#library(verification,lib.loc="/home/paulb/R/x86_64-redhat-linux-gnu-library/2.15");
source("/Volumes/shared_data/paulb/R/Functions/verify_mod.R") #I modified the function "verify" of the package to add the computation of ACC

#Parameters of the program you can change
########################################################################
XXX="multiModel" # WCT, MAC, AM, ABP or multiModel. Select the model to be tested
Directory_Data<-"/Volumes/shared_data/paulb/Data/Kenya/" #Directory where the parameters are defined
Directory_Communication<-"/Volumes/shared_data/paulb/Results/Communication/Verification/"
Directory_Output<-"/Volumes/shared_data/paulb/Results/Results/Skills/" #Directory where you want your output to be stocked. 
Begin<-366 #Time of begining of the experiment (days)
End<-9000 #Time of end of the experiment (days)
Gap<-90 
###################
# Lauch on scilab :
# exec('~/Scilab/infectedVerification/infected_XXX') and
# exec('~/Scilab/infectedVerification/Climatology.sci')
###################
pred<- as.matrix(read.csv(paste(Directory_Communication,XXX,"_",Begin,"_",Gap,"_",End,"_SimulatedCases.csv",sep=""),sep=",",header=FALSE))
obs<-as.matrix(read.csv(paste(Directory_Communication,XXX,"_",Begin,"_",Gap,"_",End,"_PositiveCases.csv",sep=""),sep=",",header=FALSE))
baseline <- as.matrix(read.csv(paste(Directory_Communication,XXX,"_",Begin,"_",Gap,"_",End,"_BaselineCases.csv",sep=""),sep=",",header=FALSE))

MAE<-0; ME<-0;MSE<-0;MSE_baseline<-0;MSE_persistence<-0;SS_baseline<-0; ACC<-0; bias<-0;

for (i in 1:(End-Begin+1)){
	A<- verify(obs[,i], pred[,i], baseline = baseline[,i],  frcst.type = "cont", obs.type = "cont")
	MAE<-MAE+A$MAE
	ME<-ME+A$ME
	MSE<-MSE+A$MSE
	MSE_baseline<-MSE_baseline+A$MSE.baseline
	MSE_persistence<-MSE_persistence+A$MSE.pers
	SS_baseline<-SS_baseline+A$SS.baseline
	ACC<-ACC+A$ACC
	bias<-bias+A$bias
}
MAE<-MAE/(End-Begin+1)
ME<-ME/(End-Begin+1)
MSE<-MSE/(End-Begin+1)
MSE_baseline<-MSE_baseline/(End-Begin+1)
MSE_persistence<-MSE_persistence/(End-Begin+1)
SS_baseline<-SS_baseline/(End-Begin+1)
ACC<-ACC/(End-Begin+1)
bias<-bias/(End-Begin+1)

Skills<-c(MAE,ME,MSE,MSE_baseline,MSE_persistence,SS_baseline,ACC,bias)
Skills<-as.data.frame(Skills)
rownames(Skills)<-c("MAE","ME","MSE","MSE baseline","MSE persistence","SS baseline","ACC","bias")

write.table(Skills,file=paste(Directory_Output,XXX,"_NEW_Continuous_Skill_Scores_",Begin,"_",Gap,"_",End,".csv",sep=""),quote=FALSE,sep=",")