R/ReadSetting.R

In KamilSJaron/ConjunctionStats: The parser of simulations of hybrid zones performed by simulator Conjunction (http://github.com/KamilSJaron/Conjunction)

#' @title ReadSetting
#'
#' @description
#' \code{ReadSetting} parses the settings file used for a simulation run using Conjunction software and converts it to a data.frame object.
#'
#' @param Inputfile A string of characters indicating the settings file to be parsed. If no file is specified via InputFile, \code{ReadSetting} reads the file \code{settings.txt} in the current working directory.
#'
#' @return A data.frame object, featuring information about the settings used in the simulation run in a R-friendly format.
#'
#' @author Kamil Jaron \email{kamiljaron at gmail.com}
#'
#' @examples{
#'    myReadSetting = ReadSetting(InputFile='./mysetting.txt')
#' }
#'
#' @export

ReadSetting <- function(InputFile = './setting.txt'){
    gradientTable <- data.frame(run = 1)
    # 'C' = numeric(0),'L' = numeric(0),'r' = numeric(0),'s' = numeric(0),'b' = numeric(0)
    summaryFile <- readLines(InputFile)
    generations <- as.numeric(strsplit(summaryFile[grepl('NUMBERofGENERATIONS',summaryFile)], "= | #")[[1]][2])
    if(length(summaryFile[grepl('DELAY',summaryFile)]) == 1){
        delay = as.numeric(strsplit(summaryFile[grepl('DELAY',summaryFile)], "= | #")[[1]][2])
    } else {
        delay = 0
    }
    replicates <- 1

    for(l in summaryFile){
        l <- unlist(strsplit(l,split='#'))[1] # cut off comments
        l <- unlist(strsplit(l,split='=')) # split parameter name and value
        # RECOMBINATIONrate was previous name for LAMBDA; it has been changed to avoid confusion with recombintion rate between pair of loci
        if(grepl('RECOMBINATIONrate',l[1]) | grepl('LAMBDA',l[1])){
            if(grepl("\\[",l[2])){
                gradientTable <- merge(gradientTable,data.frame('r' = getVectorSplit(l)))
            } else {
                gradientTable <- merge(data.frame('r' = as.numeric(l[2])),gradientTable)
            }
        }
        if(grepl('SELECTION',l[1])){
            if(grepl("\\[",l[2])){
                gradientTable <- merge(gradientTable,data.frame('s' = getVectorSplit(l)))
            } else {
                gradientTable <- merge(data.frame('s' = as.numeric(l[2])),gradientTable)
            }
        }
        if(grepl('CHROM',l[1])){
            if(grepl("\\[",l[2])){
                gradientTable <- merge(gradientTable,data.frame('C' = getVectorSplit(l)))
            } else {
                gradientTable <- merge(data.frame('C' = as.numeric(l[2])),gradientTable)
            }
        }
        if(grepl('LOCI',l[1])){
            if(grepl("\\[",l[2])){
                gradientTable <- merge(gradientTable,data.frame('L' = getVectorSplit(l)))
            } else {
                gradientTable <- merge(data.frame('L' = as.numeric(l[2])),gradientTable)
            }
        }
        if(grepl('BETA',l[1])){
            if(grepl("\\[",l[2])){
                gradientTable <- merge(gradientTable,data.frame('b' = getVectorSplit(l)))
            } else {
                gradientTable <- merge(data.frame('b' = as.numeric(l[2])),gradientTable)
            }
        }
        if(grepl('NUMBERofSAVES',l[1])){
          saves <- as.numeric(l[2])
            if(saves > 1){
              gradientTable <- merge(data.frame('G' = delay + floor(((generations - delay) / saves) * 1:saves)), gradientTable)
            } else {
              gradientTable <- merge(data.frame('G' = generations), gradientTable)
            }
        }
        if(grepl('DEMEsize',l[1])){
            if(grepl("\\[",l[2])){
                gradientTable <- merge(gradientTable,data.frame('D' = getVectorSplit(l)))
            } else {
                gradientTable <- merge(data.frame('D' = as.numeric(l[2])),gradientTable)
            }
        }
        if(grepl('SELECTEDloci',l[1])){
            if(grepl("\\[",l[2])){
                gradientTable <- merge(gradientTable,data.frame('SL' = getVectorSplit(l)))
            } else {
                gradientTable <- merge(data.frame('SL' = as.numeric(l[2])),gradientTable)
            }
        }
        if(grepl('REPLICATES',l[1])){
            replicates <- as.numeric(l[2])
        }
    }
    if(replicates > 1){
            gradientTable <- merge(gradientTable,data.frame('n' = 1:replicates))
    }
    gradientTable$run <- c()
    return(gradientTable)
}