\), denoted \\(\\zeta_i\\), change host cohort force infection \\(h_\\tau(),\\) clearance. \\[\\begin{equation} \\begin{array}{ccccccccc} \\zeta_0 &  {h\\atop \\longrightarrow} \\atop {\\longleftarrow \\atop r} & \\zeta_1 & {h\\atop \\longrightarrow} \\atop {\\longleftarrow \\atop {2r}} & \\zeta_2 & {h \\atop \\longrightarrow} \\atop {\\longleftarrow \\atop {3r}} & \\zeta_3 & {h \\atop \\longrightarrow} \\atop {\\longleftarrow \\atop {4r}}& \\ldots \\end{array} \\end{equation}\\] master equations \\(M/M/\\infty\\) :\\[\\begin{equation} \\begin{array}{rl} \\frac{d\\zeta_0}{da} &= -h_\\tau() \\zeta_0 + r \\zeta_1   \\\\ \\frac{d\\zeta_i}{da} &= -\\left( h_\\tau\\left(\\right) + r \\right) \\zeta_i + h_\\tau\\left(\\right) \\zeta_{-1} + r\\left(+1\\right) \\zeta_{+1}   \\\\ \\end{array} \\end{equation}\\] master equations describe infinite set equations, find numerical solutions, must solve finite set equations. need compute maximum MoI vanishingly small portion distribution. constant \\(h\\), steady state distribution \\(\\zeta\\) Poisson mean \\(h/r.\\) set \\(N = \\max(4h/r,24),\\) tail negligible. , set range \\(1 \\pm 10^{-7}\\) plot portion distribution covered.  must define trace FoI function.  verify works, compute MoI day first three years life. peek distribution MoI = \\(1, \\ldots, 5\\) day 500:","code":"m = seq(0.1, 24) N = pmax(24, 4*m) plot(m, ppois(N,m), type = \"l\", ylim = c(1-1e-07,1+1e-07)) solveMMinfty(3/365, foiP3) -> out"},{"path":"https://dd-harp.github.io/pf.memory/articles/MoI.html","id":"hybrid-model","dir":"Articles","previous_headings":"","what":"Hybrid Model","title":"Multiplicity of Infection","text":"can also solve hybrid equation get mean MoI (Nåsell, . 1985)\\(^1\\): \\[\\frac{dm}{da} = h - rm\\] unction dmda computes derivative, can solve hybrid equation using solve_dm plot output:","code":"solve_dm(3/365, foiP3) -> mt  plot(mt$time, mt$m, type = \"l\",       xlab = \"Age (in Days)\", ylab = expression(m[tau](a)))"},{"path":"https://dd-harp.github.io/pf.memory/articles/MoI.html","id":"verification","dir":"Articles","previous_headings":"","what":"Verification","title":"Multiplicity of Infection","text":"presented three ways computing mean MoI using cohort ages arbitrary function \\(h_\\tau()\\): Using meanMoI integrates zda: \\[\\int_0^z_\\tau(\\alpha, ) d\\alpha\\] solving queuing model \\(M/M/\\infty\\), compartmental model tracks full distribution MoI, competing mean: solving hybrid model tracking mean MoI. following plots three graph using different colors different widths, colors, patterns:  maximum errors order \\(1e-07\\)","code":"aa = 0:1825 v1 = meanMoI(aa, foiP3, hhat=5/365) v2 = solveMMinfty(5/365, foiP3, Tmax=1825)$m v3 = solve_dm(5/365, foiP3, Tmax=1825)[,2] par(mfrow = c(2,2))  plot(aa, v1, type = \"l\", col = \"red\", lwd=4,       xlab = \"Age (in Days)\",       ylab = expression(m[tau](a)),       main = \"meanMoI\")  plot(aa, v2, type = \"l\", lwd=2,       xlab = \"Age (in Days)\",       ylab = expression(m[tau](a)),       main = \"solveMMinfty\") lines(aa, v2, type = \"l\", col = \"yellow\", lwd=2, lty=2)  plot(aa, v3, type = \"l\", col = \"darkblue\", lwd=1,       xlab = \"Age (in Days)\",       ylab = expression(m[tau](a)),       main = \"solve_dm\")  plot(aa, v1, type = \"l\", col = \"red\", lwd=4,       xlab = \"Age (in Days)\",       ylab = expression(m[tau](a)),       main = \"All Three\") lines(aa, v2, type = \"l\", col = \"yellow\", lwd = 2) lines(aa, v3, type = \"l\", col = \"darkblue\", lwd = 2, lty =2) c(max(abs(v1-v2)), max(abs(v2-v3)), max(abs(v1-v3))) ## [1] 1.833689e-07 9.797276e-08 1.833689e-07"},{"path":"https://dd-harp.github.io/pf.memory/articles/Parasite_Densities.html","id":"expected-logged-densities","dir":"Articles","previous_headings":"","what":"Expected Logged Densities","title":"Parasite Density Distributions","text":"pf.memory, S3 function family developed model relationship age infection (AoI) parasite infection, \\(\\alpha\\), mean, \\(\\mu(\\alpha).\\)","code":""},{"path":"https://dd-harp.github.io/pf.memory/articles/Parasite_Densities.html","id":"alpha2mu-base","dir":"Articles","previous_headings":"Expected Logged Densities","what":"alpha2mu.base","title":"Parasite Density Distributions","text":"function alpha2mu.base following form: \\[\\begin{equation} F_\\mu(\\alpha) = \\begin{cases}     \\text{NA} \\ & \\mbox{} 0 \\leq \\alpha < 7 \\\\[10pt]       l + (b - l)  \\frac{{\\textstyle \\alpha}}{{\\delta}}   & \\mbox{} 7 \\leq \\alpha \\leq \\delta  \\\\[10pt]      l + (b - l) e^{-s_\\alpha (\\alpha-\\delta)}   & \\mbox{} \\alpha \\geq \\delta\\\\   \\end{cases} \\label{mualpha} \\end{equation}\\]","code":""},{"path":"https://dd-harp.github.io/pf.memory/articles/Parasite_Densities.html","id":"the-function-alpha2mu-chronic-has-the-following-form","dir":"Articles","previous_headings":"Expected Logged Densities","what":"The function alpha2mu.chronic has the following form:","title":"Parasite Density Distributions","text":"\\[\\begin{equation} F_\\mu(\\alpha) = l + (b - l) e^{-s_\\alpha (\\alpha-\\delta)}    \\end{equation}\\] pf.memory, functions set parameters case, -writable defaults: plot two functions : default parameters (black), parameters (dark blue): ## Parasite Density Distributions developed function family compute parasite densities function mean logged parasite densities, \\(\\mu\\)","code":"base_pars = par_Fmu_base() base_pars1 = par_Fmu_base(tildeb=11, Sa=0.0045) chronic_pars = par_Fmu_chronic() aalpha = 7:366 mu_alpha =  alpha2mu(aalpha, 0, base_pars) mu_alpha1 =  alpha2mu(aalpha, 0, base_pars1) mu_alpha2 =  alpha2mu(aalpha, 0, chronic_pars) parD = par_mu2dens_beta()  d_mu2density(9, 9, parD) ## [1] 0.4593359 par(mfrow = c(2,2)) xx = seq(0, 13, by=0.1) plot(xx, d_mu2density(xx, 9, parD), type = \"l\",       xlab = expression(xi), ylab = \"d_mu2density\", main = \"d_mu2density\") lines(xx, d_mu2density(xx, 7,  parD), col = \"darkred\") pp = seq(0,13, by = 0.01) plot(pp, p_mu2density(pp, 9,  parD), type = \"l\",       xlab = expression(xi), ylab = \"p_mu2density\", main = \"p_mu2density\") lines(xx, p_mu2density(xx, 7, parD), col = \"darkred\") hist(r_mu2density(1000, 9, parD), xlab = expression(xi),       main = \"r_mu2density\", xlim = c(0,13)) qq = seq(0.01,.99, length.out=100) plot(qq, q_mu2density(qq, 9,  parD), type = \"l\",       xlab = expression(xi), ylab = \"q_mu2density\", main = \"q_mu2density\")"},{"path":"https://dd-harp.github.io/pf.memory/articles/Parasite_Densities.html","id":"simple-infections","dir":"Articles","previous_headings":"","what":"Simple Infections","title":"Parasite Density Distributions","text":"first look density parasites simple infections – MoI = 1. compute anything, need function model exposure, FoI function age, \\(h_\\tau()\\). Notably, function accepts birth date, \\(\\tau\\) argument, can used look cohorts different birth dates. , show FoI function age two cohorts born six months apart.  one cohorts (black line), plotted density parasite cohorts. Notably, age cohorts representing infections occurred \\(\\alpha\\) days ago, \\(x-\\)axis looking past:  Now want understand parasite densities cohort humans. compute full probability distribution function cohort 5-year olds, use bits information: Mean logged parasite densities parasite infection age, \\(\\mu(\\alpha)\\) density cohorts age, \\(A_\\tau()\\)  parasite age, can plot probability density function. , show probability density function parasite infection age \\(60\\) days:  Now, parasite densities simple infections given distribution mean logged parasite densities. compute full distribution, create mesh \\(\\xi\\): every age infection, \\(\\alpha\\) compute expected parasite densities \\(\\mu(\\alpha)\\) compute full parasite density distribution, multiplied density parasites age \\(\\alpha\\): \\[\\phi(\\alpha) = P(\\mu(\\alpha))\\; f_A(\\alpha, )\\] add \\(\\phi(\\alpha)\\) appropriate bin, defined mesh \\(\\xi\\). function dPdensity computes parasite distributions function host age, given function describing history exposure.  can check ensure distribution function integrates 1:","code":"mu_alpha =  alpha2mu(a5years, 0, base_pars) dAoI(a5years, 5*365, foiP3) -> dalpha alpha = 60 fA = dAoI(alpha, 5*365, foiP3) Pmu = fA*d_alpha2density(xx, alpha, 5*365) Pa = d_Pdensity(xx, 5*365, foiP3) integrate(d_Pdensity, 0, 13, a=5*365, FoIpar=foiP3)$value ## [1] 1.000014"},{"path":[]},{"path":"https://dd-harp.github.io/pf.memory/articles/Simple_Infections.html","id":"mean-logged-parasite-densities-mualpha","dir":"Articles","previous_headings":"","what":"Mean, logged parasite densities, \\(\\mu(\\alpha)\\)","title":"Parasite Densities in Simple Infections","text":"pf.memory, S3 function family developed model relationship age infection (AoI) parasite infection, \\(\\alpha\\), mean, \\(\\mu(\\alpha).\\) function alpha2mu.base following form: \\[\\begin{equation} \\mu(\\alpha) = \\begin{cases}     \\text{NA} \\ & \\mbox{} 0 \\leq \\alpha < 7 \\\\[10pt] %      l +  (b - l)  \\frac{{\\textstyle \\alpha}}{{\\textstyle D}}   & \\mbox{} 7 \\leq \\alpha \\leq D  \\\\[10pt]       l + (b - l)  \\frac{{\\textstyle \\alpha}}{{\\textstyle \\delta}}   & \\mbox{} 7 \\leq \\alpha \\leq \\delta  \\\\[10pt]      l + (b - l) e^{-s_\\alpha (\\alpha-\\delta)}   & \\mbox{} \\alpha \\geq \\delta\\\\   \\end{cases} \\label{mualpha} \\end{equation}\\] pf.memory, functions set parameters case, -writable defaults: plot two functions : default parameters (black), parameters (dark blue):","code":"base_pars = par_alpha2mu_base() base_pars1 = par_alpha2mu_base(tildeb=11, Sa=0.0045) aalpha = 7:366 mu_alpha =  alpha2mu(aalpha, 0, base_pars) mu_alpha1 =  alpha2mu(aalpha, 0, base_pars1)"},{"path":"https://dd-harp.github.io/pf.memory/articles/Simple_Infections.html","id":"p_mu","dir":"Articles","previous_headings":"","what":"\\(P_\\mu\\)","title":"Parasite Densities in Simple Infections","text":"developed function family compute parasite densities function mean logged parasite densities, \\(\\mu\\)","code":"par(mfrow = c(2,2)) xx = seq(0, 13, by=0.1) plot(xx, dDensityPmu(xx,9), type = \"l\", xlab = expression(x), ylab = \"dDensityPmu\", main = \"dDensityPmu\") lines(xx, dDensityPmu(xx, 7), col = \"darkred\") pp = seq(0,13, by = 0.01) plot(pp, pDensityPmu(pp,9), type = \"l\", xlab = expression(x), ylab = \"pDensityPmu\", main = \"pDensityPmu\") lines(xx, pDensityPmu(xx, 7), col = \"darkred\") hist(rDensityPmu(1000, 9), main = \"rDensityPmu\", xlim = c(0,13)) qq = seq(0.01,.99, length.out=100) plot(qq, qDensityPmu(qq,9), type = \"l\", xlab = expression(x), ylab = \"qDensityPmu\", main = \"qDensityPmu\")"},{"path":"https://dd-harp.github.io/pf.memory/articles/Simple_Infections.html","id":"pxi-alpha","dir":"Articles","previous_headings":"","what":"\\(P(\\xi, \\alpha)\\)","title":"Parasite Densities in Simple Infections","text":"must specify function model exposure:  age five, distribution age infection looks like :  compute parasite density distributions, need construct mesh \\(\\xi.\\) function dDensityPa computes parasite distributions function host age, given function describing history exposure. Now, parasite densities simple infections given distribution mean logged parasite densities.","code":"meshX= seq(0, 13, by=.1) Pmu = dDensityPa(meshX,5*365, foiP3)"},{"path":"https://dd-harp.github.io/pf.memory/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"David L. Smith. Author, maintainer. John M. Henry. Author.","code":""},{"path":"https://dd-harp.github.io/pf.memory/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Smith D, Henry J (2024). pf.memory: Probabilistic Approaches Malaria Parasite Infections. R package version 0.1.0, https://dd-harp.github.io/pf.memory/.","code":"@Manual{,   title = {pf.memory: Probabilistic Approaches to Malaria Parasite Infections},   author = {David L. Smith and John M. Henry},   year = {2024},   note = {R package version 0.1.0},   url = {https://dd-harp.github.io/pf.memory/}, }"},{"path":"https://dd-harp.github.io/pf.memory/index.html","id":"pfmemory----the-age-of-infection-immunity--malaria-epidemiology","dir":"","previous_headings":"","what":"Probabilistic Approaches to Malaria Parasite Infections","title":"Probabilistic Approaches to Malaria Parasite Infections","text":"software set computational algorithms implements synthetic approach malaria epidemiology, defined narrowly include exposure bites infective mosquitoes, dynamics infection (including superinfection). epidemiology Plasmodium falciparum malaria presents unique set challenges due complex dynamics infection, immunity, disease infectiousness well treatment chemo-protection, diagnostics detection. Malaria can measured dozen different ways, difficult present simple synthesis malaria infection disease terms metrics commonly used research clinical surveillance. important metric Plasmodium falciparum parasite rate, PfPR, defined average prevalence malaria taken cross-sectional survey. Another metric, often measured covariate research studies, parasite count, number parasites blood slide field counted light microscopist. old data set, collected malariotherapy, parasite counts fluctuated substantially time course infection, strongly statistically correlated age infection AoI (Henry JM, et al., 2022)1. malaria, PfPR several old studies characterstic shape plotted age. patterns also differ diagnostic method, season, sex, location. Parasite densities used correlate disease. many interacting factors, challenge develop model deal everything. One approach studying malaria infection develop mechanistic models dynamics malaria infection within single host. prominent models type OpenMalaria eMod, several others. computational models made possible develope comprehensive individual-based simulation models, IBMs, malaria policy. approaches able replicate patterns, outputs models usually just complex data collected field studies. synthesis malaria epidemiology proven elusive. present computational algorithms support probabilistic approach malaria epidemiology. start semi-Markovian model malaria exposure infection, whose states represented random variables describe multiplicity infection (MoI) host age infection (AoI). Assuming parasite densities , least statistically, predicted AoI, can compute probability distribution functions describing parasite densities, parasite counts, detection individual chosen random population. , present model parasite detection parasite counts. approach extended predict disease, immunity, treatment anti-malarial drugs, brief period chemo-protection. probabilistic approach highly realistic descriptive, goal synthesis. synthesis involves steps: derive variables can track mean MoI, mean AoI moments, probability detection. Hybrid models MoI already exist, show approach can extended systems differential equations track mean higher order moments distribution AoI. new random variable describing age youngest infection (AoY). show variable serves basis computing parasite density distributions complex infections. derive hybrid model variable approximates mean AoY. demonstrate simple system ordinary differential equations can used place probabilistic models compute values research metrics. put another way, can reduce behavior highly complex probabilistic systems simple system equations high degree accuracy. computational conceptual simplicity hybrid models simplicity compartmental models stochastic individual-based models, supporting probabilistic framework, provide sound basis synthesis observational malaria epidemiology.","code":""},{"path":[]},{"path":"https://dd-harp.github.io/pf.memory/reference/Bda.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute \\(B_\\tau(a | h)\\) — Bda","title":"Compute \\(B_\\tau(a | h)\\) — Bda","text":"$$f_B(\\xi; , \\tau |h) = \\log_{10} \\left( \\sum_{M_\\tau(|h)>0} 10^{P_\\tau(|h)}\\right)$$","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/Bda.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute \\(B_\\tau(a | h)\\) — Bda","text":"","code":"Bda(   meshX,   a,   FoIpar,   tau = 0,   hhat = 1,   r = 1/200,   par_RBC = par_lRBC_static(),   Fmu_par = Fmu_par_base(),   mu_par = mu_par_beta(),   pWda = par_Wda_none() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/Bda.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute \\(B_\\tau(a | h)\\) — Bda","text":"meshX mesh parasite densities host cohort age FoIpar parameters define FoI function tau cohort birthday hhat local scaling parameter FoI r clearance rate simple infection par_RBC parameters compute log10RBC Fmu_par parameters compute alpha2mu mu_par parameters compute d_mu2density pWda parameters dispatch Wda","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/Bda.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute \\(B_\\tau(a | h)\\) — Bda","text":"numeric vector length meshX","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/Bdensity.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute \\(B_\\tau(a | h)\\) — Bdensity","title":"Compute \\(B_\\tau(a | h)\\) — Bdensity","text":"function first computes PDF simple infections, d_Pdensity, computes CDF full distribution, summed MoI = 1 large number using convolutions.","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/Bdensity.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute \\(B_\\tau(a | h)\\) — Bdensity","text":"","code":"Bdensity(   meshX,   a,   FoIpar,   tau = 0,   hhat = 1,   r = 1/200,   RBC_par = par_lRBC_static(),   Fmu_par = par_Fmu_base(),   mu_par = par_mu2dens_beta(),   pWda = par_Wda_none() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/Bdensity.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute \\(B_\\tau(a | h)\\) — Bdensity","text":"meshX mesh parasite densities host cohort age FoIpar parameters define FoI function tau cohort birthday hhat local scaling parameter FoI r clearance rate simple infection RBC_par parameters compute log10RBC Fmu_par parameters compute alpha2mu mu_par parameters compute d_mu2density pWda parameters dispatch Wda","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/Bdensity.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute \\(B_\\tau(a | h)\\) — Bdensity","text":"numeric vector length meshX","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/Detect.html","id":null,"dir":"Reference","previous_headings":"","what":"Detection of infection given parasitemia — Detect","title":"Detection of infection given parasitemia — Detect","text":"Detection infection given parasitemia","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/Detect.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Detection of infection given parasitemia — Detect","text":"","code":"Detect(xi, a = 0, Cpar = par_nbCounts())"},{"path":"https://dd-harp.github.io/pf.memory/reference/Detect.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Detection of infection given parasitemia — Detect","text":"xi mean \\(\\log_{10}\\) parasite densities host cohort age Cpar parameters define detection function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/Detect.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Detection of infection given parasitemia — Detect","text":"binary detection result","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/Detect.nb.html","id":null,"dir":"Reference","previous_headings":"","what":"Detection of infection given parasitemia — Detect.nb","title":"Detection of infection given parasitemia — Detect.nb","text":"Detection infection given parasitemia","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/Detect.nb.