From 1d8172c7ec016184d0ec538262b4e1c254e43f9a Mon Sep 17 00:00:00 2001
From: David Smith <smitdave@gmail.com>
Date: Fri, 15 Mar 2024 15:28:51 -0700
Subject: [PATCH] name change 2

---
 .Rproj.user/BAB4038F/pcs/files-pane.pper |  2 +-
 .Rproj.user/BAB4038F/sources/prop/INDEX  | 34 ++++++++++++++++++++++++
 DESCRIPTION                              |  6 ++---
 man/zda.Rd                               |  2 +-
 ramp.pf.infection.Rproj                  |  2 +-
 5 files changed, 40 insertions(+), 6 deletions(-)

diff --git a/.Rproj.user/BAB4038F/pcs/files-pane.pper b/.Rproj.user/BAB4038F/pcs/files-pane.pper
index b260829..a6eed4d 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"
+    "path": "~/git/ramp.pf.infection"
 }
\ No newline at end of file
diff --git a/.Rproj.user/BAB4038F/sources/prop/INDEX b/.Rproj.user/BAB4038F/sources/prop/INDEX
index 036d775..d91073e 100644
--- a/.Rproj.user/BAB4038F/sources/prop/INDEX
+++ b/.Rproj.user/BAB4038F/sources/prop/INDEX
@@ -116,3 +116,37 @@
 ~%2Fgit%2Fpf.memory%2Fvignettes%2FSimple_Infections.Rmd="C80BE1DE"
 ~%2Fgit%2Fpf.memory%2Fvignettes%2FplotCounts.Rmd="F6020077"
 ~%2Fgit%2Fpf.memory%2Fvignettes%2Fprevalence.Rmd="B4E4CCF0"
+~%2Fgit%2Framp.pf.infection%2FDESCRIPTION="3337A5D0"
+~%2Fgit%2Framp.pf.infection%2FNAMESPACE="164EB0C0"
+~%2Fgit%2Framp.pf.infection%2FR%2FFmu-base.R="90739E8D"
+~%2Fgit%2Framp.pf.infection%2FR%2FFmu-chronic.R="D1B41E0F"
+~%2Fgit%2Framp.pf.infection%2FR%2FFmu-immune.R="1883C709"
+~%2Fgit%2Framp.pf.infection%2FR%2FFmu-interface.R="D96C1ADB"
+~%2Fgit%2Framp.pf.infection%2FR%2FMMinfinity.R="F1058CC1"
+~%2Fgit%2Framp.pf.infection%2FR%2FOmega-beta.R="08BA9334"
+~%2Fgit%2Framp.pf.infection%2FR%2FOmega-interface.R="D279149E"
+~%2Fgit%2Framp.pf.infection%2FR%2FRBC.R="BC102A3E"
+~%2Fgit%2Framp.pf.infection%2FR%2Falpha2density.R="E4B7B983"
+~%2Fgit%2Framp.pf.infection%2FR%2Faoi.R="705E2A9D"
+~%2Fgit%2Framp.pf.infection%2FR%2Faoy.R="97710063"
+~%2Fgit%2Framp.pf.infection%2FR%2FaoyN.R="4B694B8D"
+~%2Fgit%2Framp.pf.infection%2FR%2Fconvolve.R="D7C7F290"
+~%2Fgit%2Framp.pf.infection%2FR%2Fcounts.R="49B2235A"
+~%2Fgit%2Framp.pf.infection%2FR%2Fdensity_clone.R="65CE1CE0"
+~%2Fgit%2Framp.pf.infection%2FR%2Fdensity_parasites.R="DA6B8858"
+~%2Fgit%2Framp.pf.infection%2FR%2Fdetection.R="098CB5FD"
+~%2Fgit%2Framp.pf.infection%2FR%2Ffoi-age.R="6D5EFECB"
+~%2Fgit%2Framp.pf.infection%2FR%2Ffoi-seasonal.R="4944D167"
+~%2Fgit%2Framp.pf.infection%2FR%2Ffoi-trend.R="613FA827"
+~%2Fgit%2Framp.pf.infection%2FR%2Ffoi.R="DE81A172"
+~%2Fgit%2Framp.pf.infection%2FR%2Fhybrid.R="5D8B3288"
+~%2Fgit%2Framp.pf.infection%2FR%2Fimmune_tracking.R="DE87FEE7"
+~%2Fgit%2Framp.pf.infection%2FR%2Finfection_dynamics.R="C2D26FE3"
+~%2Fgit%2Framp.pf.infection%2FR%2Fsample-interface.R="822374D2"
+~%2Fgit%2Framp.pf.infection%2FR%2Fsample-nb.R="4A869F6C"
+~%2Fgit%2Framp.pf.infection%2FR%2Fsample-pois.R="574E0149"
+~%2Fgit%2Framp.pf.infection%2FR%2Futils.R="C7CCDE72"
+~%2Fgit%2Framp.pf.infection%2FREADME.md="BAF66DE5"
+~%2Fgit%2Framp.pf.infection%2F_pkgdown.yml="11F35689"
+~%2Fgit%2Framp.pf.infection%2Fvignettes%2FComplex_Infections.Rmd="02F0C2B6"
+~%2Fgit%2Framp.pf.infection%2Fvignettes%2FParasite_Densities.Rmd="0A8F8731"
diff --git a/DESCRIPTION b/DESCRIPTION
index 77e913e..8901359 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,4 +1,4 @@
-Package: pf.memory
+Package: ramp.pf.infection 
 Title: Probabilistic Approaches to Malaria Parasite Infections
 Version: 0.1.0
 Authors@R: c(
@@ -9,7 +9,7 @@ Description: .
 License: GPL-3
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 LazyData: true
 Imports: 
   stats,
@@ -20,4 +20,4 @@ Suggests:
   viridis,
   viridisLite
 VignetteBuilder: knitr
-URL: https://dd-harp.github.io/pf.memory/
+URL: https://dd-harp.github.io/ramp.pf.infection/
diff --git a/man/zda.Rd b/man/zda.Rd
index ca78bdc..2aaf1a4 100644
--- a/man/zda.Rd
+++ b/man/zda.Rd
@@ -29,5 +29,5 @@ the density of parasite clones of age \eqn{\alpha} distributed among a cohort of
 age \eqn{a} is \deqn{z_\tau(\alpha, a) = e^{-r \alpha} h_\tau(a-\alpha)}
 }
 \seealso{
-\code{\link[=FoI]{FoI()}}
+\code{\link[pf.memory:FoI]{pf.memory::FoI()}}
 }
diff --git a/ramp.pf.infection.Rproj b/ramp.pf.infection.Rproj
index 270314b..f0d6187 100644
--- a/ramp.pf.infection.Rproj
+++ b/ramp.pf.infection.Rproj
@@ -18,4 +18,4 @@ StripTrailingWhitespace: Yes
 BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
-PackageRoxygenize: rd,collate,namespace
+PackageRoxygenize: rd,collate,namespace,vignette