pat<-c('mcar', 'mar','mnar','mcar0','mcar1','mar0','mar1','mnar0','mnar1')
#pat<-'test'
#rate<-c(.1,.2,.4)

for (mis in pat){
 if (substr(mis,1,3)=="mar"){
      rate<-c(1.5,4,9)
    }else{
      rate<-c(.1,.2,.4)
    }
 if (mis == 'mcar' | mis=='mar'){    
  for (i in 1:3){
     filename <- paste('/afs/crc.nd.edu/user/z/zzhang4/Private/bootmedem/mbr/MI/',mis,'/',i,'/runsim.R', sep='')
     cat('pat<-"',mis,'"\n', file=filename, sep='')
     cat('rate<-',rate[i],'\n', file=filename, append=T)
     cat("for (r in rate){",'\n', file=filename, append=T)
     cat("  resfile <- paste(pat ,'-',r,'.txt', sep='')",'\n', file=filename, append=T)
     cat("  for (i in 1:1000){",'\n', file=filename, append=T)
     cat("    datafile <-paste('cp ~/Private/bootmedem/mbr/data/',pat,'/','data-', i,'-',r,'.txt data.txt',sep='')",'\n', file=filename, 
append=T)
     cat("    system(datafile)",'\n', file=filename, append=T)
     cat("    system('sas mi.sas')",'\n', file=filename, append=T)
     cat("    if (file.exists('bcci.txt')){",'\n', file=filename, append=T)
     cat("      temp<-scan('bcci.txt')",'\n', file=filename, append=T)
     cat("      cat(c(i, temp), file=resfile, append=T)",'\n', file=filename, append=T)
     cat('      cat("\\n", file=resfile,append=T)','\n', file=filename, append=T)
     cat("      system('rm -f data.txt bcci.txt mi.log mi.lst')}}}",'\n', file=filename, append=T)
     
     ## copy sas program to the folder 
     cpsas <- paste('cp mi.sas /afs/crc.nd.edu/user/z/zzhang4/Private/bootmedem/mbr/MI/',mis,'/',i,'/mi.sas', sep='')
     system(cpsas)
     
          ## generate submission scripts
     cpsub<-paste('cp qsub.sub /afs/crc.nd.edu/user/z/zzhang4/Private/bootmedem/mbr/MI/',mis,'/',i,'/',mis,'-',i,'.sub', sep='')
     system(cpsub) 
     }
   
  }else{
    for (i in 1:3){
     filename = paste('/afs/crc.nd.edu/user/z/zzhang4/Private/bootmedem/mbr/MI/',mis,'/',i,'/runsim.R', sep='')
     cat('pat<-"',mis,'"\n', file=filename, sep='')
     cat('rate<-',rate[i],'\n', file=filename, append=T)
     cat("for (r in rate){",'\n', file=filename, append=T)
     cat("  resfile <- paste(pat ,'-',r,'.txt', sep='')",'\n', file=filename, append=T)
     cat("  for (i in 1:1000){",'\n', file=filename, append=T)
     cat("    datafile <-paste('cp ~/Private/bootmedem/mbr/data/',pat,'/','data-', i,'-',r,'.txt data.txt',sep='')",'\n', file=filename, 
append=T)
     cat("    system(datafile)",'\n', file=filename, append=T)
     cat("    system('sas mi.sas')",'\n', file=filename, append=T)
     cat("    if (file.exists('bcci.txt')){",'\n', file=filename, append=T)
     cat("      temp<-scan('bcci.txt')",'\n', file=filename, append=T)
     cat("      cat(c(i, temp), file=resfile, append=T)",'\n', file=filename, append=T)
     cat('      cat("\\n", file=resfile,append=T)','\n', file=filename, append=T)
     cat("      system('rm -f data.txt bcci.txt mi.log mi.lst')}}}",'\n', file=filename, append=T)
     ## copy sas program to the folder 
     cpsas <- paste('cp mi.aux.sas /afs/crc.nd.edu/user/z/zzhang4/Private/bootmedem/mbr/MI/',mis,'/',i,'/mi.sas', sep='')
     system(cpsas)
          ## generate submission scripts
     cpsub<-paste('cp qsub.sub /afs/crc.nd.edu/user/z/zzhang4/Private/bootmedem/mbr/MI/',mis,'/',i,'/',mis,'-',i,'.sub', sep='')
     system(cpsub) 
     }
   }            
  }


filename<-'allsub.sub'
  for (mis in pat){
for (i in 1:3){

    folder<-paste('cd /afs/crc.nd.edu/user/z/zzhang4/Private/bootmedem/mbr/MI/',mis,'/',i,'/', sep='')
    cat(folder, '\n', file=filename, append=T)
    cat('qsub *.sub', '\n', file=filename, append=T)  
  }  
}

filename<-'rm.sub'
pat<-c('mcar', 'mar','mnar','mcar0','mcar1','mar0','mar1','mnar0','mnar1')

for (i in 1:3){
  for (mis in pat){
    folder<-paste('cd /afs/crc.nd.edu/user/z/zzhang4/Private/bootmedem/mbr/MI/',mis,'/',i,'/', sep='')
    cat(folder, '\n', file=filename, append=T)
    cat('rm -f *.*', '\n', file=filename, append=T)  
  }  
}