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Detection of infection given parasitemia — Detect.nb","text":"","code":"# S3 method for nb Detect(xi, a = 0, Cpar = par_nbCounts())"},{"path":"https://dd-harp.github.io/pf.memory/reference/Detect.nb.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Detection of infection given parasitemia — Detect.nb","text":"xi mean log10 parasite densities host cohort age Cpar parameters define detection function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/Detect.nb.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Detection of infection given parasitemia — Detect.nb","text":"binary detection result","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/Detect.pois.html","id":null,"dir":"Reference","previous_headings":"","what":"Detection of infection given parasitemia — Detect.pois","title":"Detection of infection given parasitemia — Detect.pois","text":"Detection infection given parasitemia","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/Detect.pois.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Detection of infection given parasitemia — Detect.pois","text":"","code":"# S3 method for pois Detect(xi, a = 0, Cpar = par_poisCounts())"},{"path":"https://dd-harp.github.io/pf.memory/reference/Detect.pois.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Detection of infection given parasitemia — Detect.pois","text":"xi mean log10 parasite densities host cohort age Cpar parameters define detection function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/Detect.pois.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Detection of infection given parasitemia — Detect.pois","text":"binary detection result","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/DetectBda.html","id":null,"dir":"Reference","previous_headings":"","what":"Detection of infection given parasitemia — DetectBda","title":"Detection of infection given parasitemia — DetectBda","text":"Detection infection given parasitemia","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/DetectBda.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Detection of infection given parasitemia — DetectBda","text":"","code":"DetectBda(   a,   FoIpar,   dx = 0.1,   tau = 0,   hhat = 1,   r = 1/200,   par_RBC = par_lRBC_static(),   Fmu_par = par_Fmu_base(),   par_mu2dens = par_mu2dens_beta(),   pWda = par_Wda_none(),   pC = par_nbCounts() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/DetectBda.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Detection of infection given parasitemia — DetectBda","text":"host cohort age FoIpar parameters define FoI function dx width mesh tau cohort birthday hhat local scaling parameter FoI r clearance rate simple infection par_RBC parameters compute log10RBC Fmu_par parameters compute alpha2mu par_mu2dens parameters compute d_mu2density pWda parameters dispatch Wda pC parameters define detection function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/DetectBda.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Detection of infection given parasitemia — DetectBda","text":"binary detection result","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/DetectPM.html","id":null,"dir":"Reference","previous_headings":"","what":"Detection of infection given parasitemia — DetectPM","title":"Detection of infection given parasitemia — DetectPM","text":"Detection infection given parasitemia","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/DetectPM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Detection of infection given parasitemia — DetectPM","text":"","code":"DetectPM(   a,   FoIpar,   tau = 0,   hhat = 1,   r = 1/200,   par_RBC = par_lRBC_static(),   Fmu_par = par_Fmu_base(),   par_mu2dens = par_mu2dens_beta(),   pWda = par_Wda_none(),   pC = par_nbCounts() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/DetectPM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Detection of infection given parasitemia — DetectPM","text":"host cohort age FoIpar parameters define FoI function tau cohort birthday hhat local scaling parameter FoI r clearance rate simple infection par_RBC parameters compute log10RBC Fmu_par parameters compute alpha2mu par_mu2dens parameters compute d_mu2density pWda parameters dispatch Wda pC parameters define detection function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/DetectPM.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Detection of infection given parasitemia — DetectPM","text":"binary detection result","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/DetectPa.html","id":null,"dir":"Reference","previous_headings":"","what":"Detection of infection given parasitemia — DetectPa","title":"Detection of infection given parasitemia — DetectPa","text":"Detection infection given parasitemia","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/DetectPa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Detection of infection given parasitemia — DetectPa","text":"","code":"DetectPa(   a,   FoIpar,   tau = 0,   hhat = 1,   r = 1/200,   par_RBC = par_lRBC_static(),   Fmu_par = par_Fmu_base(),   par_mu2dens = par_mu2dens_beta(),   pWda = par_Wda_none(),   pC = par_nbCounts() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/DetectPa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Detection of infection given parasitemia — DetectPa","text":"host cohort age FoIpar parameters define FoI function tau cohort birthday hhat local scaling parameter FoI r clearance rate simple infection par_RBC parameters compute log10RBC Fmu_par parameters compute alpha2mu par_mu2dens parameters compute d_mu2density pWda parameters dispatch Wda pC parameters define detection function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/DetectPa.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Detection of infection given parasitemia — DetectPa","text":"numeric vector length()","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/FoI.html","id":null,"dir":"Reference","previous_headings":"","what":"Force of Infection, \\(h_\\tau(a)\\) — FoI","title":"Force of Infection, \\(h_\\tau(a)\\) — FoI","text":"Given birth day, \\(\\tau,\\) age related time formula \\(t = +\\tau\\). FoI computed $$\\bar h \\; \\omega() S(+\\tau) T(+\\tau)$$","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/FoI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Force of Infection, \\(h_\\tau(a)\\) — FoI","text":"","code":"FoI(a, FoIpar, tau = 0)"},{"path":"https://dd-harp.github.io/pf.memory/reference/FoI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Force of Infection, \\(h_\\tau(a)\\) — FoI","text":"host age FoIpar compound list compute \\(h_\\tau()\\) tau host cohort's birthday","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/FoI.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Force of Infection, \\(h_\\tau(a)\\) — FoI","text":"numeric","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/MoIDistPlot.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot the output of solveMMinfty — MoIDistPlot","title":"Plot the output of solveMMinfty — MoIDistPlot","text":"Plot output solveMMinfty","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/MoIDistPlot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot the output of solveMMinfty — MoIDistPlot","text":"","code":"MoIDistPlot(moi, t, clr1 = \"red\")"},{"path":"https://dd-harp.github.io/pf.memory/reference/MoIDistPlot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot the output of solveMMinfty — MoIDistPlot","text":"moi mean moi t time clr1 color","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/MoIPM.html","id":null,"dir":"Reference","previous_headings":"","what":"Detection of infection given parasitemia — MoIPM","title":"Detection of infection given parasitemia — MoIPM","text":"Detection infection given parasitemia","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/MoIPM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Detection of infection given parasitemia — MoIPM","text":"","code":"MoIPM(   a,   FoIpar,   tau = 0,   hhat = 1,   r = 1/200,   par_RBC = par_lRBC_static(),   Fmu_par = par_Fmu_base(),   par_mu2dens = par_mu2dens_beta(),   pWda = par_Wda_none(),   pC = par_nbCounts() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/MoIPM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Detection of infection given parasitemia — MoIPM","text":"host cohort age FoIpar parameters define FoI function tau cohort birthday hhat local scaling parameter FoI r clearance rate simple infection par_RBC parameters compute log10RBC Fmu_par parameters compute alpha2mu par_mu2dens parameters compute d_mu2density pWda parameters dispatch Wda pC parameters define detection function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/MoIPM.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Detection of infection given parasitemia — MoIPM","text":"detection probability","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/Wda.0.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute immune tracking variables as a function of host age and exposure — Wda.0","title":"Compute immune tracking variables as a function of host age and exposure — Wda.0","text":"Compute immune tracking variables function host age exposure","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/Wda.0.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute immune tracking variables as a function of host age and exposure — Wda.0","text":"","code":"# S3 method for `0` Wda(a, FoIpar, hhat = NULL, tau = 0, par = par_Wda.0())"},{"path":"https://dd-harp.github.io/pf.memory/reference/Wda.0.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute immune tracking variables as a function of host age and exposure — Wda.0","text":"age host cohort FoIpar parameters define FoI function hhat overrides value hbar par tau cohort birthday par parameters list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/Wda.0.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute immune tracking variables as a function of host age and exposure — Wda.0","text":"numeric vector 0's length()","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/Wda.delta.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute immune tracking variables as a function of host age and exposure — Wda.delta","title":"Compute immune tracking variables as a function of host age and exposure — Wda.delta","text":"Compute immune tracking variables function host age exposure","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/Wda.delta.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute immune tracking variables as a function of host age and exposure — Wda.delta","text":"","code":"# S3 method for delta Wda(a, FoIpar, tau = 0, hhat = 1, par = par_Wda_delta())"},{"path":"https://dd-harp.github.io/pf.memory/reference/Wda.delta.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute immune tracking variables as a function of host age and exposure — Wda.delta","text":"age host cohort FoIpar parameters define FoI function tau cohort birthday hhat overrides value hbar par par parameters list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/Wda.delta.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute immune tracking variables as a function of host age and exposure — Wda.delta","text":"numeric vector length()","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/Wda.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute immune tracking variables as a function of host age and exposure — Wda","title":"Compute immune tracking variables as a function of host age and exposure — Wda","text":"function dispatches class(par)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/Wda.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute immune tracking variables as a function of host age and exposure — Wda","text":"","code":"Wda(a, FoIpar, tau = 0, hhat = 1, par = par_Wda_none())"},{"path":"https://dd-harp.github.io/pf.memory/reference/Wda.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute immune tracking variables as a function of host age and exposure — Wda","text":"age host cohort FoIpar parameters define FoI function tau cohort birthday hhat overrides value hbar par par parameters list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/Wda.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute immune tracking variables as a function of host age and exposure — Wda","text":"numeric vector length()","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/Wda.none.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute immune tracking variables as a function of host age and exposure — Wda.none","title":"Compute immune tracking variables as a function of host age and exposure — Wda.none","text":"Compute immune tracking variables function host age exposure","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/Wda.none.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute immune tracking variables as a function of host age and exposure — Wda.none","text":"","code":"# S3 method for none Wda(a, FoIpar, tau = 0, hhat = 1, par = par_Wda_none())"},{"path":"https://dd-harp.github.io/pf.memory/reference/Wda.none.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute immune tracking variables as a function of host age and exposure — Wda.none","text":"age host cohort FoIpar parameters define FoI function tau cohort birthday hhat overrides value hbar par par parameters list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/Wda.none.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute immune tracking variables as a function of host age and exposure — Wda.none","text":"numeric vector 0's length()","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/ageFoI.flat.html","id":null,"dir":"Reference","previous_headings":"","what":"A function that does not modify the FoI by age — ageFoI.flat","title":"A function that does not modify the FoI by age — ageFoI.flat","text":"function modify FoI age","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/ageFoI.flat.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A function that does not modify the FoI by age — ageFoI.flat","text":"","code":"# S3 method for flat ageFoI(a, par)"},{"path":"https://dd-harp.github.io/pf.memory/reference/ageFoI.flat.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A function that does not modify the FoI by age — ageFoI.flat","text":"host age par list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/ageFoI.flat.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"A function that does not modify the FoI by age — ageFoI.flat","text":"numeric","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/ageFoI.html","id":null,"dir":"Reference","previous_headings":"","what":"Functions to modify the FoI by age — ageFoI","title":"Functions to modify the FoI by age — ageFoI","text":"method dispatches par.","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/ageFoI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Functions to modify the FoI by age — ageFoI","text":"","code":"ageFoI(a, par)"},{"path":"https://dd-harp.github.io/pf.memory/reference/ageFoI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Functions to modify the FoI by age — ageFoI","text":"host age par list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/ageFoI.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Functions to modify the FoI by age — ageFoI","text":"numeric","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/ageFoI.type2.html","id":null,"dir":"Reference","previous_headings":"","what":"A function that does not modify the FoI by age — ageFoI.type2","title":"A function that does not modify the FoI by age — ageFoI.type2","text":"function modify FoI age","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/ageFoI.type2.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A function that does not modify the FoI by age — ageFoI.type2","text":"","code":"# S3 method for type2 ageFoI(a, par)"},{"path":"https://dd-harp.github.io/pf.memory/reference/ageFoI.type2.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A function that does not modify the FoI by age — ageFoI.type2","text":"host age par list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/ageFoI.type2.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"A function that does not modify the FoI by age — ageFoI.type2","text":"numeric","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/alpha2mu.0.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute expected log10 parasite densities, mu, as a function of the age of infection alpha — alpha2mu.0","title":"Compute expected log10 parasite densities, mu, as a function of the age of infection alpha — alpha2mu.0","text":"Compute mean log10 parasites model immunity","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/alpha2mu.0.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute expected log10 parasite densities, mu, as a function of the age of infection alpha — alpha2mu.0","text":"","code":"# S3 method for `0` alpha2mu(alpha, W, par)"},{"path":"https://dd-harp.github.io/pf.memory/reference/alpha2mu.0.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute expected log10 parasite densities, mu, as a function of the age of infection alpha — alpha2mu.0","text":"alpha age parasite infection W immune tracking variables par list defines model","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/alpha2mu.0.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute expected log10 parasite densities, mu, as a function of the age of infection alpha — alpha2mu.0","text":"mean log10 parasite densities","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/alpha2mu.W.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute expected log10 parasite densities, mu, as a function of the age of infection alpha — alpha2mu.W","title":"Compute expected log10 parasite densities, mu, as a function of the age of infection alpha — alpha2mu.W","text":"Compute mean log10 parasites model immunity","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/alpha2mu.W.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute expected log10 parasite densities, mu, as a function of the age of infection alpha — alpha2mu.W","text":"","code":"# S3 method for W alpha2mu(alpha, W, par_Fmu)"},{"path":"https://dd-harp.github.io/pf.memory/reference/alpha2mu.W.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute expected log10 parasite densities, mu, as a function of the age of infection alpha — alpha2mu.W","text":"alpha age parasite infection W immune tracking variables par_Fmu list defines model","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/alpha2mu.W.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute expected log10 parasite densities, mu, as a function of the age of infection alpha — alpha2mu.W","text":"mean log10 parasite densities","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/alpha2mu.base.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute expected log10 parasite densities, mu, as a function of the age of infection alpha — alpha2mu.base","title":"Compute expected log10 parasite densities, mu, as a function of the age of infection alpha — alpha2mu.base","text":"Compute mean log10 parasites model immunity","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/alpha2mu.base.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute expected log10 parasite densities, mu, as a function of the age of infection alpha — alpha2mu.base","text":"","code":"# S3 method for base alpha2mu(alpha, W, par_Fmu)"},{"path":"https://dd-harp.github.io/pf.memory/reference/alpha2mu.base.