finalPlotFuncs.R

In aaronm70/batMods: fitsSEIR

library("miscTools")
library("ggpubr")
library("binom")
library("reshape2")
library("loo")
library("ggplot2")
library(miscTools)
library(reshape2)
library(cowplot)

##File locations##
if(Sys.info()['sysname']=="Darwin"){
  fileLoc="/Users/alm204/OneDrive/emma aaron/data/Boonah/hendra-virus-test-results-flying-foxes.csv"
  fileLocUrine="/Users/alm204/OneDrive/emma aaron/data/Boonah/henrda-underRoostUrine.csv"
  prmFileLoc="/Users/alm204/Documents/ModelSetups.csv"
}else{
  fileLoc="C:\\Users\\aaron\\Documents\\batMods\\batMods\\data\\hendra-virus-test-results-flying-foxes.csv"
  fileLocUrine="C:\\Users\\aaron\\Documents\\batMods\\batMods\\data\\henrda-underRoostUrine.csv"
  prmFileLoc="C:\\Users\\aaron\\Documents\\batMods\\batMods\\data\\ModelSetups.csv"

}
prmLst<-prmLstFunc(prmFileLoc)

#location of pMCMC results
resultsFile<-"C:\\Users\\aaron\\Documents\\batMods\\chain2\\"
prmFile<-read.csv("C:\\Users\\aaron\\Documents\\batMods\\batMods\\data\\ModelSetups.csv")#read in model setups
saveLoc<-"C:\\Users\\aaron\\Documents\\batMods\\figures\\" #location to save figures
burn<-100000 #any additional burning
modNums<-c(2,4,8)#model numbers to plot (see model setups table, prmFile)
thin=10 #any thinning, if using rds files, set to 0 as these are already thinned

#Plot Rt values
plotAllRt(resultsFile= resultsFile,Rt=T,saveLoc=saveLoc,burn=burn,modNums=modNums,prmFile=prmFile,thin)
#Plot fitted simulation
plotAllRt(resultsFile= resultsFile,Rt=F,saveLoc=saveLoc,burn=burn,modNums=modNums,prmFile=prmFile,thin)
plotEnvForc(resultsFile= resultsFile,burn=burn,modNums=modNums,saveLoc=saveLoc,prmFile=prmFile,thin)
#run function to obtain looic vals, R0's, contributing bats etc
parmVals<-looicFunc(resultsFile=resultsFile,prmFile=prmFile,burn=burn,samples=0,prmLst=prmLst,thin)

#parmVals<-readRDS("/Users/alm204/Documents/looDat.rds")
looicVal<-parmVals[[1]]
zetaS<-parmVals[[5]]
zetaP<-parmVals[[4]]
contBats<-parmVals[[3]]

fNm<-"C:\\Users\\aaron\\Documents\\batMods\\figures\\"

p1<-plotLooic(fileNme=paste0(fNm,"looicVals.png"),loicVals=looicVal,type="loo")
p2<-plotLooic(fileNme=paste0(fNm,"contBatsX.png"),loicVals=contBats,type="batCont")
p3<-plotLooic(fileNme=paste0(fNm,"zetaPlotsS.png"),loicVals=zetaS,type="zetaS")
p4<-plotLooic(fileNme=paste0(fNm,"zetaPlotsP.png"),loicVals=zetaP,type="zetaP")
p5<-plotLooic(fileNme=paste0(fNm,"zetaPlotsU.png"),loicVals=zetaU,type="zetaU")
p6<-plotLooic(fileNme=paste0(fNm,"r0Val.png"),loicVals=r0Val,type="R0")

gx<-ggarrange(p1,p2,p3,p4,p5,p6,common.legend = T)

ggsave(
  paste0(fNm,"loZetVals.png"),
  plot = gx,
  height = 25,
  width = 40,
  units = "cm"
)