updated main and sensitivity plot by Chiabrando

Main.R

@@ -32,7 +32,7 @@ end_time <- Sys.time()-start_time
 ##############################
 source("./Rfunction/SensitivityPlot.R")
 
-pl = SensitivityPlot(folder = "SIR_sensitivity/")
+pl = SensitivityPlot(folder = "SIR_sensitivity/", scd_folder = "SIR_analysis/")
 
 pl$TrajS
 pl$TrajI
@@ -85,9 +85,9 @@ source("Rfunction/ModelAnalysisPlot.R")
 
 AnalysisPlot = ModelAnalysisPlot(Stoch = F ,print = F,
                                  trace_path = "./SIR_analysis/SIR-analysis-1.trace")
-AnalysisPlot$plI
+AnalysisPlot$plAll
 
-model_analysis(solver_fname = "Net/SIR.solver",
+model.analysis(solver_fname = "Net/SIR.solver",
                parameters_fname = "Input/Functions_list_ModelAnalysis.csv",
                solver_type = "SSA",
                n_run = 500,
@@ -98,6 +98,6 @@ model_analysis(solver_fname = "Net/SIR.solver",
 
 AnalysisPlot = ModelAnalysisPlot(Stoch = T ,print = F,
                                  trace_path = "./SIR_analysis/SIR-analysis-1.trace")
-AnalysisPlot$plI
-AnalysisPlot$HistI
-plS
+
+AnalysisPlot$plAll
+AnalysisPlot$plAllMean 

Rfunction/FunctionSensitivity.R

@@ -25,4 +25,4 @@ mse<-function(reference, output)
   diff.Infect <- 1/length(times_ref)*sum(( Infect - I_ref )^2 )
 
   return(diff.Infect)
-}
+}

Rfunction/SensitivityPlot.R

@@ -1,13 +1,14 @@
 library(ggplot2)
 
-SensitivityPlot <-function(rank=T,folder){
-  load(paste0(folder,"SIR-sensitivity.RData"))
+SensitivityPlot <-function(rank=T,folder, scd_folder){
+  #Changed the folder in which is contained the .RData file
+  load(paste0(scd_folder,"SIR-analysis.RData"))  
   # Then, we read all the trajectories generated saving them in a list called
   # ListTraces. List that will be rewritten as a data frame in order to use ggplot.
   # ConfigID represents the initial condition associated to each trajectory,
   # which was generated by using the function implemented in the file Functions.R .
 
-  listFile<-list.files(folder,
+  listFile<-list.files(scd_folder,
                        pattern = ".trace")
 
   configID<-t(sapply(1:length(listFile),
@@ -32,11 +33,11 @@ SensitivityPlot <-function(rank=T,folder){
   ListTraces<-lapply(id.traces,
                      function(x){
                        trace.tmp=read.csv(paste0(
-                        folder,"/SIR-sensitivity-",
+                         scd_folder,"SIR-analysis-",
                          x,
                          ".trace"), sep = "")
                        trace.tmp=data.frame(trace.tmp,ID= x,
-                                            rank = rank[which(rank[,2]==paste0("SIR-sensitivity-",
+                                            rank = rank[which(rank[,2]==paste0("SIR-analysis-",
                                                                                x,
                                                                                ".trace")),1])
                        return(trace.tmp)
@@ -46,13 +47,14 @@ SensitivityPlot <-function(rank=T,folder){
                 function(x){
                   recovery<-config[[4]][[x]][[3]]
                   infection<-config[[5]][[x]][[3]]
-                  rnk.tmp=data.frame(ID=x,distance = rank[which(rank[,2]==paste0("SIR-sensitivity-",
+                  rnk.tmp=data.frame(ID=x,distance = rank[which(rank[,2]==paste0("SIR-analysis-",
                                                                                  x,
                                                                                  ".trace")),1],
                                      rec_rate=recovery, inf_rate=infection)
                   return(rnk.tmp)
                 })
 
+
   rank2 <- do.call("rbind", rank2)
   traces <- do.call("rbind", ListTraces)