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute expected log10 parasite densities, mu, as a function of the age of infection alpha — alpha2mu.base","text":"alpha age parasite infection W immune tracking variables par_Fmu list defines model","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/alpha2mu.base.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute expected log10 parasite densities, mu, as a function of the age of infection alpha — alpha2mu.base","text":"mean log10 parasite densities","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/alpha2mu.chronic.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute expected log10 parasite densities, mu, as a function of the age of infection alpha — alpha2mu.chronic","title":"Compute expected log10 parasite densities, mu, as a function of the age of infection alpha — alpha2mu.chronic","text":"Compute mean log10 parasites model immunity","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/alpha2mu.chronic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute expected log10 parasite densities, mu, as a function of the age of infection alpha — alpha2mu.chronic","text":"","code":"# S3 method for chronic alpha2mu(alpha, W, par_Fmu)"},{"path":"https://dd-harp.github.io/pf.memory/reference/alpha2mu.chronic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute expected log10 parasite densities, mu, as a function of the age of infection alpha — alpha2mu.chronic","text":"alpha age parasite infection W immune tracking variables par_Fmu list defines model","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/alpha2mu.chronic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute expected log10 parasite densities, mu, as a function of the age of infection alpha — alpha2mu.chronic","text":"mean log10 parasite densities","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/alpha2mu.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute mean, expected parasite densities mu as a function of the age of infection alpha — alpha2mu","title":"Compute mean, expected parasite densities mu as a function of the age of infection alpha — alpha2mu","text":"Compute mean, expected parasite densities mu function age infection alpha","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/alpha2mu.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute mean, expected parasite densities mu as a function of the age of infection alpha — alpha2mu","text":"","code":"alpha2mu(alpha, W, par_Fmu)"},{"path":"https://dd-harp.github.io/pf.memory/reference/alpha2mu.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute mean, expected parasite densities mu as a function of the age of infection alpha — alpha2mu","text":"alpha age parasite infection W immune tracking variables par_Fmu list defines model","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/alpha2mu.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute mean, expected parasite densities mu as a function of the age of infection alpha — alpha2mu","text":"mean log10 parasite densities, numeric vector length(alpha)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/binnedCounts.html","id":null,"dir":"Reference","previous_headings":"","what":"Detection of infection given parasitemia — binnedCounts","title":"Detection of infection given parasitemia — binnedCounts","text":"Detection infection given parasitemia","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/binnedCounts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Detection of infection given parasitemia — binnedCounts","text":"","code":"binnedCounts(xi, a, bins, Cpar = par_nbCounts())"},{"path":"https://dd-harp.github.io/pf.memory/reference/binnedCounts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Detection of infection given parasitemia — binnedCounts","text":"xi mean log10 parasite densities host cohort age bins breakpoints summarizing outputs Cpar parameters define detection function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/binnedCounts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Detection of infection given parasitemia — binnedCounts","text":"binary detection result","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/binnedCounts.nb.html","id":null,"dir":"Reference","previous_headings":"","what":"Detection of infection given parasitemia — binnedCounts.nb","title":"Detection of infection given parasitemia — binnedCounts.nb","text":"Detection infection given parasitemia","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/binnedCounts.nb.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Detection of infection given parasitemia — binnedCounts.nb","text":"","code":"# S3 method for nb binnedCounts(xi, a, bins, Cpar = par_nbCounts())"},{"path":"https://dd-harp.github.io/pf.memory/reference/binnedCounts.nb.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Detection of infection given parasitemia — binnedCounts.nb","text":"xi mean log10 parasite densities host cohort age bins break points binning counts data Cpar parameters define detection function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/binnedCounts.nb.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Detection of infection given parasitemia — binnedCounts.nb","text":"binary detection result","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/binnedCounts.pois.html","id":null,"dir":"Reference","previous_headings":"","what":"Detection of infection given parasitemia — binnedCounts.pois","title":"Detection of infection given parasitemia — binnedCounts.pois","text":"Detection infection given parasitemia","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/binnedCounts.pois.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Detection of infection given parasitemia — binnedCounts.pois","text":"","code":"# S3 method for pois binnedCounts(xi, a, bins, Cpar = par_poisCounts())"},{"path":"https://dd-harp.github.io/pf.memory/reference/binnedCounts.pois.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Detection of infection given parasitemia — binnedCounts.pois","text":"xi mean log10 parasite densities host cohort age bins breakpoints binning data Cpar parameters define detection function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/binnedCounts.pois.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Detection of infection given parasitemia — binnedCounts.pois","text":"binary detection result","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/cdfConvolve2.html","id":null,"dir":"Reference","previous_headings":"","what":"The density function for the sum of two infections — cdfConvolve2","title":"The density function for the sum of two infections — cdfConvolve2","text":"density function sum two infections","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/cdfConvolve2.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The density function for the sum of two infections — cdfConvolve2","text":"","code":"cdfConvolve2(meshX, CDF1, CDF2)"},{"path":"https://dd-harp.github.io/pf.memory/reference/cdfConvolve2.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The density function for the sum of two infections — cdfConvolve2","text":"meshX mesh host cohort ages CDF1 CDF complex distribution CDF2 CDF complex distribution","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/cdfConvolve2.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The density function for the sum of two infections — cdfConvolve2","text":"numeric vector length(meshX)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/cdfConvolve2a.html","id":null,"dir":"Reference","previous_headings":"","what":"The density function for the sum of two infections, method b — cdfConvolve2a","title":"The density function for the sum of two infections, method b — cdfConvolve2a","text":"density function sum two infections, method b","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/cdfConvolve2a.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The density function for the sum of two infections, method b — cdfConvolve2a","text":"","code":"cdfConvolve2a(meshX, CDF1, CDF2)"},{"path":"https://dd-harp.github.io/pf.memory/reference/cdfConvolve2a.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The density function for the sum of two infections, method b — cdfConvolve2a","text":"meshX mesh host cohort ages CDF1 CDF complex distribution CDF2 CDF complex distribution","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/cdfConvolve2a.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The density function for the sum of two infections, method b — cdfConvolve2a","text":"numeric vector length(meshX)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/cdfConvolve2b.html","id":null,"dir":"Reference","previous_headings":"","what":"The density function for the sum of two infections, method a — cdfConvolve2b","title":"The density function for the sum of two infections, method a — cdfConvolve2b","text":"density function sum two infections, method ","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/cdfConvolve2b.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The density function for the sum of two infections, method a — cdfConvolve2b","text":"","code":"cdfConvolve2b(meshX, CDF1, CDF2)"},{"path":"https://dd-harp.github.io/pf.memory/reference/cdfConvolve2b.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The density function for the sum of two infections, method a — cdfConvolve2b","text":"meshX mesh host cohort ages CDF1 CDF complex distribution CDF2 CDF complex distribution","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/cdfConvolve2b.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The density function for the sum of two infections, method a — cdfConvolve2b","text":"numeric vector length(meshX)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dAoI.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the density function for AoI — dAoI","title":"Compute the density function for AoI — dAoI","text":"density AoI given $$f_A(\\alpha | , \\tau, h) = \\frac{\\int_0^z(\\alpha, )}{m_\\tau()}$$","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dAoI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the density function for AoI — dAoI","text":"","code":"dAoI(alpha, a, FoIpar, tau = 0, hhat = 1, r = 1/200)"},{"path":"https://dd-harp.github.io/pf.memory/reference/dAoI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the density function for AoI — dAoI","text":"alpha age infection, \\(\\alpha\\) host age FoIpar compound list compute \\(h_\\tau()\\) tau host cohort's birthday hhat scaling parameter FoI r clearance rate simple infection","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dAoI.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the density function for AoI — dAoI","text":"numeric vector length(alpha)","code":""},{"path":[]},{"path":"https://dd-harp.github.io/pf.memory/reference/dAoIda.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the derivatives of the AoI moments dynamically — dAoIda","text":"","code":"dAoIda(a, M, p, FoIpar)"},{"path":"https://dd-harp.github.io/pf.memory/reference/dAoIda.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the derivatives of the AoI moments dynamically — dAoIda","text":"host age M state variables p parameters FoIpar parameters define FoI function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dAoIda.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the derivatives of the AoI moments dynamically — dAoIda","text":"derivatives MoI AoI list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dAoY.html","id":null,"dir":"Reference","previous_headings":"","what":"The density function for the age of the youngest infection (AoY) — dAoY","title":"The density function for the age of the youngest infection (AoY) — dAoY","text":"density function age youngest infection (AoY)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dAoY.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The density function for the age of the youngest infection (AoY) — dAoY","text":"","code":"dAoY(alpha, a, FoIpar, tau = 0, hhat = 1, r = 1/200)"},{"path":"https://dd-harp.github.io/pf.memory/reference/dAoY.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The density function for the age of the youngest infection (AoY) — dAoY","text":"alpha age infection, \\(\\alpha\\) host age FoIpar compound list compute \\(h_\\tau()\\) tau host cohort's birthday hhat scaling parameter FoI r clearance rate simple infection","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dAoY.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The density function for the age of the youngest infection (AoY) — dAoY","text":"numeric vector length(alpha)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dAoYN.html","id":null,"dir":"Reference","previous_headings":"","what":"The youngest of N infections, density function — dAoYN","title":"The youngest of N infections, density function — dAoYN","text":"youngest N infections, density function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dAoYN.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The youngest of N infections, density function — dAoYN","text":"","code":"dAoYN(N, a, FoIpar, hhat = NULL, tau = 0, r = 1/200)"},{"path":"https://dd-harp.github.io/pf.memory/reference/dAoYN.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The youngest of N infections, density function — dAoYN","text":"N number infections age cohort FoIpar parameters define FoI function hhat local scaling parameter FoI tau cohort birthday r clearance rate simple infection","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dAoYN.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The youngest of N infections, density function — dAoYN","text":"numeric vector length + 1","code":""},{"path":[]},{"path":"https://dd-harp.github.io/pf.memory/reference/dAoYda.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the derivatives of the approximate moments of the AoY dynamically — dAoYda","text":"","code":"dAoYda(a, vars, pars, FoIpar)"},{"path":"https://dd-harp.github.io/pf.memory/reference/dAoYda.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the derivatives of the approximate moments of the AoY dynamically — dAoYda","text":"host age vars state variables pars parameters FoIpar parameters define FoI function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dAoYda.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the derivatives of the approximate moments of the AoY dynamically — dAoYda","text":"derivatives MoI AoI list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dBda.html","id":null,"dir":"Reference","previous_headings":"","what":"The density function for parasite densities in a host cohort — dBda","title":"The density function for parasite densities in a host cohort — dBda","text":"density function parasite densities host cohort","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dBda.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The density function for parasite densities in a host cohort — dBda","text":"","code":"dBda(   meshX,   a,   FoIpar,   hhat = NULL,   tau = 0,   r = 1/200,   pMu = par_alpha2mu_base(),   pPDens = par_mu2density_beta(),   pWda = par_Wda_none() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/dBda.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The density function for parasite densities in a host cohort — dBda","text":"meshX mesh parasite densities host cohort age FoIpar parameters define FoI function hhat local scaling parameter FoI tau cohort birthday r clearance rate simple infection pMu parameters compute alpha2mu pPDens parameters defining parasite densities function mu pWda parameters dispatch Wda","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dBda.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The density function for parasite densities in a host cohort — dBda","text":"numeric vector length meshX","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dCounts.html","id":null,"dir":"Reference","previous_headings":"","what":"density function of counts — dCounts","title":"density function of counts — dCounts","text":"density function counts","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dCounts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"density function of counts — dCounts","text":"","code":"dCounts(hatxi, xi, a = 0, Cpar = par_nbCounts())"},{"path":"https://dd-harp.github.io/pf.memory/reference/dCounts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"density function of counts — dCounts","text":"hatxi mean \\(\\log_{10}\\) parasite counts xi mean \\(\\log_{10}\\) parasite densities host cohort age Cpar parameters define detection function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dCounts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"density function of counts — dCounts","text":"binary detection result","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dCounts.nb.html","id":null,"dir":"Reference","previous_headings":"","what":"Detection of infection given parasitemia — dCounts.nb","title":"Detection of infection given parasitemia — dCounts.nb","text":"Detection infection given parasitemia","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dCounts.nb.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Detection of infection given parasitemia — dCounts.nb","text":"","code":"# S3 method for nb dCounts(hatxi, xi, a = 0, Cpar = par_nbCounts())"},{"path":"https://dd-harp.github.io/pf.memory/reference/dCounts.nb.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Detection of infection given parasitemia — dCounts.nb","text":"hatxi mean log10 parasite counts xi mean log10 parasite densities host cohort age Cpar parameters define detection function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dCounts.nb.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Detection of infection given parasitemia — dCounts.nb","text":"binary detection result","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dCounts.pois.html","id":null,"dir":"Reference","previous_headings":"","what":"Detection of infection given parasitemia — dCounts.pois","title":"Detection of infection given parasitemia — dCounts.pois","text":"Detection infection given parasitemia","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dCounts.pois.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Detection of infection given parasitemia — dCounts.pois","text":"","code":"# S3 method for pois dCounts(hatxi, xi, a = 0, Cpar = par_poisCounts())"},{"path":"https://dd-harp.github.io/pf.memory/reference/dCounts.pois.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Detection of infection given parasitemia — dCounts.pois","text":"hatxi mean log10 parasite densities xi mean log10 parasite densities host cohort age Cpar parameters define detection function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dCounts.pois.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Detection of infection given parasitemia — dCounts.pois","text":"binary detection result","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dCountsBa.