New version

.gitignore

@@ -2,4 +2,3 @@
 .Rhistory
 .RData
 .Ruserdata
-*.Rproj

main.R

 #header
 
-library(here)
 
-here("output")
+rm(list=ls(all=T))
+set_wd <- function() {
+  
+  
+  if(!require(rstudioapi)){
+    install.packages("rstudioapi")
+  }
+  library(rstudioapi)
+  
+  current_path <- getActiveProject()
+  setwd(paste(current_path))
+  print( getwd() )
+  }
+
+wd<-set_wd()
 
 dir.create("Output",showWarnings = F)
 dir.create("Figures",showWarnings = F)
 
 source(file.path("Scripts","dynamic.R"))
+model(10,200,500,16)
+
+
+
+human_prev<-list()
+prev_diff<-list()
+log_diff<-list()
+prev<-list()
+
+
+for (i in 1:16){
+  
+  human_prev[[i]]<-read.table(paste(wd,"/","Output","/","output_scenario",i,"/","data1.txt",sep=""),header = TRUE)
+  
+  prev_diff[[i]]<-(human_prev[[i]]$H[[length(human_prev[[i]]$H)]]-
+                     human_prev[[1]]$H[[length(human_prev[[1]]$H)]])
+  
+  log_diff[[i]]<-log(human_prev[[i]]$H[[length(human_prev[[i]]$H)]]/
+                       human_prev[[1]]$H[[length(human_prev[[1]]$H)]])
+  
+  prev[[i]]<-human_prev[[i]]$H[[length(human_prev[[i]]$H)]]
+  
+  
+}
+
+plot(1:200,human_prev[[1]]$H,type="l",col=1,lwd=2,ylab="ESBL prevalence in the open community",xlab="Time in weeks")
+lines(1:200,human_prev[[15]]$H,type="l",col=15)
+lines(1:200,human_prev[[9]]$H,type="l",col=9)
+lines(1:200,human_prev[[14]]$H,type="l",col=14)
+lines(1:200,human_prev[[12]]$H,type="l",col=12)
+lines(1:200,human_prev[[4]]$H,type="l",col=4)
+lines(1:200,human_prev[[5]]$H,type="l",col=5)
+lines(1:200,human_prev[[2]]$H,type="l",col=2)
+
+nome2<-c("Baseline","No_far&No_food", "Cross=0.15",  "No_food_consum",  "High_slaugh_contaminaiton","Short_OC" ,"Fade_ch=0.5"   ,"Long_OC"  )
+
 
-rm(list=ls())
+legend(130, 0.05, legend=nome2,
+       col=c(1,15,9,14,12,4,5,2), lty=1,lwd=c(2,1,1,1,1,1,1,1), cex=0.8, text.font=4)