## for the analysis with uniform priors
## The results are saved in the folder of *R

gen.script<-function(DATA, N){
folder<-paste(DATA,'R', sep='')
folder1<-paste(DATA, sep='')
NSS<-paste('N',N,sep='')

## create a folder for a given sample size
mkNSS<-paste('mkdir ../',folder,'/',NSS, sep='')
system(mkNSS)

## replace "NS" in model.txt by the sample size
repNS<-paste("sed 's/NS/",N,"/g' model.txt > tempmodel.txt",sep='')
system(repNS)

for (i in 1:10){
	## create a folder
	mkfolder<-paste('mkdir ../',folder,'/',NSS,'/',i, sep='')
	system(mkfolder)
	
	## copy files to the folder
	## copy model, initial, and script files
	cpmodel<-paste('cp tempmodel.txt ../',folder,'/',NSS,'/', i, '/model.txt', sep='')
	system(cpmodel)
	
	cpini<-paste('cp inits.txt ../',folder,'/',NSS,'/', i, '/inits.txt', sep='')
	system(cpini)
	
	cpscript<-paste('cp script.txt ../',folder,'/',NSS,'/', i, '/script.txt', sep='')
	system(cpscript)
	
	## replace analysis situation
	repfolder<-paste("sed 's/folder1/",DATA,"/g' runsim.sas > temp00.sas", sep='')
	system(repfolder)
	repfolder<-paste("sed 's/folder/",folder,"/g' temp00.sas > temp01.sas", sep='')
	system(repfolder)
	repdata<-paste("sed 's/DATA/",DATA,"/g' temp01.sas > temp.sas", sep='')
	system(repdata)
	
	## replace iteration numbers
	start<-1001+(i-1)*100
	end<-1000+i*100
	
	repstart<-paste("sed 's/1001/",start,"/g' temp.sas > temp1.sas", sep='')
	
	system(repstart)
	
	repend<-paste("sed 's/1100/",end,"/g' temp1.sas > temp2.sas",sep='')
		
	system(repend)
	
	repcodans<-paste("sed 's/codans/",N,"/g' temp2.sas > temp3.sas",sep='')
	system(repcodans)
	
	## move the sas file to the folder
	cpsas<-paste('cp temp3.sas ../',folder,'/',NSS,'/',i,'/runsim.sas', sep='')
	system(cpsas)
	
	system('rm -f temp*.sas')
	
	## copy submit file
	cpqsub<-paste('cp qsub.sh ../',folder,'/',NSS,'/',i,'/qsub-',i,'.sh',sep='')
	system(cpqsub)
	}
	
	system('rm -f temp*')
## generate submission script
subfile<-paste('../',folder,'/',NSS,'/submitall.sh',sep='')
cat('',file=subfile)

for (i in 1:10){
	cmmd<-paste('cd /pscratch/zzhang4/Private/student-grm/Analysis/',folder, '/', NSS ,'/', i,'/\n qsub qsub* \n',sep='')
	cat(cmmd, file=subfile,  append=T)
	}
system(paste('chmod 777 ', subfile, sep=''))
}

DATA<-'Tdata'
N<-300

gen.script<-function(DATA, N){
folder<-paste(DATA,sep='')
NSS<-paste('N',N,sep='')

## create a folder for a given sample size
mkNSS<-paste('mkdir ../',folder,'/',NSS, sep='')
system(mkNSS)

## replace "NS" in model.txt by the sample size
repNS<-paste("sed 's/NS/",N,"/g' model.txt > tempmodel.txt",sep='')
system(repNS)

for (i in 1:10){
	## create a folder
	mkfolder<-paste('mkdir ../',folder,'/',NSS,'/',i, sep='')
	system(mkfolder)
	
	## copy files to the folder
	## copy model, initial, and script files
	cpmodel<-paste('cp tempmodel.txt ../',folder,'/',NSS,'/', i, '/model.txt', sep='')
	system(cpmodel)
	
	cpini<-paste('cp inits.txt ../',folder,'/',NSS,'/', i, '/inits.txt', sep='')
	system(cpini)
	
	cpscript<-paste('cp script.txt ../',folder,'/',NSS,'/', i, '/script.txt', sep='')
	system(cpscript)
	
	## replace analysis situation
	repfolder<-paste("sed 's/folder/",folder,"/g' runsim.sas > temp00.sas", sep='')
	system(repfolder)
	repdata<-paste("sed 's/DATA/",DATA,"/g' temp00.sas > temp.sas", sep='')
	system(repdata)
	
	## replace iteration numbers
	start<-1001+(i-1)*100
	end<-1000+i*100
	
	repstart<-paste("sed 's/1001/",start,"/g' temp.sas > temp1.sas", sep='')
	
	system(repstart)
	
	repend<-paste("sed 's/1100/",end,"/g' temp1.sas > temp2.sas",sep='')
		
	system(repend)
	
	repcodans<-paste("sed 's/codans/",N,"/g' temp2.sas > temp3.sas",sep='')
	system(repcodans)
	
	## move the sas file to the folder
	cpsas<-paste('cp temp3.sas ../',folder,'/',NSS,'/',i,'/runsim.sas', sep='')
	system(cpsas)
	
	system('rm -f temp*.sas')
	
	## copy submit file
	cpqsub<-paste('cp qsub.sh ../',folder,'/',NSS,'/',i,'/qsub-',i,'.sh',sep='')
	system(cpqsub)
	}
	
	system('rm -f temp*')
## generate submission script
subfile<-paste('../',folder,'/',NSS,'/submitall.sh',sep='')
cat('',file=subfile)

for (i in 1:10){
	cmmd<-paste('cd /pscratch/zzhang4/Private/student-grm/Analysis/',folder, '/', NSS ,'/', i,'/\n qsub qsub* \n',sep='')
	cat(cmmd, file=subfile,  append=T)
	}
system(paste('chmod 777 ', subfile, sep=''))
}