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the density of parasite counts in complex infections — dCountsBa","title":"Compute the density of parasite counts in complex infections — dCountsBa","text":"Compute density parasite counts complex infections","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dCountsBa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the density of parasite counts in complex infections — dCountsBa","text":"","code":"dCountsBa(   a,   FoIpar,   bins = 1,   dx = 0.1,   hhat = 1,   tau = 0,   r = 1/200,   RBC_par = par_lRBC_static(),   Fmu_par = par_Fmu_base(),   mu_par = par_mu2dens_beta(),   pWda = par_Wda_none(),   Cpar = par_nbCounts() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/dCountsBa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the density of parasite counts in complex infections — dCountsBa","text":"host cohort age FoIpar parameters define FoI function bins set break points computing counts dx width mesh computing CDF parasite densities hhat local scaling parameter FoI tau cohort birthday r clearance rate simple infection RBC_par parameters compute log10RBC Fmu_par parameters compute alpha2mu mu_par parameters defining parasite densities function mu pWda parameters dispatch Wda Cpar parameters define detection function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dCountsBa.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the density of parasite counts in complex infections — dCountsBa","text":"list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dCountsPa.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the density of parasite counts for simple infections — dCountsPa","title":"Compute the density of parasite counts for simple infections — dCountsPa","text":"Compute density parasite counts simple infections","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dCountsPa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the density of parasite counts for simple infections — dCountsPa","text":"","code":"dCountsPa(   a,   FoIpar,   bins = 1,   dx = 0.1,   hhat = 1,   tau = 0,   r = 1/200,   RBC_par = par_lRBC_static(),   Fmu_par = par_Fmu_base(),   mu_par = par_mu2dens_beta(),   pWda = par_Wda_none(),   Cpar = par_nbCounts() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/dCountsPa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the density of parasite counts for simple infections — dCountsPa","text":"host cohort age FoIpar parameters define FoI function bins set break points computing counts dx width mesh computing CDF parasite densities hhat local scaling parameter FoI tau cohort birthday r clearance rate simple infection RBC_par parameters compute log10RBC Fmu_par parameters compute alpha2mu mu_par parameters defining parasite densities function mu pWda parameters dispatch Wda Cpar parameters define detection function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dCountsPa.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the density of parasite counts for simple infections — dCountsPa","text":"list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dDensityPa.html","id":null,"dir":"Reference","previous_headings":"","what":"The density function for parasite densities from a host cohort population of age a — dDensityPa","title":"The density function for parasite densities from a host cohort population of age a — dDensityPa","text":"density function parasite densities host cohort population age ","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dDensityPa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The density function for parasite densities from a host cohort population of age a — dDensityPa","text":"","code":"dDensityPa(   x,   a,   FoIpar,   hhat = NULL,   tau = 0,   r = 1/200,   pMu = par_alpha2mu_base(),   pPDens = par_mu2density_beta(),   pWda = par_Wda_none() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/dDensityPa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The density function for parasite densities from a host cohort population of age a — dDensityPa","text":"x host cohort age host cohort age FoIpar parameters define FoI function hhat local scaling parameter FoI tau cohort birthday r clearance rate simple infection pMu parameters compute alpha2mu pPDens parameters defining parasite densities function mu pWda parameters dispatch Wda","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dDensityPa.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The density function for parasite densities from a host cohort population of age a — dDensityPa","text":"numeric vector length(x)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dDensityPaConvolve2.html","id":null,"dir":"Reference","previous_headings":"","what":"The density function for the sum of two infections — dDensityPaConvolve2","title":"The density function for the sum of two infections — dDensityPaConvolve2","text":"density function sum two infections","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dDensityPaConvolve2.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The density function for the sum of two infections — dDensityPaConvolve2","text":"","code":"dDensityPaConvolve2(   x,   a,   FoIpar,   hhat = NULL,   tau = 0,   r = 1/200,   par_RBC = par_lRBC_static(),   par_Fmu = par_Fmu_base(),   par_mu2dens = par_mu2dens_beta(),   pWda = par_Wda_none() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/dDensityPaConvolve2.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The density function for the sum of two infections — dDensityPaConvolve2","text":"x host cohort age host cohort age FoIpar parameters define FoI function hhat local scaling parameter FoI tau cohort birthday r clearance rate simple infection par_RBC parameters compute log10RBC par_Fmu parameters compute alpha2mu par_mu2dens parameters compute d_mu2density pWda parameters dispatch Wda","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dDensityPaConvolve2.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The density function for the sum of two infections — dDensityPaConvolve2","text":"numeric value","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dDensityPalpha.html","id":null,"dir":"Reference","previous_headings":"","what":"The density function for parasite densities in a simple malaria infection of age alpha — dDensityPalpha","title":"The density function for parasite densities in a simple malaria infection of age alpha — dDensityPalpha","text":"density function parasite densities simple malaria infection age alpha","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dDensityPalpha.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The density function for parasite densities in a simple malaria infection of age alpha — dDensityPalpha","text":"","code":"dDensityPalpha(   x,   alpha,   W = 0,   a = 0,   pMu = par_alpha2mu_base(),   pRBC = par_lRBC_static(),   pSig = par_sigma_abc() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/dDensityPalpha.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The density function for parasite densities in a simple malaria infection of age alpha — dDensityPalpha","text":"x vector quantiles alpha age parasite infection W immune tracking variables host cohort age pMu parameters compute alpha2mu pRBC parameters compute log10RBC pSig parameters dispatch sigma_mu","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dDensityPalpha.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The density function for parasite densities in a simple malaria infection of age alpha — dDensityPalpha","text":"numeric vector length(x)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dDensityPmu.html","id":null,"dir":"Reference","previous_headings":"","what":"The density function for parasite densities in a simple malaria infection — dDensityPmu","title":"The density function for parasite densities in a simple malaria infection — dDensityPmu","text":"density function parasite densities simple malaria infection","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dDensityPmu.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The density function for parasite densities in a simple malaria infection — dDensityPmu","text":"","code":"dDensityPmu(xi, mu, a = 0, pRBC = par_lRBC_static(), pSig = par_sigma_abc())"},{"path":"https://dd-harp.github.io/pf.memory/reference/dDensityPmu.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The density function for parasite densities in a simple malaria infection — dDensityPmu","text":"xi vector quantiles mu expected value log10 parasite densities host cohort age pRBC parameters compute log10RBC pSig parameters dispatch sigma_mu","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dDensityPmu.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The density function for parasite densities in a simple malaria infection — dDensityPmu","text":"numeric vector length(xi)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dMoIda.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivatives for the queuing model \\(M/M/\\infty\\) — dMoIda","title":"Derivatives for the queuing model \\(M/M/\\infty\\) — dMoIda","text":"queuing model \\(M/M/\\infty\\) tracks MoI cohort humans ages. assumes time- age-dependent hazard rate infection, called force infection (FoI, \\(h_\\tau()\\)). Infections affect , one clears independently rate \\(r\\). Let \\(\\zeta_i\\) fraction population MoI = , $$\\frac{d\\zeta_0}{da}= -h_\\tau() \\zeta_0 + r \\zeta_1$$ \\(\\geq 1\\) $$\\frac{d\\zeta_i}{da}= h_\\tau() \\left( \\zeta_{-1} - \\zeta_i \\right)  - ri \\zeta_i + r(+1)\\zeta_{+1}$$ function computes derivatives form can used deSolve::ode.","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dMoIda.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivatives for the queuing model \\(M/M/\\infty\\) — dMoIda","text":"","code":"dMoIda(a, M, pars, FoIpar)"},{"path":"https://dd-harp.github.io/pf.memory/reference/dMoIda.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivatives for the queuing model \\(M/M/\\infty\\) — dMoIda","text":"host age M state variables pars parameters FoIpar \\(h_\\tau()\\), list formatted compute FoI","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dMoIda.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivatives for the queuing model \\(M/M/\\infty\\) — dMoIda","text":"derivatives list","code":""},{"path":[]},{"path":"https://dd-harp.github.io/pf.memory/reference/d_Bdensity.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the distribution function for \\(B_\\tau(a)\\) — d_Bdensity","title":"Compute the distribution function for \\(B_\\tau(a)\\) — d_Bdensity","text":"Call Bdensity return PDF: $$f_B(\\xi; , \\tau |h) = \\log_{10} \\left( \\sum_{M_\\tau(|h)>0} 10^{P_\\tau(|h)}\\right)$$","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/d_Bdensity.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the distribution function for \\(B_\\tau(a)\\) — d_Bdensity","text":"","code":"d_Bdensity(   meshX,   a,   FoIpar,   tau = 0,   hhat = 1,   r = 1/200,   RBC_par = par_lRBC_static(),   Fmu_par = par_Fmu_base(),   mu_par = par_mu2dens_beta(),   pWda = par_Wda_none() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/d_Bdensity.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the distribution function for \\(B_\\tau(a)\\) — d_Bdensity","text":"meshX mesh parasite densities host cohort age FoIpar parameters define FoI function tau cohort birthday hhat local scaling parameter FoI r clearance rate simple infection RBC_par parameters compute log10RBC Fmu_par parameters compute alpha2mu mu_par parameters compute d_mu2density pWda parameters dispatch Wda","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/d_Bdensity.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the distribution function for \\(B_\\tau(a)\\) — d_Bdensity","text":"numeric vector length meshX","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/d_Pdensity.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute \\(P_\\tau(a |h)\\) — d_Pdensity","title":"Compute \\(P_\\tau(a |h)\\) — d_Pdensity","text":"Compute $$P_\\tau(| h) \\sim f_P(\\xi; , \\tau |h ) = \\int_0^\\Omega(\\xi|F_\\mu(\\alpha)) \\; f_A(\\alpha; , \\tau | h) d\\alpha$$ Compute $$P_\\tau(| h) \\sim f_P(\\xi; , \\tau |h ) = \\int_0^\\Omega(\\xi|F_\\mu(\\alpha)) \\; f_A(\\alpha; , \\tau | h) d\\alpha$$","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/d_Pdensity.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute \\(P_\\tau(a |h)\\) — d_Pdensity","text":"","code":"d_Pdensity(   xi,   a,   FoIpar,   tau = 0,   hhat = 1,   r = 1/200,   par_RBC = par_lRBC_static(),   par_Fmu = par_Fmu_base(),   par_mu2dens = par_mu2dens_beta(),   pWda = par_Wda_none() )  d_Pdensity(   xi,   a,   FoIpar,   tau = 0,   hhat = 1,   r = 1/200,   par_RBC = par_lRBC_static(),   par_Fmu = par_Fmu_base(),   par_mu2dens = par_mu2dens_beta(),   pWda = par_Wda_none() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/d_Pdensity.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute \\(P_\\tau(a |h)\\) — d_Pdensity","text":"xi log10 host cohort age FoIpar parameters define FoI function tau cohort birthday hhat local scaling parameter FoI r clearance rate simple infection par_RBC parameters compute log10RBC par_Fmu parameters compute alpha2mu par_mu2dens parameters compute d_mu2density pWda parameters dispatch Wda","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/d_Pdensity.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute \\(P_\\tau(a |h)\\) — d_Pdensity","text":"numeric vector length(x) numeric vector length(x)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/d_alpha2density.html","id":null,"dir":"Reference","previous_headings":"","what":"The density function for parasite densities in a simple malaria infection of age alpha — d_alpha2density","title":"The density function for parasite densities in a simple malaria infection of age alpha — d_alpha2density","text":"density function parasite densities simple malaria infection age alpha","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/d_alpha2density.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The density function for parasite densities in a simple malaria infection of age alpha — d_alpha2density","text":"","code":"d_alpha2density(   xi,   alpha,   W = 0,   a = 0,   par_RBC = par_lRBC_static(),   par_Fmu = par_Fmu_base(),   par_mu2dens = par_mu2dens_beta() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/d_alpha2density.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The density function for parasite densities in a simple malaria infection of age alpha — d_alpha2density","text":"xi vector quantiles alpha age parasite infection W immune tracking variables host cohort age par_RBC parameters compute log10RBC par_Fmu parameters compute alpha2mu par_mu2dens parameters compute d_mu2density","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/d_alpha2density.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The density function for parasite densities in a simple malaria infection of age alpha — d_alpha2density","text":"numeric vector length(x)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/d_mu2density.beta.html","id":null,"dir":"Reference","previous_headings":"","what":"Modified beta distribution, density function — d_mu2density.beta","title":"Modified beta distribution, density function — d_mu2density.beta","text":"beta distribution, parameterized mean variance, modified return number 0 bvm (number red blood cells)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/d_mu2density.beta.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Modified beta distribution, density function — d_mu2density.beta","text":"","code":"# S3 method for beta d_mu2density(xi, mu, par_mu2dens = par_mu2dens_beta(), bvm = 13)"},{"path":"https://dd-harp.github.io/pf.memory/reference/d_mu2density.beta.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Modified beta distribution, density function — d_mu2density.beta","text":"xi vector quantiles \\(log_{10}\\) parasite densities mu expected value \\(log_{10}\\) parasite densities par_mu2dens parameters compute parasite densities function mu bvm blood volume \\(log_{10}\\) red blood cells","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/d_mu2density.beta.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Modified beta distribution, density function — d_mu2density.beta","text":"numeric vector length(xi)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/d_mu2density.html","id":null,"dir":"Reference","previous_headings":"","what":"The density function for parasite densities in a simple malaria infection — d_mu2density","title":"The density function for parasite densities in a simple malaria infection — d_mu2density","text":"density function parasite densities simple malaria infection","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/d_mu2density.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The density function for parasite densities in a simple malaria infection — d_mu2density","text":"","code":"d_mu2density(xi, mu, par_mu2dens = par_mu2dens_beta(), bvm = 13)"},{"path":"https://dd-harp.github.io/pf.memory/reference/d_mu2density.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The density function for parasite densities in a simple malaria infection — d_mu2density","text":"xi vector quantiles \\(log_{10}\\) parasite densities mu expected value \\(log_{10}\\) parasite densities par_mu2dens parameters compute parasite densities function mu bvm blood volume \\(log_{10}\\) red blood cells","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/d_mu2density.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The density function for parasite densities in a simple malaria infection — d_mu2density","text":"numeric vector length(xi)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dbeta1.html","id":null,"dir":"Reference","previous_headings":"","what":"Density function for the beta distribution, an alternative parameterization — dbeta1","title":"Density function for the beta distribution, an alternative parameterization — dbeta1","text":"beta distribution parameterized using mean function sigma_mu computes variance function mean","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dbeta1.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Density function for the beta distribution, an alternative parameterization — dbeta1","text":"","code":"dbeta1(x, mu, pSig = par_sigma_abc())"},{"path":"https://dd-harp.github.io/pf.memory/reference/dbeta1.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Density function for the beta distribution, an alternative parameterization — dbeta1","text":"x vector quantiles mu mean value distribution (0 <= mu <= 1) pSig parameters dispatch S3 function sigma_mu","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dbeta1.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Density function for the beta distribution, an alternative parameterization — dbeta1","text":"numeric vector length(x)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dmda.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the derivatives for MoI using a hybrid model — dmda","title":"Compute the derivatives for MoI using a hybrid model — dmda","text":"Compute derivatives MoI using hybrid model","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dmda.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the derivatives for MoI using a hybrid model — dmda","text":"","code":"dmda(a, M, p, FoIpar)"},{"path":"https://dd-harp.github.io/pf.memory/reference/dmda.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the derivatives for MoI using a hybrid model — dmda","text":"host age M state variables p parameters FoIpar parameters define FoI function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dmda.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the derivatives for MoI using a hybrid model — dmda","text":"derivatives list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dpda.