Draft paper

.Rproj.user/BAB4038F/pcs/files-pane.pper

@@ -5,5 +5,5 @@
             "ascending": true
         }
     ],
-    "path": "~/git/pf.memory/R"
+    "path": "~/git/pf.memory/vignettes"
 }

.Rproj.user/BAB4038F/pcs/source-pane.pper

@@ -1,3 +1,3 @@
 {
-    "activeTab": 10
+    "activeTab": 3
 }

.Rproj.user/BAB4038F/pcs/windowlayoutstate.pper

@@ -1,12 +1,12 @@
 {
     "left": {
-        "splitterpos": 457,
+        "splitterpos": 372,
         "topwindowstate": "NORMAL",
         "panelheight": 1172,
         "windowheight": 1210
     },
     "right": {
-        "splitterpos": 614,
+        "splitterpos": 385,
         "topwindowstate": "NORMAL",
         "panelheight": 1172,
         "windowheight": 1210

.Rproj.user/BAB4038F/pcs/workbench-pane.pper

@@ -1,5 +1,5 @@
 {
     "TabSet1": 1,
-    "TabSet2": 5,
+    "TabSet2": 0,
     "TabZoom": {}
 }

.Rproj.user/BAB4038F/sources/prop/INDEX

@@ -4,6 +4,15 @@
 ~%2Fgit%2Fmozy_ecology.R="24C7EAB6"
 ~%2Fgit%2Fpf.memory%2FDESCRIPTION="6683BFBF"
 ~%2Fgit%2Fpf.memory%2FNAMESPACE="534057AC"
+~%2Fgit%2Fpf.memory%2FR%2FFmu-base.R="5BAA819E"
+~%2Fgit%2Fpf.memory%2FR%2FFmu-chronic.R="36BCD81E"
+~%2Fgit%2Fpf.memory%2FR%2FFmu-immune.R="B31465E0"
+~%2Fgit%2Fpf.memory%2FR%2FFmu-interface.R="D32BC313"
+~%2Fgit%2Fpf.memory%2FR%2FMMinfinity.R="B7C5F496"
+~%2Fgit%2Fpf.memory%2FR%2FOmega-beta.R="A060A2F0"
+~%2Fgit%2Fpf.memory%2FR%2FOmega-interface.R="5D88E9B4"
+~%2Fgit%2Fpf.memory%2FR%2FRBC.R="71153DE9"
+~%2Fgit%2Fpf.memory%2FR%2FTheta.R="57BD1419"
 ~%2Fgit%2Fpf.memory%2FR%2Falpha2density-beta.R="7B0E571F"
 ~%2Fgit%2Fpf.memory%2FR%2Falpha2density.R="7BF3E52A"
 ~%2Fgit%2Fpf.memory%2FR%2Falpha2mu-W.R="0615E065"
@@ -17,13 +26,27 @@
 ~%2Fgit%2Fpf.memory%2FR%2FaoyN.R="6F2904AF"
 ~%2Fgit%2Fpf.memory%2FR%2Fbeta.R="FBD39C0C"
 ~%2Fgit%2Fpf.memory%2FR%2Fblood_volume.R="CFD4D0B3"
