## THIS FILE IS RESTRICTED TO READING INPUT FILES, ALGORITHM IS IN ANOTHER FILE
#this function gets the file name from the user
#' This function reads user file
#'
#' @param x A file name
#' @return A dataframe with user selected fields in a tab-delimited text file.
#' @export
#' @examples
#' my.df<-cc_read_file("filename.txt")
cc_read_file<-function(x) {
read_file<-x
cc_read_file_name(read_file)
}
# this function reads the files
cc_read_file_name<-function(y){
#read file data into R
f_read_with_Header<-read.csv(y, header=F, sep="\t")
f_read_without_Header<-read.csv(y, header=T, sep="\t", skip = 1)
f_inclusionAs<-t(f_read_with_Header[1,])
f_columnsAs<-t(f_read_with_Header[2,])
ignored<-table(f_inclusionAs)
print(paste0("Total variables read: ", length(f_inclusionAs), " ignored: ", ignored[["x"]][1]))
#cc_dataset<<-data.frame(1:length(f_read_without_Header[[1]]))
nr<-seq(1,length(f_read_without_Header[[1]]))
cc_dataset<-data.frame(nr)
cc_dataset_names<-vector()
cc_list<-list()
for (i in 1:22){
#print(i)
data_type_by_user<-f_inclusionAs[i]
#print(data_type_by_user)
cc_dataset_names[1] <-"Nr"
switch(data_type_by_user,
"n"={
#create nominal variables
aa<-f_columnsAs[i]
#print(paste0(" ",aa))
cc_list[[i]]<-as.factor(f_read_without_Header[[aa]])
cc_dataset<-cbind(cc_dataset,cc_list[[i]])
cc_dataset_names[i+1]<-aa
},
"o"={
#create ordered variables
aa<-f_columnsAs[i]
#print(paste0(" ",aa))
cc_list[[i]]<-as.ordered(f_read_without_Header[[aa]])
# cc_dataset<<-data.frame(as.ordered(f_read_without_Header[[aa]]))
cc_dataset<-cbind(cc_dataset,cc_list[[i]])
cc_dataset_names[i+1]<-aa
},
"c"={
#create continuous variables
aa<-f_columnsAs[i]
#print(paste0(" ",aa))
cc_list[[i]]<-as.numeric(f_read_without_Header[[aa]])
# cc_dataset<<-data.frame(as.ordered(f_read_without_Header[[aa]]))
cc_dataset<-cbind(cc_dataset,cc_list[[i]])
cc_dataset_names[i+1]<-aa
#cc_dataset_names<-c(cc_dataset_names,aa)
},
"x"={
#list deleted variables
aa<-f_columnsAs[i]
#print(paste0(" to be deleted ",aa))
#cc_dataset<<-data.frame(as.factor(f_read_without_Header[[aa]]))
},
{
#print("default")
}
)
}
for (i in 1:19){
# print(paste0(i,"--", length(cc_list[[i]])))
}
#cc_dataset<<-cc_dataset
cc_prepare_data_frame(cc_dataset_names,cc_dataset)
}
cc_prepare_data_frame<-function(x,y){
#print("hello")
cc_names<-na.omit(x)
cc_names<-c( cc_names)
colnames(y)<-cc_names
return(y)
}
#mydata<-cc_define_file("aidwork3.txt") # release this line when testing
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