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the derivatives for MoI and true PR — dpda","title":"Compute the derivatives for MoI and true PR — dpda","text":"Compute derivatives MoI true PR","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dpda.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the derivatives for MoI and true PR — dpda","text":"","code":"dpda(a, M, par, FoIpar)"},{"path":"https://dd-harp.github.io/pf.memory/reference/dpda.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the derivatives for MoI and true PR — dpda","text":"host age M state variables par model parameters FoIpar parameters define FoI function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/dpda.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the derivatives for MoI and true PR — dpda","text":"derivatives, list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/log10RBC.0.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute log10 of the red blood cell population — log10RBC.0","title":"Compute log10 of the red blood cell population — log10RBC.0","text":"static model","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/log10RBC.0.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute log10 of the red blood cell population — log10RBC.0","text":"","code":"# S3 method for `0` log10RBC(a, par)"},{"path":"https://dd-harp.github.io/pf.memory/reference/log10RBC.0.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute log10 of the red blood cell population — log10RBC.0","text":"age host cohort par list parameters","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/log10RBC.0.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute log10 of the red blood cell population — log10RBC.0","text":"numeric vector length()","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/log10RBC.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute log10 of the red blood cell population — log10RBC","title":"Compute log10 of the red blood cell population — log10RBC","text":"Compute log10 red blood cell population","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/log10RBC.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute log10 of the red blood cell population — log10RBC","text":"","code":"log10RBC(a, par)"},{"path":"https://dd-harp.github.io/pf.memory/reference/log10RBC.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute log10 of the red blood cell population — log10RBC","text":"age host cohort par list parameters","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/log10RBC.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute log10 of the red blood cell population — log10RBC","text":"numeric vector length()","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/log10RBC.static.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute log10 of the red blood cell population — log10RBC.static","title":"Compute log10 of the red blood cell population — log10RBC.static","text":"static model","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/log10RBC.static.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute log10 of the red blood cell population — log10RBC.static","text":"","code":"# S3 method for static log10RBC(a, par)"},{"path":"https://dd-harp.github.io/pf.memory/reference/log10RBC.static.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute log10 of the red blood cell population — log10RBC.static","text":"age host cohort par list parameters","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/log10RBC.static.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute log10 of the red blood cell population — log10RBC.static","text":"numeric vector length()","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/make_FoI.html","id":null,"dir":"Reference","previous_headings":"","what":"Trace Function - Force of Infection — make_FoI","title":"Trace Function - Force of Infection — make_FoI","text":"Trace Function - Force Infection","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/make_FoI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Trace Function - Force of Infection — make_FoI","text":"","code":"make_FoI(par, maxAge = 50)"},{"path":"https://dd-harp.github.io/pf.memory/reference/make_FoI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Trace Function - Force of Infection — make_FoI","text":"par formatted list maxAge age years normalize ","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/make_FoI.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Trace Function - Force of Infection — make_FoI","text":"numeric","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/meanCountsBa.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the mean parasite counts in complex infections — meanCountsBa","title":"Compute the mean parasite counts in complex infections — meanCountsBa","text":"Compute mean parasite counts complex infections","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/meanCountsBa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the mean parasite counts in complex infections — meanCountsBa","text":"","code":"meanCountsBa(   a,   FoIpar,   dx = 0.1,   hhat = 1,   tau = 0,   r = 1/200,   Fmu_par = par_Fmu_base(),   mu_par = par_mu2dens_beta(),   pWda = par_Wda_none(),   Cpar = par_nbCounts() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/meanCountsBa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the mean parasite counts in complex infections — meanCountsBa","text":"host cohort age FoIpar parameters define FoI function dx width mesh computing CDF parasite densities hhat local scaling parameter FoI tau cohort birthday r clearance rate simple infection Fmu_par parameters compute alpha2mu mu_par parameters defining parasite densities function mu pWda parameters dispatch Wda Cpar parameters define detection function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/meanCountsBa.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the mean parasite counts in complex infections — meanCountsBa","text":"list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/meanCountsPa.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the mean parasite counts in simple infections — meanCountsPa","title":"Compute the mean parasite counts in simple infections — meanCountsPa","text":"Compute mean parasite counts simple infections","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/meanCountsPa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the mean parasite counts in simple infections — meanCountsPa","text":"","code":"meanCountsPa(   a,   FoIpar,   dx = 0.1,   hhat = 1,   tau = 0,   r = 1/200,   Fmu_par = par_Fmu_base(),   mu_par = par_mu2dens_beta(),   pWda = par_Wda_none(),   Cpar = par_nbCounts() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/meanCountsPa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the mean parasite counts in simple infections — meanCountsPa","text":"host cohort age FoIpar parameters define FoI function dx width mesh computing CDF parasite densities hhat local scaling parameter FoI tau cohort birthday r clearance rate simple infection Fmu_par parameters compute alpha2mu mu_par parameters defining parasite densities function mu pWda parameters dispatch Wda Cpar parameters define detection function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/meanCountsPa.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the mean parasite counts in simple infections — meanCountsPa","text":"list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/meanMoI.html","id":null,"dir":"Reference","previous_headings":"","what":"The mean MoI in a host cohort of age \\(a\\) — meanMoI","title":"The mean MoI in a host cohort of age \\(a\\) — meanMoI","text":"mean multiplicity infection (MoI) $$m_\\tau() = \\int_0^z_\\tau(\\alpha, ) d \\alpha$$","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/meanMoI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The mean MoI in a host cohort of age \\(a\\) — meanMoI","text":"","code":"meanMoI(a, FoIpar, tau = 0, hhat = 1, r = 1/200)"},{"path":"https://dd-harp.github.io/pf.memory/reference/meanMoI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The mean MoI in a host cohort of age \\(a\\) — meanMoI","text":"host age FoIpar compound list compute \\(h_\\tau()\\) tau host cohort's birthday hhat local scaling parameter FoI r clearance rate simple infection","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/meanMoI.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The mean MoI in a host cohort of age \\(a\\) — meanMoI","text":"numeric vector length()","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/momentAoI.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the moments for the AoI density function for a cohort of age a — momentAoI","title":"Compute the moments for the AoI density function for a cohort of age a — momentAoI","text":"Compute moments AoI density function cohort age ","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/momentAoI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the moments for the AoI density function for a cohort of age a — momentAoI","text":"","code":"momentAoI(a, FoIpar, tau = 0, hhat = 1, r = 1/200, n = 1)"},{"path":"https://dd-harp.github.io/pf.memory/reference/momentAoI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the moments for the AoI density function for a cohort of age a — momentAoI","text":"host age FoIpar compound list compute \\(h_\\tau()\\) tau host cohort's birthday hhat local scaling parameter FoI r clearance rate simple infection n moment desired","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/momentAoI.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the moments for the AoI density function for a cohort of age a — momentAoI","text":"numeric vector length()","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/momentAoY.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the moments for the AoY density function for a cohort of age a — momentAoY","title":"Compute the moments for the AoY density function for a cohort of age a — momentAoY","text":"Compute moments AoY density function cohort age ","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/momentAoY.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the moments for the AoY density function for a cohort of age a — momentAoY","text":"","code":"momentAoY(a, FoIpar, tau = 0, hhat = 1, r = 1/200, n = 1)"},{"path":"https://dd-harp.github.io/pf.memory/reference/momentAoY.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the moments for the AoY density function for a cohort of age a — momentAoY","text":"host age FoIpar compound list compute \\(h_\\tau()\\) tau host cohort's birthday hhat local scaling parameter FoI r clearance rate simple infection n moment desired","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/momentAoY.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the moments for the AoY density function for a cohort of age a — momentAoY","text":"numeric vector length()","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/nzPois.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute N non-zero values from a Poisson distribution with a given MoI — nzPois","title":"Compute N non-zero values from a Poisson distribution with a given MoI — nzPois","text":"Compute N non-zero values Poisson distribution given MoI","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/nzPois.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute N non-zero values from a Poisson distribution with a given MoI — nzPois","text":"","code":"nzPois(N, moi)"},{"path":"https://dd-harp.github.io/pf.memory/reference/nzPois.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute N non-zero values from a Poisson distribution with a given MoI — nzPois","text":"N number random variates return moi mean moi","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/nzPois.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute N non-zero values from a Poisson distribution with a given MoI — nzPois","text":"numeric vector length N","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pAoI.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the distribution function for AoI — pAoI","title":"Compute the distribution function for AoI — pAoI","text":"Compute distribution function AoI","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pAoI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the distribution function for AoI — pAoI","text":"","code":"pAoI(alpha, a, FoIpar, tau = 0, hhat = 1, r = 1/200)"},{"path":"https://dd-harp.github.io/pf.memory/reference/pAoI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the distribution function for AoI — pAoI","text":"alpha age infection, \\(\\alpha\\) host age FoIpar compound list compute \\(h_\\tau()\\) tau host cohort's birthday hhat scaling parameter FoI r clearance rate simple infection","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pAoI.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the distribution function for AoI — pAoI","text":"numeric vector length(alpha)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pAoY.html","id":null,"dir":"Reference","previous_headings":"","what":"The distribution function for the age of the youngest infection (AoY) — pAoY","title":"The distribution function for the age of the youngest infection (AoY) — pAoY","text":"distribution function age youngest infection (AoY)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pAoY.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The distribution function for the age of the youngest infection (AoY) — pAoY","text":"","code":"pAoY(alpha, a, FoIpar, tau = 0, hhat = 1, r = 1/200)"},{"path":"https://dd-harp.github.io/pf.memory/reference/pAoY.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The distribution function for the age of the youngest infection (AoY) — pAoY","text":"alpha age infection, \\(\\alpha\\) host age FoIpar compound list compute \\(h_\\tau()\\) tau host cohort's birthday hhat scaling parameter FoI r clearance rate simple infection","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pAoY.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The distribution function for the age of the youngest infection (AoY) — pAoY","text":"numeric vector length(alpha)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pAoYN.html","id":null,"dir":"Reference","previous_headings":"","what":"The youngest of N infections, distribution function — pAoYN","title":"The youngest of N infections, distribution function — pAoYN","text":"youngest N infections, distribution function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pAoYN.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The youngest of N infections, distribution function — pAoYN","text":"","code":"pAoYN(N, a, FoIpar, hhat = NULL, tau = 0, r = 1/200)"},{"path":"https://dd-harp.github.io/pf.memory/reference/pAoYN.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The youngest of N infections, distribution function — pAoYN","text":"N MoI age cohort FoIpar parameters define FoI function hhat local scaling parameter FoI tau cohort birthday r clearance rate simple infection","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pAoYN.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The youngest of N infections, distribution function — pAoYN","text":"numeric vector length + 1","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pAoY_long.html","id":null,"dir":"Reference","previous_headings":"","what":"Alternative method for computing the distribution function for the age of the youngest infection (AoY) — pAoY_long","title":"Alternative method for computing the distribution function for the age of the youngest infection (AoY) — pAoY_long","text":"method computes distribution function AoY summing AoI distributions","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pAoY_long.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Alternative method for computing the distribution function for the age of the youngest infection (AoY) — pAoY_long","text":"","code":"pAoY_long(alpha, a, FoIpar, tau = 0, hhat = 1, r = 1/200)"},{"path":"https://dd-harp.github.io/pf.memory/reference/pAoY_long.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Alternative method for computing the distribution function for the age of the youngest infection (AoY) — pAoY_long","text":"alpha age infection, \\(\\alpha\\) host age FoIpar compound list compute \\(h_\\tau()\\) tau host cohort's birthday hhat scaling parameter FoI r clearance rate simple infection","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pAoY_long.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Alternative method for computing the distribution function for the age of the youngest infection (AoY) — pAoY_long","text":"numeric vector length(alpha)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pBda.html","id":null,"dir":"Reference","previous_headings":"","what":"The distribution function for parasite densities in a host cohort — pBda","title":"The distribution function for parasite densities in a host cohort — pBda","text":"distribution function parasite densities host cohort","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pBda.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The distribution function for parasite densities in a host cohort — pBda","text":"","code":"pBda(   meshX,   a,   FoIpar,   hhat = NULL,   tau = 0,   r = 1/200,   pMu = par_alpha2mu_base(),   pPDens = par_mu2density_beta(),   pWda = par_Wda_none() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/pBda.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The distribution function for parasite densities in a host cohort — pBda","text":"meshX mesh parasite densities host cohort age FoIpar parameters define FoI function hhat local scaling parameter FoI tau cohort birthday r clearance rate simple infection pMu parameters compute alpha2mu pPDens parameters defining parasite densities function mu pWda parameters dispatch Wda","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pBda.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The distribution function for parasite densities in a host cohort — pBda","text":"numeric vector length meshX","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pCounts.html","id":null,"dir":"Reference","previous_headings":"","what":"cumulative density function of counts — pCounts","title":"cumulative density function of counts — pCounts","text":"cumulative density function counts","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pCounts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"cumulative density function of counts — pCounts","text":"","code":"pCounts(hatxi, xi, a = 0, Cpar = par_nbCounts())"},{"path":"https://dd-harp.github.io/pf.memory/reference/pCounts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"cumulative density function of counts — pCounts","text":"hatxi mean log10 parasite densities xi mean \\(\\log_{10}\\) parasite densities host cohort age Cpar parameters define detection function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pCounts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"cumulative density function of counts — pCounts","text":"binary detection result","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pCounts.nb.html","id":null,"dir":"Reference","previous_headings":"","what":"Detection of infection given parasitemia — pCounts.nb","title":"Detection of infection given parasitemia — pCounts.nb","text":"Detection infection given parasitemia","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pCounts.nb.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Detection of infection given parasitemia — pCounts.nb","text":"","code":"# S3 method for nb pCounts(hatxi, xi, a = 0, Cpar = par_nbCounts())"},{"path":"https://dd-harp.github.io/pf.memory/reference/pCounts.nb.