+~%2Fgit%2Fpf.memory%2FR%2Fclonal_counts.R="2ABD17C1"
+~%2Fgit%2Fpf.memory%2FR%2Fclonal_densities.Rmd="1A7B5D93"
+~%2Fgit%2Fpf.memory%2FR%2Fclonal_density.R="91FB5CE3"
+~%2Fgit%2Fpf.memory%2FR%2Fclonal_detection.R="7644269F"
+~%2Fgit%2Fpf.memory%2FR%2Fclone_counts.R="4BB8024B"
+~%2Fgit%2Fpf.memory%2FR%2Fclone_density.R="B7D443C0"
+~%2Fgit%2Fpf.memory%2FR%2Fclone_detection.R="746DA46A"
 ~%2Fgit%2Fpf.memory%2FR%2Fcohort_counts.R="44AB2D5D"
 ~%2Fgit%2Fpf.memory%2FR%2Fcohort_detect.R="80E3C356"
 ~%2Fgit%2Fpf.memory%2FR%2Fcohort_parasites_clones.R="D759A9B3"
 ~%2Fgit%2Fpf.memory%2FR%2Fcohort_parasites_complex.R="42884925"
 ~%2Fgit%2Fpf.memory%2FR%2Fcohort_parasites_simple.R="6C8EA019"
 ~%2Fgit%2Fpf.memory%2FR%2Fconvolve.R="912073C6"
+~%2Fgit%2Fpf.memory%2FR%2Fcount_parasites.R="4B4677E9"
 ~%2Fgit%2Fpf.memory%2FR%2Fcounts.R="6DB6CAA1"
+~%2Fgit%2Fpf.memory%2FR%2Fcounts_clone.R="47B7018F"
+~%2Fgit%2Fpf.memory%2FR%2Fcounts_parasites.R="1C0FAD32"
+~%2Fgit%2Fpf.memory%2FR%2Fdensity_clone.R="81AE25DE"
+~%2Fgit%2Fpf.memory%2FR%2Fdensity_parasites.R="51C0BF39"
+~%2Fgit%2Fpf.memory%2FR%2Fdetect_clone.R="DE4F2A82"
+~%2Fgit%2Fpf.memory%2FR%2Fdetect_parasites.R="BDBFDDB0"
 ~%2Fgit%2Fpf.memory%2FR%2Fdetection-interface.R="6B78DF9F"
 ~%2Fgit%2Fpf.memory%2FR%2Fdetection-nb.R="8A490595"
 ~%2Fgit%2Fpf.memory%2FR%2Fdetection-pois.R="EAFCEBC2"
@@ -38,30 +61,43 @@
 ~%2Fgit%2Fpf.memory%2FR%2Fhost_cohorts.R="84C0B865"
 ~%2Fgit%2Fpf.memory%2FR%2Fhybrid.R="0E8F467C"
 ~%2Fgit%2Fpf.memory%2FR%2Fimmune_tracking.R="A048ED65"
+~%2Fgit%2Fpf.memory%2FR%2Finfection_dynamics.R="E4269552"
 ~%2Fgit%2Fpf.memory%2FR%2Fmodified_beta.R="60B42952"
 ~%2Fgit%2Fpf.memory%2FR%2Fmoi.R="C75BDA96"
 ~%2Fgit%2Fpf.memory%2FR%2Fmu2density-beta.R="3D56436C"
+~%2Fgit%2Fpf.memory%2FR%2Fmu2density-interface.R="D21B11A3"
 ~%2Fgit%2Fpf.memory%2FR%2Fmu2density.R="72434DC4"
