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dostats<-function(){
#' Create QC statistical summary
#' @description This function creates two report files (Mystats.txt and CasesSummary.txt) with a statistical summary
#' of QCs performed over the whole data set
#' @return files with QC summary
#' @export
#Get value of 'Global variable' 'homefolder'
homefolder <- getOption("homefolder")
myfolder<-paste0(homefolder,'QCSummary/')
mycases<-paste0(myfolder,'CasesSummary.txt');if(file.exists(mycases)){file.remove(mycases)}
mystats<-paste0(myfolder,'Mystats.txt');if(file.exists(mystats)){file.remove(mystats)}
nyu<-list.files(myfolder)
nyunames<-substring(nyu,8,21)
n<-length(nyu)
for(i in 1:n){
ja<-utils::read.table(paste0(myfolder,nyu[i]))
emu<-data.frame(variable=substring(nyunames[i],1,2),STAID=substring(nyunames[i],9,14),ITEM=ja[,1],CASES=ja[,2])
divide<-which(emu$ITEM=='QC_Code')
if(divide!=1){
utils::write.table(emu[1:(divide-1),],mycases,sep='\t',append=TRUE,row.names=FALSE,quote=FALSE,col.names=FALSE)
}
utils::write.table(emu[(divide+1):nrow(emu),],mystats,sep='\t',append=TRUE,row.names=FALSE,quote=FALSE,col.names=FALSE)
}
nyu<-utils::read.table(mystats)
nyu<-stats::aggregate(nyu[,4],by=list(nyu[,1],nyu[,3]),FUN=sum);names(nyu)<-c('Variable','Code','Freq')
nyutotal<-stats::aggregate(nyu[,3],list(nyu[,1]),FUN=sum);names(nyutotal)<-c('Variable','Total')
nyu<-merge(nyu,nyutotal)
nyu<-nyu[order(nyu[,1],nyu[,2]),]
nyu$Percentage<-round(nyu$Freq/nyu$Total*100,2)
utils::write.table(nyu,mystats,sep='\t',row.names=FALSE,quote=FALSE,col.names=FALSE)
nyi<-utils::read.table(mycases)
nyi<-stats::aggregate(nyi[,4],by=list(nyi[,1],nyi[,3]),FUN=sum);names(nyi)<-c('Variable','Test','Freq')
nyitotal<-stats::aggregate(nyi[,3],list(nyi[,1]),FUN=sum);names(nyitotal)<-c('Variable','Total')
nyu<-merge(nyi,nyitotal)
nyi[order(nyi[,1],nyi[,2]),]
utils::write.table(nyi,mycases,sep='\t',row.names=FALSE,quote=FALSE,col.names=FALSE)
}
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