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Detection of infection given parasitemia — pCounts.nb","text":"hatxi mean log10 parasite counts xi mean log10 parasite densities host cohort age Cpar parameters define detection function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pCounts.nb.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Detection of infection given parasitemia — pCounts.nb","text":"binary detection result","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pCounts.pois.html","id":null,"dir":"Reference","previous_headings":"","what":"Detection of infection given parasitemia — pCounts.pois","title":"Detection of infection given parasitemia — pCounts.pois","text":"Detection infection given parasitemia","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pCounts.pois.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Detection of infection given parasitemia — pCounts.pois","text":"","code":"# S3 method for pois pCounts(hatxi, xi, a = 0, Cpar = par_poisCounts())"},{"path":"https://dd-harp.github.io/pf.memory/reference/pCounts.pois.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Detection of infection given parasitemia — pCounts.pois","text":"hatxi mean log10 parasite counts xi mean log10 parasite densities host cohort age Cpar parameters define detection function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pCounts.pois.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Detection of infection given parasitemia — pCounts.pois","text":"binary detection result","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pCountsBa.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the distribution of parasite counts in complex infections — pCountsBa","title":"Compute the distribution of parasite counts in complex infections — pCountsBa","text":"Compute distribution parasite counts complex infections","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pCountsBa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the distribution of parasite counts in complex infections — pCountsBa","text":"","code":"pCountsBa(   a,   FoIpar,   bins = 1,   dx = 0.1,   hhat = 1,   tau = 0,   r = 1/200,   RBC_par = par_lRBC_static(),   Fmu_par = par_Fmu_base(),   mu_par = par_mu2dens_beta(),   pWda = par_Wda_none(),   Cpar = par_nbCounts() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/pCountsBa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the distribution of parasite counts in complex infections — pCountsBa","text":"host cohort age FoIpar parameters define FoI function bins set break points computing counts dx width mesh computing CDF parasite densities hhat local scaling parameter FoI tau cohort birthday r clearance rate simple infection RBC_par parameters compute log10RBC Fmu_par parameters compute alpha2mu mu_par parameters defining parasite densities function mu pWda parameters dispatch Wda Cpar parameters define detection function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pCountsBa.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the distribution of parasite counts in complex infections — pCountsBa","text":"list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pCountsPa.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the distribution of parasite counts for simple infections — pCountsPa","title":"Compute the distribution of parasite counts for simple infections — pCountsPa","text":"Compute distribution parasite counts simple infections","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pCountsPa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the distribution of parasite counts for simple infections — pCountsPa","text":"","code":"pCountsPa(   a,   FoIpar,   bins = c(1:5, 13),   dx = 0.1,   hhat = 1,   tau = 0,   r = 1/200,   RBC_par = par_lRBC_static(),   Fmu_par = par_Fmu_base(),   mu_par = par_mu2dens_beta(),   pWda = par_Wda_none(),   Cpar = par_nbCounts() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/pCountsPa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the distribution of parasite counts for simple infections — pCountsPa","text":"host cohort age FoIpar parameters define FoI function bins set break points computing counts dx width mesh computing CDF parasite densities hhat local scaling parameter FoI tau cohort birthday r clearance rate simple infection RBC_par parameters compute log10RBC Fmu_par parameters compute alpha2mu mu_par parameters defining parasite densities function mu pWda parameters dispatch Wda Cpar parameters define detection function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pCountsPa.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the distribution of parasite counts for simple infections — pCountsPa","text":"list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pDensityPalpha.html","id":null,"dir":"Reference","previous_headings":"","what":"The distribution function for parasite densities in a simple malaria infection of age alpha — pDensityPalpha","title":"The distribution function for parasite densities in a simple malaria infection of age alpha — pDensityPalpha","text":"distribution function parasite densities simple malaria infection age alpha","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pDensityPalpha.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The distribution function for parasite densities in a simple malaria infection of age alpha — pDensityPalpha","text":"","code":"pDensityPalpha(   x,   alpha,   W = 0,   a = 0,   pMu = par_alpha2mu_base(),   pRBC = par_lRBC_static(),   pSig = par_sigma_abc() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/pDensityPalpha.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The distribution function for parasite densities in a simple malaria infection of age alpha — pDensityPalpha","text":"x vector probabilities alpha age parasite infection W immune tracking variables host cohort age pMu parameters compute alpha2mu pRBC parameters compute log10RBC pSig parameters dispatch sigma_mu","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pDensityPalpha.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The distribution function for parasite densities in a simple malaria infection of age alpha — pDensityPalpha","text":"numeric vector length(x)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pDensityPmu.html","id":null,"dir":"Reference","previous_headings":"","what":"The density function for parasite densities as a function of the mean — pDensityPmu","title":"The density function for parasite densities as a function of the mean — pDensityPmu","text":"density function parasite densities function mean","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pDensityPmu.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The density function for parasite densities as a function of the mean — pDensityPmu","text":"","code":"pDensityPmu(xi, mu, a = 0, pRBC = par_lRBC_static(), pSig = par_sigma_abc())"},{"path":"https://dd-harp.github.io/pf.memory/reference/pDensityPmu.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The density function for parasite densities as a function of the mean — pDensityPmu","text":"xi vector probabilities mu expected value log10 parasite densities host cohort age pRBC parameters compute log10RBC pSig parameters dispatch sigma_mu","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/pDensityPmu.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The density function for parasite densities as a function of the mean — pDensityPmu","text":"numeric vector length(xi)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/p_Bdensity.html","id":null,"dir":"Reference","previous_headings":"","what":"Call Bdensity and return the density vector — p_Bdensity","title":"Call Bdensity and return the density vector — p_Bdensity","text":"Call Bdensity return density vector","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/p_Bdensity.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Call Bdensity and return the density vector — p_Bdensity","text":"","code":"p_Bdensity(   meshX,   a,   FoIpar,   tau = 0,   hhat = 1,   r = 1/200,   RBC_par = par_lRBC_static(),   Fmu_par = par_Fmu_base(),   mu_par = par_mu2dens_beta(),   pWda = par_Wda_none() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/p_Bdensity.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Call Bdensity and return the density vector — p_Bdensity","text":"meshX mesh parasite densities host cohort age FoIpar parameters define FoI function tau cohort birthday hhat local scaling parameter FoI r clearance rate simple infection RBC_par parameters compute log10RBC Fmu_par parameters compute alpha2mu mu_par parameters compute d_mu2density pWda parameters dispatch Wda","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/p_Bdensity.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Call Bdensity and return the density vector — p_Bdensity","text":"numeric vector length meshX","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/p_alpha2density.html","id":null,"dir":"Reference","previous_headings":"","what":"The distribution function for parasite densities in a simple malaria infection of age alpha — p_alpha2density","title":"The distribution function for parasite densities in a simple malaria infection of age alpha — p_alpha2density","text":"distribution function parasite densities simple malaria infection age alpha","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/p_alpha2density.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The distribution function for parasite densities in a simple malaria infection of age alpha — p_alpha2density","text":"","code":"p_alpha2density(   x,   alpha,   W = 0,   a = 0,   par_RBC = par_lRBC_static(),   par_Fmu = par_Fmu_base(),   par_mu2dens = par_mu2dens_beta() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/p_alpha2density.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The distribution function for parasite densities in a simple malaria infection of age alpha — p_alpha2density","text":"x vector probabilities alpha age parasite infection W immune tracking variables host cohort age par_RBC parameters compute log10RBC par_Fmu parameters compute alpha2mu par_mu2dens parameters compute p_mu2density","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/p_alpha2density.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The distribution function for parasite densities in a simple malaria infection of age alpha — p_alpha2density","text":"numeric vector length(x)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/p_mu2density.beta.html","id":null,"dir":"Reference","previous_headings":"","what":"Modified beta distribution, distribution function — p_mu2density.beta","title":"Modified beta distribution, distribution function — p_mu2density.beta","text":"Modified beta distribution, distribution function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/p_mu2density.beta.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Modified beta distribution, distribution function — p_mu2density.beta","text":"","code":"# S3 method for beta p_mu2density(xi, mu, par_mu2dens = par_mu2dens_beta(), bvm = 13)"},{"path":"https://dd-harp.github.io/pf.memory/reference/p_mu2density.beta.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Modified beta distribution, distribution function — p_mu2density.beta","text":"xi vector probabilities \\(log_{10}\\) parasite densities mu expected value \\(log_{10}\\) parasite densities par_mu2dens parameters defining parasite densities function mu bvm blood volume \\(log_{10}\\) red blood cells","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/p_mu2density.beta.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Modified beta distribution, distribution function — p_mu2density.beta","text":"numeric vector length(xi)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/p_mu2density.html","id":null,"dir":"Reference","previous_headings":"","what":"The density function for parasite densities as a function of the mean — p_mu2density","title":"The density function for parasite densities as a function of the mean — p_mu2density","text":"density function parasite densities function mean","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/p_mu2density.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The density function for parasite densities as a function of the mean — p_mu2density","text":"","code":"p_mu2density(xi, mu, par_mu2dens = par_mu2dens_beta(), bvm = 13)"},{"path":"https://dd-harp.github.io/pf.memory/reference/p_mu2density.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The density function for parasite densities as a function of the mean — p_mu2density","text":"xi vector probabilities \\(log_{10}\\) parasite densities mu expected value \\(log_{10}\\) parasite densities par_mu2dens parameters defining parasite densities function mu bvm blood volume \\(log_{10}\\) red blood cells","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/p_mu2density.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The density function for parasite densities as a function of the mean — p_mu2density","text":"numeric vector length(xi)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_Fmu_W.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up parameters for alpha2mu.W — par_Fmu_W","title":"Set up parameters for alpha2mu.W — par_Fmu_W","text":"Set parameters alpha2mu.W","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_Fmu_W.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up parameters for alpha2mu.W — par_Fmu_W","text":"","code":"par_Fmu_W(   peak = 20,   liver = 7,   tildeb = 10.3,   tildel = 2,   Sa = 0.0033,   Sw = 0.001 )"},{"path":"https://dd-harp.github.io/pf.memory/reference/par_Fmu_W.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up parameters for alpha2mu.W — par_Fmu_W","text":"peak age infection (days) parasite densities peak liver age infection (days) parasites emerge liver tildeb maximum expected log10 parasite densities tildel minimum expected log10 parasite densities Sa decline mu respect alpha Sw decline mu respect immunity","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_Fmu_W.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up parameters for alpha2mu.W — par_Fmu_W","text":"mean log10 parasite densities","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_Fmu_base.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up parameters for alpha2mu.base — par_Fmu_base","title":"Set up parameters for alpha2mu.base — par_Fmu_base","text":"Set parameters alpha2mu.base","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_Fmu_base.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up parameters for alpha2mu.base — par_Fmu_base","text":"","code":"par_Fmu_base(peak = 20, liver = 7, tildeb = 10.3, tildel = 2, Sa = 0.0033)"},{"path":"https://dd-harp.github.io/pf.memory/reference/par_Fmu_base.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up parameters for alpha2mu.base — par_Fmu_base","text":"peak age infection (days) parasite densities peak liver age infection (days) parasites emerge liver tildeb maximum expected log10 parasite densities tildel minimum expected log10 parasite densities Sa decline mu respect alpha","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_Fmu_base.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up parameters for alpha2mu.base — par_Fmu_base","text":"list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_Fmu_chronic.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up parameters for alpha2mu.chronic — par_Fmu_chronic","title":"Set up parameters for alpha2mu.chronic — par_Fmu_chronic","text":"Set parameters alpha2mu.chronic","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_Fmu_chronic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up parameters for alpha2mu.chronic — par_Fmu_chronic","text":"","code":"par_Fmu_chronic(tildeb = 10.3, tildel = 2, Sa = 0.0033)"},{"path":"https://dd-harp.github.io/pf.memory/reference/par_Fmu_chronic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up parameters for alpha2mu.chronic — par_Fmu_chronic","text":"tildeb maximum expected log10 parasite densities tildel minimum expected log10 parasite densities Sa decline mu respect alpha","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_Fmu_chronic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up parameters for alpha2mu.chronic — par_Fmu_chronic","text":"list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_Wda.0.html","id":null,"dir":"Reference","previous_headings":"","what":"Make a parameter set for Wda.0 — par_Wda.0","title":"Make a parameter set for Wda.0 — par_Wda.0","text":"Make parameter set Wda.0","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_Wda.0.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make a parameter set for Wda.0 — par_Wda.0","text":"","code":"par_Wda.0()"},{"path":"https://dd-harp.github.io/pf.memory/reference/par_Wda.0.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make a parameter set for Wda.0 — par_Wda.0","text":"list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_Wda.delta.html","id":null,"dir":"Reference","previous_headings":"","what":"Make a parameter set for Wda.delta — par_Wda.delta","title":"Make a parameter set for Wda.delta — par_Wda.delta","text":"Make parameter set Wda.delta","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_Wda.delta.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make a parameter set for Wda.delta — par_Wda.delta","text":"","code":"par_Wda.delta(delta = 0.001)"},{"path":"https://dd-harp.github.io/pf.memory/reference/par_Wda.delta.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make a parameter set for Wda.delta — par_Wda.delta","text":"delta decay rate","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_Wda.delta.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make a parameter set for Wda.delta — par_Wda.delta","text":"list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_Wda_delta.html","id":null,"dir":"Reference","previous_headings":"","what":"Make a parameter set for Wda.none — par_Wda_delta","title":"Make a parameter set for Wda.none — par_Wda_delta","text":"Make parameter set Wda.none","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_Wda_delta.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make a parameter set for Wda.none — par_Wda_delta","text":"","code":"par_Wda_delta(delta = 0.001)"},{"path":"https://dd-harp.github.io/pf.memory/reference/par_Wda_delta.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make a parameter set for Wda.none — par_Wda_delta","text":"delta decay rate","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_Wda_delta.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make a parameter set for Wda.none — par_Wda_delta","text":"list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_Wda_none.html","id":null,"dir":"Reference","previous_headings":"","what":"Make a parameter set for Wda.none — par_Wda_none","title":"Make a parameter set for Wda.none — par_Wda_none","text":"Make parameter set Wda.none","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_Wda_none.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make a parameter set for Wda.none — par_Wda_none","text":"","code":"par_Wda_none()"},{"path":"https://dd-harp.github.io/pf.memory/reference/par_Wda_none.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make a parameter set for Wda.none — par_Wda_none","text":"list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_alpha2mu.0.