+~%2Fgit%2Fpf.memory%2FR%2Fomega-interface.R="3EC86BE4"
 ~%2Fgit%2Fpf.memory%2FR%2Fpar_dens_complex.R="DB0E72E9"
 ~%2Fgit%2Fpf.memory%2FR%2Fpar_dens_simple.R="D0F27E38"
 ~%2Fgit%2Fpf.memory%2FR%2Fparasite_cohorts.R="6EB5B99B"
+~%2Fgit%2Fpf.memory%2FR%2Fparasite_counts.R="D26138E7"
 ~%2Fgit%2Fpf.memory%2FR%2Fparasite_dens_complex.R="328463D5"
 ~%2Fgit%2Fpf.memory%2FR%2Fparasite_dens_simple.R="919ADC01"
 ~%2Fgit%2Fpf.memory%2FR%2Fparasite_densities.R="2D02006A"
 ~%2Fgit%2Fpf.memory%2FR%2Fparasite_densities_complex.R="A563775B"
 ~%2Fgit%2Fpf.memory%2FR%2Fparasite_densities_simple.R="20F45A82"
+~%2Fgit%2Fpf.memory%2FR%2Fparasite_density.R="9D367F2B"
+~%2Fgit%2Fpf.memory%2FR%2Fparasite_detection.R="DC442C1E"
 ~%2Fgit%2Fpf.memory%2FR%2Fparasite_simple.R="09250A2A"
 ~%2Fgit%2Fpf.memory%2FR%2Fparasites_simple.R="DE5F9651"
 ~%2Fgit%2Fpf.memory%2FR%2Fpr.R="CB713F73"
 ~%2Fgit%2Fpf.memory%2FR%2Fpr.Rmd="1950C552"
 ~%2Fgit%2Fpf.memory%2FR%2Fprevalence.R="1B2C829C"
 ~%2Fgit%2Fpf.memory%2FR%2Frbc.R="55313469"
+~%2Fgit%2Fpf.memory%2FR%2Fsample-interface.R="AED269A3"
+~%2Fgit%2Fpf.memory%2FR%2Fsample-nb.R="74561104"
+~%2Fgit%2Fpf.memory%2FR%2Fsample-pois.R="5D82C219"
+~%2Fgit%2Fpf.memory%2FR%2Fsampling-interface.R="022079D8"
+~%2Fgit%2Fpf.memory%2FR%2Fsampling-nb.R="E683D640"
+~%2Fgit%2Fpf.memory%2FR%2Fsampling-pois.R="94A976BD"
 ~%2Fgit%2Fpf.memory%2FR%2Futils.R="016A8C62"
 ~%2Fgit%2Fpf.memory%2FREADME.Rmd="02662E0A"
 ~%2Fgit%2Fpf.memory%2FREADME.md="5CA253FF"
 ~%2Fgit%2Fpf.memory%2F_pkgdown.yml="33F34E18"
 ~%2Fgit%2Fpf.memory%2Fdocs%2Findex.html="6399C0D0"
 ~%2Fgit%2Fpf.memory%2Fdocs%2Freference%2Fout="B693E1D7"
+~%2Fgit%2Fpf.memory%2Fman%2Fd_detect.Rd="4AA32B57"
 ~%2Fgit%2Fpf.memory%2Fman%2Fout="D565CA5D"
 ~%2Fgit%2Fpf.memory%2Fvignettes%2FAoI-Hybrid.Rmd="11869B4B"
 ~%2Fgit%2Fpf.memory%2Fvignettes%2FAoI.Rmd="35C9761C"

