R/NMreadCsv.R

In NMdata: Preparation, Checking and Post-Processing Data for PK/PD Modeling

##' Read input data formatted for Nonmem
##'
##' This function is especially useful if the csv file was written
##' using NMwriteData.
##' 
##' @param file The file to read. Must be pure text.
##' @param args.fread List of arguments passed to fread. Notice that
##'     except for "file", you need to supply all arguments to fread
##'     if you use this argument. Default values can be configured
##'     using NMdataConf.
##' @param as.fun The default is to return data as a data.frame. Pass
##'     a function (say tibble::as_tibble) in as.fun to convert to
##'     something else. If data.tables are wanted, use
##'     as.fun="data.table". The default can be configured using
##'     NMdataConf.
##' @param format Format of file to read. Can be of length>1 in which
##'     case the first format found will be used (i.e. format is a
##'     prioritized vector). If not one of "rds" or "fst", it is
##'     assumed to be a delimited text file. Default is to determine
##'     this from the file name extension. Notice, if a delimited
##'     format is used, the extension can very well be different from
##'     "csv" (say file name is
##'     "input.tab")". This will work for any delimited format supported by fread.
##' @param args.fst Optional arguments to pass to \code{read_fst} if \code{format="fst"} is used.
##' @details This is almost just a shortcut to fread so you don't have to remember how to read the data that was exported for Nonmem. The only added feature is that meta data as written by NMwriteData is read and attached as NMdata metadata before data is returned.
##' @return A data set of class as defined by as.fun.
##' @importFrom data.table fread
##' @importFrom fst read_fst
##' @family DataRead
##' @seealso NMwriteData
##' @export

NMreadCsv <- function(file,args.fread,as.fun=NULL,format,args.fst){

#### Section start: Dummy variables, only not to get NOTE's in pacakge checks ####

    ext.found <- NULL
    file.found <- NULL
    ext.interpret <- NULL
    priority <- NULL

### Section end: Dummy variables, only not to get NOTE's in pacakge checks



    
    if(missing(format)) format <- NULL
### If format is not provided
    if(is.null(format)) format <- fnExtension(file)

    if( !is.character(format) ){
        stop("format must be character strings.")
    }
    as.fun <- NMdataDecideOption("as.fun",as.fun)

    
    
### we take the first file available. format is file name
### extension. If not fst or rds, it is expected to be a delimited
### text file.

    fn.root <- basename(file)
    fn.root <- fnExtension(fn.root,"")
    dt.files <- data.table(
        file.found=list.files(dirname(file),pattern=paste0(fn.root,".*"))
    ) [ ,ext.found:=fnExtension(file.found)]
    dt.files[,ext.interpret:=ext.found]
    dt.files[ext.interpret %in% c("rds","fst"),ext.interpret:="text"]

    format <- unique(format)
    format[!format%in%c("rds","fst")] <- "text"
    dt.files[,priority:=match(ext.interpret,format)]
    setorder(dt.files,priority)
    file.read <- dt.files[1,file.found]
    format.read <- dt.files[1,ext.interpret]
    
    if(FALSE){
### we take the first file available. format is file name
### extension. If not fst or rds, it is expected to be a delimited
### text file.
        format <- unique(format)
        exts <- format
        files <- fnExtension(file,exts)
        exists <- file.exists(files)
        exts <- exts[exists][1]
        format[!format%in%c("rds","fst")] <- "text"
        format <- format[exists][1]
        file <- files[exists][1]
    }


    dt <- switch(format,
                 text={
                     if(missing(args.fread)) args.fread <- NULL
                     args.fread <- NMdataDecideOption("args.fread",args.fread)
                     do.call(fread,c(list(file=file),args.fread))
                 },
                 rds={
                     as.data.table(readRDS(file=file))
                 },
                 fst={
                     ## if (!requireNamespace("fst", quietly = TRUE)) {
                     ##     stop("fst package could not be loaded. Either install fst or drop fst from formats.")
                     ## }
                     if(missing(args.fst)){
                         args.fst <- list(as.data.table=TRUE)
                     }
                     do.call(read_fst,c(list(path=file),args.fst))
                 }
                 )
    
    dt <- as.fun(dt)
    file.csv.meta <- fnAppend(fnExtension(file,ext="txt"),"meta")
    
    if(file.exists(file.csv.meta)){
        
        meta <- fread(file.csv.meta,sep=",",header=TRUE)
        meta.list <- setNames(as.list(meta$value),meta$parameter)
        writeNMinfo(dt,list(dataCreate=meta.list))
    }
    
    return(dt)
}