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up parameters for alpha2mu.0 — par_alpha2mu.0","title":"Set up parameters for alpha2mu.0 — par_alpha2mu.0","text":"Set parameters alpha2mu.0","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_alpha2mu.0.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up parameters for alpha2mu.0 — par_alpha2mu.0","text":"","code":"par_alpha2mu.0(D = 20, liver = 7, tildeb = 10.3, tildel = 2, Sa = 0.0033)"},{"path":"https://dd-harp.github.io/pf.memory/reference/par_alpha2mu.0.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up parameters for alpha2mu.0 — par_alpha2mu.0","text":"D age infection (days) parasite densities peak liver age infection (days) parasites emerge liver tildeb maximum expected log10 parasite densities tildel minimum expected log10 parasite densities Sa decline mu respect alpha","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_alpha2mu.0.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up parameters for alpha2mu.0 — par_alpha2mu.0","text":"list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_alpha2mu.W.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up parameters for alpha2mu.W — par_alpha2mu.W","title":"Set up parameters for alpha2mu.W — par_alpha2mu.W","text":"Set parameters alpha2mu.W","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_alpha2mu.W.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up parameters for alpha2mu.W — par_alpha2mu.W","text":"","code":"par_alpha2mu.W(   peak = 20,   liver = 7,   tildeb = 10.3,   tildel = 2,   Sa = 0.0033,   Sw = 0.001 )"},{"path":"https://dd-harp.github.io/pf.memory/reference/par_alpha2mu.W.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up parameters for alpha2mu.W — par_alpha2mu.W","text":"peak age infection (days) parasite densities peak liver age infection (days) parasites emerge liver tildeb maximum expected log10 parasite densities tildel minimum expected log10 parasite densities Sa decline mu respect alpha Sw decline mu respect immunity","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_alpha2mu.W.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up parameters for alpha2mu.W — par_alpha2mu.W","text":"mean log10 parasite densities","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_alpha2mu_base.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up parameters for alpha2mu.base — par_alpha2mu_base","title":"Set up parameters for alpha2mu.base — par_alpha2mu_base","text":"Set parameters alpha2mu.base","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_alpha2mu_base.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up parameters for alpha2mu.base — par_alpha2mu_base","text":"","code":"par_alpha2mu_base(peak = 20, liver = 7, 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par_alpha2mu_chronic","text":"list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_expSeason.html","id":null,"dir":"Reference","previous_headings":"","what":"Return a list to dispatch seasonalFoI.exp — par_expSeason","title":"Return a list to dispatch seasonalFoI.exp — par_expSeason","text":"Return list dispatch seasonalFoI.exp","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_expSeason.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return a list to dispatch seasonalFoI.exp — par_expSeason","text":"","code":"par_expSeason(phase = 0, pwr = 1, lift = 0, shift = 0)"},{"path":"https://dd-harp.github.io/pf.memory/reference/par_expSeason.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return a list to dispatch seasonalFoI.exp — par_expSeason","text":"phase shift phase / time year pwr raise seasonal pattern power lift amplitude shift shift everything 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for parasite densities in a simple malaria infection — par_mu2density_beta","text":"","code":"par_mu2density_beta(par_lRBC = par_lRBC_static(), par_sigma = par_sigma_abc())"},{"path":"https://dd-harp.github.io/pf.memory/reference/par_mu2density_beta.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The quantile function for parasite densities in a simple malaria infection — par_mu2density_beta","text":"par_lRBC parameters compute log10 RBC density par_sigma parameters compute sigma_mu","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_mu2density_beta.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The quantile function for parasite densities in a simple malaria infection — par_mu2density_beta","text":"compound list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_nbCounts.html","id":null,"dir":"Reference","previous_headings":"","what":"Detection of infection given 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par_nbCounts","text":"binary detection result","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_poisCounts.html","id":null,"dir":"Reference","previous_headings":"","what":"Detection of infection given parasitemia — par_poisCounts","title":"Detection of infection given parasitemia — par_poisCounts","text":"Detection infection given parasitemia","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_poisCounts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Detection of infection given parasitemia — par_poisCounts","text":"","code":"par_poisCounts(q = 6, bvm = par_lRBC_static())"},{"path":"https://dd-harp.github.io/pf.memory/reference/par_poisCounts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Detection of infection given parasitemia — par_poisCounts","text":"q fraction blood volume sampled bvm blood volume log10 red blood 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sigma.0 — par_sigma.0","text":"aa shape parameter bb shape parameter cc shape parameter","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_sigma.0.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parameters to configure sigma.0 — par_sigma.0","text":"list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_sigma_abc.html","id":null,"dir":"Reference","previous_headings":"","what":"Parameters to configure sigma_mu.abc — par_sigma_abc","title":"Parameters to configure sigma_mu.abc — par_sigma_abc","text":"Parameters configure sigma_mu.abc","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/par_sigma_abc.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parameters to configure sigma_mu.abc — par_sigma_abc","text":"","code":"par_sigma_abc(aa = 3.11, bb = 2.14, cc = 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sigma_mu","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/qDensityPalpha.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The quantile function for parasite densities in a simple malaria infection of age alpha — qDensityPalpha","text":"numeric vector length(x)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/qDensityPmu.html","id":null,"dir":"Reference","previous_headings":"","what":"The quantile function for parasite densities in a simple malaria infection — qDensityPmu","title":"The quantile function for parasite densities in a simple malaria infection — qDensityPmu","text":"quantile function parasite densities simple malaria infection","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/qDensityPmu.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The quantile function for parasite densities in a simple malaria infection — 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age parasite infection W immune tracking variables host cohort age par_RBC parameters compute log10RBC par_Fmu parameters compute alpha2mu par_mu2dens parameters compute q_mu2density","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/q_alpha2density.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The quantile function for parasite densities in a simple malaria infection of age alpha — q_alpha2density","text":"numeric vector length(x)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/q_mu2density.beta.html","id":null,"dir":"Reference","previous_headings":"","what":"Modified beta distribution, distribution function — q_mu2density.beta","title":"Modified beta distribution, distribution function — q_mu2density.beta","text":"Modified beta distribution, distribution function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/q_mu2density.beta.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Modified beta distribution, distribution function — q_mu2density.beta","text":"","code":"# S3 method for beta q_mu2density(xi, mu, par_mu2dens = par_mu2dens_beta(), bvm = 13)"},{"path":"https://dd-harp.github.io/pf.memory/reference/q_mu2density.beta.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Modified beta distribution, distribution function — q_mu2density.beta","text":"xi vector quantiles mu expected value \\(log_{10}\\) parasite densities par_mu2dens parameters defining parasite densities function mu bvm blood volume \\(log_{10}\\) red blood cells","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/q_mu2density.beta.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Modified beta distribution, distribution function — q_mu2density.beta","text":"numeric vector length(xi)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/q_mu2density.html","id":null,"dir":"Reference","previous_headings":"","what":"The quantile function for parasite densities in a simple malaria infection — q_mu2density","title":"The quantile function for parasite densities in a simple malaria infection — q_mu2density","text":"quantile function parasite densities simple malaria infection","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/q_mu2density.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The quantile function for parasite densities in a simple malaria infection — q_mu2density","text":"","code":"q_mu2density(xi, mu, par_mu2dens = par_mu2dens_beta(), bvm = 13)"},{"path":"https://dd-harp.github.io/pf.memory/reference/q_mu2density.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The quantile function for parasite densities in a simple malaria infection — q_mu2density","text":"xi vector quantiles mu expected value \\(log_{10}\\) parasite densities par_mu2dens parameters defining parasite densities function mu bvm blood volume \\(log_{10}\\) red blood cells","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/q_mu2density.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The quantile function for parasite densities in a simple malaria infection — q_mu2density","text":"numeric vector length(xi)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/qbeta1.html","id":null,"dir":"Reference","previous_headings":"","what":"The quantile function for the beta distribution, an alternative parameterization — qbeta1","title":"The quantile function for the beta distribution, an alternative parameterization — qbeta1","text":"quantile function beta distribution, alternative parameterization","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/qbeta1.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The quantile function for the beta distribution, an alternative parameterization — qbeta1","text":"","code":"qbeta1(x, mu, pSig = par_sigma_abc())"},{"path":"https://dd-harp.github.io/pf.memory/reference/qbeta1.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The quantile function for the beta distribution, an alternative parameterization — qbeta1","text":"x vector quantiles mu mean value distribution (0 <= mu <= 1) pSig parameters dispatch S3 function sigma_mu","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/qbeta1.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The quantile function for the beta distribution, an alternative parameterization — qbeta1","text":"numeric vector length(x)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/rAoI.html","id":null,"dir":"Reference","previous_headings":"","what":"Random numbers for the AoI — rAoI","title":"Random numbers for the AoI — rAoI","text":"Random numbers AoI","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/rAoI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Random numbers for the AoI — rAoI","text":"","code":"rAoI(N, a, FoIpar, tau = 0, hhat = 1, r = 1/200, alphamin = 0)"},{"path":"https://dd-harp.github.io/pf.memory/reference/rAoI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Random numbers for the AoI — rAoI","text":"N number observations host age FoIpar compound list compute \\(h_\\tau()\\) tau host cohort's birthday hhat local scaling parameter FoI r clearance rate simple infection alphamin minimum value AoI return","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/rAoI.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Random numbers for the AoI — rAoI","text":"numeric vector length(alpha)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/rAoY.html","id":null,"dir":"Reference","previous_headings":"","what":"The random generation function for the age of the youngest infection (AoY) — rAoY","title":"The random generation function for the age of the youngest infection (AoY) — rAoY","text":"random generation function age youngest infection (AoY)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/rAoY.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The random generation function for the age of the youngest infection (AoY) — rAoY","text":"","code":"rAoY(N, a, FoIpar, tau = 0, hhat = 1, r = 1/200, alphamin = 0)"},{"path":"https://dd-harp.github.io/pf.memory/reference/rAoY.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The random generation function for the age of the youngest infection (AoY) — rAoY","text":"N number observations host age FoIpar compound list compute \\(h_\\tau()\\) tau host cohort's birthday hhat local scaling parameter FoI r clearance rate simple infection alphamin minimum value AoI return","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/rAoY.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The random generation function for the age of the youngest infection (AoY) — rAoY","text":"numeric vector length(N)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/rAoYN.html","id":null,"dir":"Reference","previous_headings":"","what":"The youngest of N infections, random numbers — rAoYN","title":"The youngest of N infections, random numbers — rAoYN","text":"youngest N infections, random numbers","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/rAoYN.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The youngest of N infections, random numbers — rAoYN","text":"","code":"rAoYN(R, N, a, FoIpar, hhat = NULL, tau = 0, r = 1/200, alphamin = 0)"},{"path":"https://dd-harp.github.io/pf.memory/reference/rAoYN.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The youngest of N infections, random numbers — rAoYN","text":"R number observations N number infections per person host cohort age FoIpar parameters define FoI function hhat local scaling parameter FoI tau cohort birthday r clearance rate simple infection alphamin minimum value AoI return","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/rAoYN.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The youngest of N infections, random numbers — rAoYN","text":"numeric vector length R","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/rBda.html","id":null,"dir":"Reference","previous_headings":"","what":"Random generation for parasite densities in a host cohort — rBda","title":"Random generation for parasite densities in a host cohort — rBda","text":"Random generation parasite densities host cohort","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/rBda.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Random generation for parasite densities in a host cohort — rBda","text":"","code":"rBda(   N,   a,   FoIpar,   hhat = NULL,   r = 1/200,   tau = 0,   alphamin = 7,   pMu = par_alpha2mu_base(),   pPDens = par_mu2density_beta(),   pWda = par_Wda_none() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/rBda.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Random generation for parasite densities in a host cohort — rBda","text":"N number observations host cohort age FoIpar parameters define FoI function hhat local scaling parameter FoI r clearance rate simple infection tau cohort birthday alphamin minimum value alpha allowed pMu parameters compute alpha2mu pPDens parameters defining parasite densities function mu pWda parameters dispatch Wda","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/rBda.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Random generation for parasite densities in a host cohort — rBda","text":"numeric vector length N","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/rDensityPalpha.html","id":null,"dir":"Reference","previous_headings":"","what":"The distribution function for parasite densities in a simple malaria infection of age alpha — rDensityPalpha","title":"The distribution function for parasite densities in a simple malaria infection of age alpha — rDensityPalpha","text":"distribution function parasite densities simple malaria infection age alpha","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/rDensityPalpha.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The distribution function for parasite densities in a simple malaria infection of age alpha — rDensityPalpha","text":"","code":"rDensityPalpha(   n,   alpha,   W = 0,   a = 0,   pMu = par_alpha2mu_base(),   pRBC = par_lRBC_static(),   pSig = par_sigma_abc() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/rDensityPalpha.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The distribution function for parasite densities in a simple malaria infection of age alpha — rDensityPalpha","text":"n number observations alpha age parasite infection W immune tracking variables host cohort age pMu parameters compute alpha2mu pRBC parameters compute log10RBC pSig parameters compute sigma_mu","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/rDensityPalpha.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The distribution function for parasite densities in a simple malaria infection of age alpha — rDensityPalpha","text":"numeric vector length(n)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/rDensityPmu.html","id":null,"dir":"Reference","previous_headings":"","what":"Random generation of parasite densities from a simple malaria infection — rDensityPmu","title":"Random generation of parasite densities from a simple malaria infection — rDensityPmu","text":"Random generation parasite densities simple malaria infection","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/rDensityPmu.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Random generation of parasite densities from a simple malaria infection — rDensityPmu","text":"","code":"rDensityPmu(n, mu, a = 0, pRBC = par_lRBC_static(), pSig = par_sigma_abc())"},{"path":"https://dd-harp.github.io/pf.memory/reference/rDensityPmu.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Random generation of parasite densities from a simple malaria infection — rDensityPmu","text":"n number observations mu expected value log10 parasite densities host cohort age pRBC parameters compute log10RBC pSig parameters dispatch sigma_mu","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/rDensityPmu.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Random generation of parasite densities from a simple malaria infection — rDensityPmu","text":"numeric vector length(n)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/rRda.html","id":null,"dir":"Reference","previous_headings":"","what":"Random generation for M parasite densities in a host cohort with MoI — rRda","title":"Random generation for M parasite densities in a host cohort with MoI — rRda","text":"Random generation M parasite densities host cohort MoI","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/rRda.