NAMESPACE

@@ -1,41 +1,34 @@
 # Generated by roxygen2: do not edit by hand
 
-S3method(Detect,nb)
-S3method(Detect,pois)
+S3method(Fmu,W)
+S3method(Fmu,base)
+S3method(Fmu,chronic)
 S3method(Wda,delta)
 S3method(Wda,none)
 S3method(ageFoI,flat)
 S3method(ageFoI,type2)
-S3method(alpha2mu,W)
-S3method(alpha2mu,base)
-S3method(alpha2mu,chronic)
-S3method(binnedCounts,nb)
-S3method(binnedCounts,pois)
-S3method(dCounts,nb)
-S3method(dCounts,pois)
-S3method(d_mu2density,beta)
+S3method(d_Omega,beta)
+S3method(d_counts,nb)
+S3method(d_counts,pois)
+S3method(d_detect,nb)
+S3method(d_detect,pois)
 S3method(log10RBC,static)
-S3method(pCounts,nb)
-S3method(pCounts,pois)
-S3method(p_mu2density,beta)
-S3method(q_mu2density,beta)
-S3method(r_mu2density,beta)
+S3method(p_Omega,beta)
+S3method(p_counts,nb)
+S3method(p_counts,pois)
+S3method(q_Omega,beta)
+S3method(r_Omega,beta)
 S3method(seasonalFoI,exp)
 S3method(seasonalFoI,flat)
 S3method(seasonalFoI,sin)
 S3method(sigma_mu,abc)
 S3method(trendFoI,flat)
-export(Bdensity)
-export(Detect)
-export(DetectBda)
-export(DetectPM)
+export(FQ)
+export(Fmu)
 export(FoI)
 export(MoIDistPlot)
-export(MoIPM)
 export(Wda)
 export(ageFoI)
-export(alpha2mu)
-export(binnedCounts)
 export(cdfConvolve2)
 export(cdfConvolve2a)
 export(cdfConvolve2b)
@@ -44,66 +37,76 @@ export(dAoIda)
 export(dAoY)
 export(dAoYN)
 export(dAoYda)
-export(dCounts)
-export(dCountsBa)
-export(dCountsPa)
 export(dDensityPaConvolve2)
 export(dMoIda)
-export(d_Bdensity)
-export(d_Pdensity)
+export(d_Omega)
 export(d_alpha2density)
-export(d_mu2density)
+export(d_clone_counts)
+export(d_clone_density)
+export(d_counts)
+export(d_detect)
+export(d_detect_mesh)
+export(d_moi_count)
+export(d_nz_counts_log)
+export(d_nz_counts_log_binned)
+export(d_parasite_counts)
+export(d_parasite_density)
+export(d_parasite_detect)
+export(d_parasite_detect_moi)
 export(dbeta1)
 export(dmda)
 export(dpda)
 export(log10RBC)
-export(meanCountsBa)
-export(meanCountsPa)
 export(meanMoI)
+export(mean_clone_counts)
+export(mean_parasite_counts)
 export(momentAoI)
 export(momentAoY)
-export(moment_Bdensity)
-export(moment_Pdensity)
+export(moments_clone_density)
+export(moments_parasite_density)
 export(nzPois)
 export(pAoI)
 export(pAoY)
 export(pAoYN)
 export(pAoY_long)
-export(pCounts)
-export(pCountsBa)
-export(pCountsPa)
-export(p_Bdensity)
+export(p_Omega)
 export(p_alpha2density)
-export(p_mu2density)
+export(p_clone_counts)
+export(p_counts)
+export(p_nz_counts_log)
+export(p_nz_counts_log_binned)
+export(p_parasite_counts)
+export(p_parasite_density)
 export(par_Fmu_W)
 export(par_Fmu_base)
 export(par_Fmu_chronic)
+export(par_Omega_beta)
 export(par_Wda_delta)
 export(par_Wda_none)
 export(par_expSeason)
 export(par_flatAge)
 export(par_flatSeason)
 export(par_flatTrend)
 export(par_lRBC_static)
-export(par_mu2dens_beta)
-export(par_nbCounts)
-export(par_poisCounts)
+export(par_nb)
+export(par_pois)
 export(par_sigma_abc)
 export(par_sinSeason)
 export(par_type2Age)
+export(parasite_density)
 export(pbeta1)
+export(q_Omega)
 export(q_alpha2density)
-export(q_mu2density)
 export(qbeta1)
 export(rAoI)
 export(rAoY)
 export(rAoYN)
 export(rRda)
-export(r_Bdensity)
+export(r_Omega)
 export(r_alpha2density)
-export(r_mu2density)
+export(r_parasite_density)
 export(rbeta1)
-export(salpha2mu)
+export(sFmu)
 export(seasonalFoI)
 export(sigma_mu)
 export(solveMMinfty)
@@ -112,5 +115,5 @@ export(solve_dAoYda)
 export(solve_dm)
 export(solve_dpda)
 export(trendFoI)
-export(truePRa)
+export(truePR)
 export(zda)

R/alpha2mu-base.R → R/Fmu-base.R

@@ -2,12 +2,12 @@
 #' Compute expected log10 parasite densities, `mu`, as a function of the age of infection `alpha`
 #' @description Compute mean log10 parasites for a model with no immunity
 #'
-#' @inheritParams alpha2mu
+#' @inheritParams Fmu
 #'
 #' @return mean log10 parasite densities
 #' @export
 #'
-alpha2mu.base = function(alpha, W, par_Fmu){with(par_Fmu,{
+Fmu.base = function(alpha, W, par_Fmu){with(par_Fmu,{
   B = tildel + (tildeb-tildel)*exp(-(Sa*(alpha-peak)))
   ix = which(alpha<peak)
   if(length(ix>0)) B[ix] = tildel+(tildeb-tildel)*alpha[ix]/peak
@@ -16,7 +16,7 @@ alpha2mu.base = function(alpha, W, par_Fmu){with(par_Fmu,{
   B
 })}
 
