From 4adbcad64ff018fdc06de1c49e2488ef268b842d Mon Sep 17 00:00:00 2001
From: Lydia Haile <l.haile@imperial.ac.uk>
Date: Mon, 29 Jan 2024 10:29:36 +0000
Subject: [PATCH] renaming profile to see if this resolves cluster issues

---
 R/interventions.R             |  14 +++++++-------
 data/{profile.rda => r21.rda} | Bin
 site.Rproj                    |  20 ++++++++++++++++++++
 3 files changed, 27 insertions(+), 7 deletions(-)
 rename data/{profile.rda => r21.rda} (100%)
 create mode 100644 site.Rproj

diff --git a/R/interventions.R b/R/interventions.R
index ccb4589..6a2b8a7 100644
--- a/R/interventions.R
+++ b/R/interventions.R
@@ -239,7 +239,7 @@ add_smc <- function(p, interventions){
 #'
 #' @return modified parameter list
 add_pev_epi <- function(p, interventions){
-  
+
 
   month <- 365 / 12
   timesteps <- 1 + (interventions$year - p$baseline_year) * 365
@@ -250,19 +250,19 @@ add_pev_epi <- function(p, interventions){
       coverage = ifelse(vaccine == 'R21', r21_coverage, rtss_coverage),
       booster_coverage = ifelse(vaccine == 'R21', r21_booster_coverage, rtss_coverage)
     )
-  
+
 
   if (unique(interventions$vaccine)== 'R21'){
 
-    initial_profile<- profile$r21_profile
-    booster_profile<- profile$r21_booster_profile
+    initial_profile<- r21$r21_profile
+    booster_profile<- r21$r21_booster_profile
 
   }else {
-    
+
     initial_profile<- malariasimulation::rtss_profile
     booster_profile<- malariasimulation::rtss_booster_profile
   }
-  
+
   # specify flat booster coverage scenarios (90% for routine and 100% for blue sky)
 
   p <- malariasimulation::set_pev_epi(
@@ -276,7 +276,7 @@ add_pev_epi <- function(p, interventions){
     booster_coverage = matrix(interventions$booster_coverage),
     booster_profile = list(booster_profile)
   )
-  
+
 
   return(p)
 }
diff --git a/data/profile.rda b/data/r21.rda
similarity index 100%
rename from data/profile.rda
rename to data/r21.rda
diff --git a/site.Rproj b/site.Rproj
new file mode 100644
index 0000000..497f8bf
--- /dev/null
+++ b/site.Rproj
@@ -0,0 +1,20 @@
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source