devel/movedToNMdata/NMtransInput.R

In philipdelff/pmxtricks: Every-day pharmacometrics helper functions

##' read input data and translate names according to the $INPUT section
##' 
##' @description Based on a nonmem run, this function finds the input data and
##'     reads it. But it reads it like the nonmem run by applying DROP arguments
##'     and alternative naming of columns in the nonmem run.
##' @param file a .lst or a .mod. No matter which you provide, the .mod is
##'     required and is the only one to be read.
##' @param useRDS If an rds file is found with the exact same name (except for
##'     .rds instead of say .csv) as the text file mentioned in the Nonmem
##'     control stream, should this be used instead? The default is yes, and
##'     NMwriteData will create this by default too.
##' @param dir.data The data directory can only be read from the control stream
##'     (.mod) and not from the output file (.lst). So if you only have the
##'     output file, use dir.data to tell in which directory to find the data file.
##' @param quiet Default is to inform a little, but TRUE is useful for
##'     non-interactive stuff.
##' @param debug start by running browser()?
##' @family Nonmem

NMtransInput <- function(file,useRDS=TRUE,dir.data,quiet=FALSE,debug=F){

    if(debug) browser()
    
### the lst file only contains the name of the data file, not the path to it. So we need to find the .mod instead.
    if(missing(dir.data)){
        if(grepl("\\.lst$",file)) file <- sub("\\.lst$","\\.mod",file)
    }
    
    lines <- NMgetSection(file,section="INPUT",keepName=F)

    line <- gsub(" +"," ",paste(lines,collapse=" "))
    line <- sub("^ ","",line)
    line <- sub(" $","",line)

    nms <- strsplit(line," ")[[1]]

    ## find all equals. drop or rename?
    ## drop <- grepl("= *DROP",nms)
### this is if they are not intended to be kept.
    ## nms <- sub(".*=(.*)","\\1",nms)
    ## nms[nms=="DROP"] <- paste0("DROP",1:sum(nms=="DROP"))
### this is to keep even dropped columns
    nms <- sub("(.*) *= *DROP","\\1",nms)
    nms <- sub(".*=(.*)","\\1",nms)


    ## get input data file name. Nonmem manual says:
###  The first character string appearing after $DATA is the name of the file
### containing the data. Since it is to be used in a FORTRAN OPEN statement,
### this name may not include embedded commas, semi-colons, parentheses, or
### spaces.
    lines.data <- NMgetSection(file,section="DATA",keepName=F,keepComments=F,keepEmpty=F)

    ## pick $DATA and the next string
    lines.data2 <- paste(lines.data,collapse=" ")
    path.data.input <- sub(" *([^ ]+) +.*","\\1",lines.data2)

    if(missing(dir.data)){
        pathIsAbs <- function(path) grepl("^/",path)
        if(pathIsAbs(path.data.input)){
### assuming we are on windows
            stop("absolute paths not supported")
        } else {
            path.data.input <- file.path(dirname(file),path.data.input)
        }
    } else {
        path.data.input <- filePathSimple(dir.data,basename(path.data.input))
    }

    path.data.input.rds <- sub("^(.+)\\..+$","\\1.rds",path.data.input)
    if(useRDS && file.exists(path.data.input.rds)){
        if(!quiet) message("found rds input file. This will be used.")
        path.data.input <- path.data.input.rds
        data.input <- readRDS(path.data.input)
    } else {
        if(file.exists(path.data.input)){
            if(!quiet) message("Found input data file. Reading with NMreadCsv")
            data.input <- NMreadCsv(path.data.input)
        } else {
            stop(paste("Input data file not found. Was expecting to find",path.data.input))
            ##        use.input <- FALSE
        }
    }
    

    cnames.input <- colnames(data.input)
    cnames.input[1:length(nms)] <- nms
    colnames(data.input) <- cnames.input
    data.input

}