-#' Set up parameters for [alpha2mu.base]
+#' Set up parameters for [Fmu.base]
 #'
 #' @param peak The age of infection (in days) when parasite densities peak
 #' @param liver The age of infection (in days) when parasites emerge from the liver

R/alpha2mu-chronic.R → R/Fmu-chronic.R

@@ -1,16 +1,16 @@
 #' Compute expected log10 parasite densities, `mu`, as a function of the age of infection `alpha`
 #' @description Compute mean log10 parasites for a model with no immunity
 #'
-#' @inheritParams alpha2mu
+#' @inheritParams Fmu
 #'
 #' @return mean log10 parasite densities
 #' @export
 #'
-alpha2mu.chronic = function(alpha, W, par_Fmu){with(par_Fmu,{
+Fmu.chronic = function(alpha, W, par_Fmu){with(par_Fmu,{
   B = tildel + (tildeb-tildel)*exp(-(Sa*(alpha)))
 })}
 
-#' Set up parameters for [alpha2mu.chronic]
+#' Set up parameters for [Fmu.chronic]
 #'
 #' @param tildeb The maximum expected log10 parasite densities
 #' @param tildel The minimum expected log10 parasite densities

R/alpha2mu-immune.R → R/Fmu-immune.R

@@ -2,12 +2,12 @@
 #' Compute expected log10 parasite densities, `mu`, as a function of the age of infection `alpha`
 #' @description Compute mean log10 parasites for a model with no immunity
 #'
-#' @inheritParams alpha2mu
+#' @inheritParams Fmu
 #'
 #' @return mean log10 parasite densities
 #' @export
 #'
-alpha2mu.W = function(alpha, W, par_Fmu){with(par_Fmu,{
+Fmu.W = function(alpha, W, par_Fmu){with(par_Fmu,{
   B = tildel + (tildeb-tildel)*exp(-Sa*(alpha-peak)-Sw*W)
   ix = which(alpha<=peak)
   if(length(ix>0)) B[ix] = tildel+(tildeb-tildel)*exp(-Sw*W)*alpha[ix]/peak
@@ -16,7 +16,7 @@ alpha2mu.W = function(alpha, W, par_Fmu){with(par_Fmu,{
   B
 })}
 
-#' Set up parameters for [alpha2mu.W]
+#' Set up parameters for [Fmu.W]
 #'
 #' @param peak The age of infection (in days) when parasite densities peak
 #' @param liver The age of infection (in days) when parasites emerge from the liver

R/alpha2mu-interface.R → R/Fmu-interface.R

@@ -7,8 +7,8 @@
 #' @return mean log10 parasite densities, a [numeric] vector of length(alpha)
 #' @export
 #'
-alpha2mu = function(alpha, W, par_Fmu){
-  UseMethod("alpha2mu", par_Fmu)
+Fmu = function(alpha, W, par_Fmu){
+  UseMethod("Fmu", par_Fmu)
 }
 
 #' Compute mean, expected parasite densities `mu` for multiple values of the age of infection `alpha`
@@ -20,8 +20,8 @@ alpha2mu = function(alpha, W, par_Fmu){
 #' @return mean log10 parasite densities, a [numeric] vector of length(alpha)
 #' @export
 #'
-salpha2mu = function(alpha, W, par_Fmu){
-  sapply(alpha, alpha2mu, W=W, par_Fmu=par_Fmu)
+sFmu = function(alpha, W, par_Fmu){
+  sapply(alpha, Fmu, W=W, par_Fmu=par_Fmu)
 }