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Random generation for M parasite densities in a host cohort with MoI — rRda","text":"","code":"rRda(   M,   R,   a,   FoIpar,   tau = 0,   hhat = 1,   r = 1/200,   alphamin = 7,   RBC_par = par_lRBC_static(),   Fmu_par = par_Fmu_base(),   mu_par = par_mu2dens_beta(),   pWda = par_Wda_none() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/rRda.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Random generation for M parasite densities in a host cohort with MoI — rRda","text":"M MoI R number observations host cohort age FoIpar parameters define FoI function tau cohort birthday hhat local scaling parameter FoI r clearance rate simple infection alphamin minimum value alpha allowed RBC_par parameters compute log10RBC Fmu_par parameters compute alpha2mu mu_par parameters defining parasite densities function mu pWda parameters dispatch Wda","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/rRda.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Random generation for M parasite densities in a host cohort with MoI — rRda","text":"R M matrix","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/r_Bdensity.html","id":null,"dir":"Reference","previous_headings":"","what":"Random generation for parasite densities in a host cohort — r_Bdensity","title":"Random generation for parasite densities in a host cohort — r_Bdensity","text":"Random generation parasite densities host cohort","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/r_Bdensity.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Random generation for parasite densities in a host cohort — r_Bdensity","text":"","code":"r_Bdensity(   N,   a,   FoIpar,   tau = 0,   hhat = 1,   r = 1/200,   alphamin = 7,   RBC_par = par_lRBC_static(),   Fmu_par = par_Fmu_base(),   mu_par = par_mu2dens_beta(),   pWda = par_Wda_none() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/r_Bdensity.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Random generation for parasite densities in a host cohort — r_Bdensity","text":"N number observations host cohort age FoIpar parameters define FoI function tau cohort birthday hhat local scaling parameter FoI r clearance rate simple infection alphamin minimum value alpha allowed RBC_par parameters compute log10RBC Fmu_par parameters compute alpha2mu mu_par parameters compute d_mu2density pWda parameters dispatch Wda","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/r_Bdensity.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Random generation for parasite densities in a host cohort — r_Bdensity","text":"numeric vector length N","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/r_alpha2density.html","id":null,"dir":"Reference","previous_headings":"","what":"The distribution function for parasite densities in a simple malaria infection of age alpha — r_alpha2density","title":"The distribution function for parasite densities in a simple malaria infection of age alpha — r_alpha2density","text":"distribution function parasite densities simple malaria infection age alpha","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/r_alpha2density.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The distribution function for parasite densities in a simple malaria infection of age alpha — r_alpha2density","text":"","code":"r_alpha2density(   n,   alpha,   W = 0,   a = 0,   par_RBC = par_lRBC_static(),   par_Fmu = par_Fmu_base(),   par_mu2dens = par_mu2dens_beta() )"},{"path":"https://dd-harp.github.io/pf.memory/reference/r_alpha2density.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The distribution function for parasite densities in a simple malaria infection of age alpha — r_alpha2density","text":"n number observations alpha age parasite infection W immune tracking variables host cohort age par_RBC parameters compute log10RBC par_Fmu parameters compute alpha2mu par_mu2dens parameters compute r_mu2density","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/r_alpha2density.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The distribution function for parasite densities in a simple malaria infection of age alpha — r_alpha2density","text":"numeric vector length(n)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/r_mu2density.beta.html","id":null,"dir":"Reference","previous_headings":"","what":"Modified beta distribution, random numbers — r_mu2density.beta","title":"Modified beta distribution, random numbers — r_mu2density.beta","text":"beta distribution, parameterized mean variance, modified return number 0 bvm (number red blood cells)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/r_mu2density.beta.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Modified beta distribution, random numbers — r_mu2density.beta","text":"","code":"# S3 method for beta r_mu2density(n, mu, par_mu2dens = par_mu2dens_beta(), bvm = 13)"},{"path":"https://dd-harp.github.io/pf.memory/reference/r_mu2density.beta.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Modified beta distribution, random numbers — r_mu2density.beta","text":"n number observations mu expected value \\(log_{10}\\) parasite densities par_mu2dens parameters defining parasite densities function mu bvm blood volume \\(log_{10}\\) red blood cells","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/r_mu2density.beta.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Modified beta distribution, random numbers — r_mu2density.beta","text":"numeric vector length(xi)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/r_mu2density.html","id":null,"dir":"Reference","previous_headings":"","what":"Random generation of parasite densities from a simple malaria infection — r_mu2density","title":"Random generation of parasite densities from a simple malaria infection — r_mu2density","text":"Random generation parasite densities simple malaria infection","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/r_mu2density.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Random generation of parasite densities from a simple malaria infection — r_mu2density","text":"","code":"r_mu2density(n, mu, par_mu2dens = par_mu2dens_beta(), bvm = 13)"},{"path":"https://dd-harp.github.io/pf.memory/reference/r_mu2density.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Random generation of parasite densities from a simple malaria infection — r_mu2density","text":"n number observations mu expected value \\(log_{10}\\) parasite densities par_mu2dens parameters defining parasite densities function mu bvm blood volume \\(log_{10}\\) red blood cells","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/r_mu2density.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Random generation of parasite densities from a simple malaria infection — r_mu2density","text":"numeric vector length(n)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/rbeta1.html","id":null,"dir":"Reference","previous_headings":"","what":"The random generation function for the beta distribution, an alternative parameterization\nTitle — rbeta1","title":"The random generation function for the beta distribution, an alternative parameterization\nTitle — rbeta1","text":"random generation function beta distribution, alternative parameterization Title","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/rbeta1.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The random generation function for the beta distribution, an alternative parameterization\nTitle — rbeta1","text":"","code":"rbeta1(n, mu, pSig = par_sigma_abc())"},{"path":"https://dd-harp.github.io/pf.memory/reference/rbeta1.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The random generation function for the beta distribution, an alternative parameterization\nTitle — rbeta1","text":"n number observations mu mean value distribution (0 <= mu <= 1) pSig parameters dispatch S3 function sigma_mu","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/rbeta1.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The random generation function for the beta distribution, an alternative parameterization\nTitle — rbeta1","text":"numeric vector length n","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/salpha2mu.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute mean, expected parasite densities mu for multiple values of the age of infection alpha — salpha2mu","title":"Compute mean, expected parasite densities mu for multiple values of the age of infection alpha — salpha2mu","text":"Compute mean, expected parasite densities mu multiple values age infection alpha","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/salpha2mu.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute mean, expected parasite densities mu for multiple values of the age of infection alpha — salpha2mu","text":"","code":"salpha2mu(alpha, W, par_Fmu)"},{"path":"https://dd-harp.github.io/pf.memory/reference/salpha2mu.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute mean, expected parasite densities mu for multiple values of the age of infection alpha — salpha2mu","text":"alpha parasite's age infection W immune tracking variables par_Fmu list defines model","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/salpha2mu.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute mean, expected parasite densities mu for multiple values of the age of infection alpha — salpha2mu","text":"mean log10 parasite densities, numeric vector length(alpha)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/seasonalFoI.exp.html","id":null,"dir":"Reference","previous_headings":"","what":"A generalized sinusoidal seasonal pattern, exponentiated — seasonalFoI.exp","title":"A generalized sinusoidal seasonal pattern, exponentiated — seasonalFoI.exp","text":"generalized sinusoidal seasonal pattern, exponentiated","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/seasonalFoI.exp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A generalized sinusoidal seasonal pattern, exponentiated — seasonalFoI.exp","text":"","code":"# S3 method for exp seasonalFoI(t, par = par_expSeason())"},{"path":"https://dd-harp.github.io/pf.memory/reference/seasonalFoI.exp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A generalized sinusoidal seasonal pattern, exponentiated — seasonalFoI.exp","text":"t time par list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/seasonalFoI.exp.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"A generalized sinusoidal seasonal pattern, exponentiated — seasonalFoI.exp","text":"numeric","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/seasonalFoI.flat.html","id":null,"dir":"Reference","previous_headings":"","what":"The ","title":"The ","text":"\"seasonality\" function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/seasonalFoI.flat.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The ","text":"","code":"# S3 method for flat seasonalFoI(t, par)"},{"path":"https://dd-harp.github.io/pf.memory/reference/seasonalFoI.flat.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The ","text":"t time par list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/seasonalFoI.flat.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The ","text":"numeric","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/seasonalFoI.html","id":null,"dir":"Reference","previous_headings":"","what":"Add a seasonal pattern to the FoI trace function — seasonalFoI","title":"Add a seasonal pattern to the FoI trace function — seasonalFoI","text":"Add seasonal pattern FoI trace function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/seasonalFoI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add a seasonal pattern to the FoI trace function — seasonalFoI","text":"","code":"seasonalFoI(t, par)"},{"path":"https://dd-harp.github.io/pf.memory/reference/seasonalFoI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add a seasonal pattern to the FoI trace function — seasonalFoI","text":"t time par list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/seasonalFoI.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add a seasonal pattern to the FoI trace function — seasonalFoI","text":"numeric","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/seasonalFoI.sin.html","id":null,"dir":"Reference","previous_headings":"","what":"A generalized sinusoidal seasonal pattern — seasonalFoI.sin","title":"A generalized sinusoidal seasonal pattern — seasonalFoI.sin","text":"generalized sinusoidal seasonal pattern","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/seasonalFoI.sin.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A generalized sinusoidal seasonal pattern — seasonalFoI.sin","text":"","code":"# S3 method for sin seasonalFoI(t, par = par_sinSeason())"},{"path":"https://dd-harp.github.io/pf.memory/reference/seasonalFoI.sin.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A generalized sinusoidal seasonal pattern — seasonalFoI.sin","text":"t time par list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/seasonalFoI.sin.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"A generalized sinusoidal seasonal pattern — seasonalFoI.sin","text":"numeric","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/sigma.0.html","id":null,"dir":"Reference","previous_headings":"","what":"A function that returns constrained values of the variance for the beta distrution as a function of the mean. — sigma.0","title":"A function that returns constrained values of the variance for the beta distrution as a function of the mean. — sigma.0","text":"function returns constrained values variance beta distrution function mean.","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/sigma.0.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A function that returns constrained values of the variance for the beta distrution as a function of the mean. — sigma.0","text":"","code":"# S3 method for `0` sigma(mu, par)"},{"path":"https://dd-harp.github.io/pf.memory/reference/sigma.0.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A function that returns constrained values of the variance for the beta distrution as a function of the mean. — sigma.0","text":"mu mean value distribution (0 <= mu <= 1) par parameters dispatch configure instances","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/sigma.0.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"A function that returns 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compute","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/solve_dAoI.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Solve the system of differential equations to compute the moments of the AoI over time. — solve_dAoI","text":"data.frame orbits","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/solve_dAoYda.html","id":null,"dir":"Reference","previous_headings":"","what":"Solve the system of differential equations to compute the approximate moments of the AoY over time. — solve_dAoYda","title":"Solve the system of differential equations to compute the approximate moments of the AoY over time. — solve_dAoYda","text":"Solve system differential equations compute approximate moments AoY time.","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/solve_dAoYda.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Solve the system of differential equations to compute the approximate moments of the AoY over time. — solve_dAoYda","text":"","code":"solve_dAoYda(h, FoIpar, r = 1/200, tau = 0, Amax = 730, dt = 1, n = 8)"},{"path":"https://dd-harp.github.io/pf.memory/reference/solve_dAoYda.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Solve the system of differential equations to compute the approximate moments of the AoY over time. — solve_dAoYda","text":"h force infection FoIpar FoI trace function r clearance rate simple infection tau cohort birthday Amax maximum runtime (days) dt output frequency (days) n number terms use \\(\\phi(r,m)\\)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/solve_dAoYda.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Solve the system of differential equations to compute the approximate moments of the AoY over time. — solve_dAoYda","text":"data.frame describing orbits","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/solve_dm.html","id":null,"dir":"Reference","previous_headings":"","what":"Solve the hybrid model for the MoI — solve_dm","title":"Solve the hybrid model for the MoI — solve_dm","text":"Solve hybrid model MoI","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/solve_dm.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Solve the hybrid model for the MoI — solve_dm","text":"","code":"solve_dm(h, FoIpar, r = 1/200, tau = 0, Amax = 730, dt = 1)"},{"path":"https://dd-harp.github.io/pf.memory/reference/solve_dm.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Solve the hybrid model for the MoI — solve_dm","text":"h average, annual force infection FoIpar FoI trace function r clearance rate simple infection tau cohort birthday Amax maximum runtime (days) dt output frequency (days)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/solve_dm.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Solve the hybrid model for the MoI — solve_dm","text":"matrix orbits","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/solve_dpda.html","id":null,"dir":"Reference","previous_headings":"","what":"Solve a system of differential equations to compute the true PR and the MoI — solve_dpda","title":"Solve a system of differential equations to compute the true PR and the MoI — solve_dpda","text":"Solve system differential equations compute true PR MoI","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/solve_dpda.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Solve a system of differential equations to compute the true PR and the MoI — solve_dpda","text":"","code":"solve_dpda(h, FoIpar, r = 1/200, tau = 0, Amax = 730, dt = 1)"},{"path":"https://dd-harp.github.io/pf.memory/reference/solve_dpda.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Solve a system of differential equations to compute the true PR and the MoI — solve_dpda","text":"h scaling factor FoI FoIpar parameters define FoI function r clearance rate simple infection tau cohort birthday Amax maximum runtime (days) dt output frequency (days)","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/solve_dpda.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Solve a system of differential equations to compute the true PR and the MoI — solve_dpda","text":"data.frame orbits","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/trendFoI.flat.html","id":null,"dir":"Reference","previous_headings":"","what":"The ","title":"The ","text":"\"trend\" function","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/trendFoI.flat.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The ","text":"","code":"# S3 method for flat trendFoI(t, par)"},{"path":"https://dd-harp.github.io/pf.memory/reference/trendFoI.flat.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The ","text":"t time par list","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/trendFoI.flat.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The ","text":"numeric","code":""},{"path":"https://dd-harp.github.io/pf.memory/reference/trendFoI.html","id":null,"dir":"Reference","previous_headings":"","what":"Add a trend to the FoI trace function — trendFoI","title":"Add a trend to the FoI trace function — trendFoI","text":"Add trend FoI trace 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