R/gl.make.recode.ind.r

Defines functions gl.make.recode.ind

Documented in gl.make.recode.ind

#' @name gl.make.recode.ind
#' @title Creates a proforma recode_ind file for reassigning individual
#'  (=specimen) names
#' @description
#' Renaming individuals may be required when there have been errors in
#' labelling arising in the process from sample to DArT files. There may be
#' occasions where renaming individuals is required for preparation of figures.
#' Caution needs to be exercised because of the potential for breaking the
#' 'chain of evidence' between the samples themselves and the analyses. Recoding
#' individuals can be done with a recode table (csv).
#' @details
#' This script facilitates the construction of a recode table by producing a
#'  proforma file with current individual (=specimen) names in two identical
#'  columns. Edit the second column to reassign individual names. Use keyword
#'  Delete to delete an individual.
#'
#' Apply the recoding using gl.recode.ind(). Deleting individuals can
#' potentially generate monomorphic loci or loci with all values missing. Clean
#' this up with gl.filter.monomorphic().
#'
#' @param x Name of the genlight object containing the SNP data [required].
#' @param out.recode.file File name of the output file (including extension)
#'  [default default_recode_ind.csv].
#' @param outpath Path where to save the output file
#' [default tempdir(), mandated by CRAN]. Use outpath=getwd() or outpath='.'
#' when calling this function to direct output files to your working directory.
#' @param verbose Verbosity: 0, silent or fatal errors; 1, begin and end; 2,
#' progress log; 3, progress and results summary; 5, full report
#' [default 2 or as specified using gl.set.verbosity].
#' @return A vector containing the new individual names.
#' @export
#' @author Custodian: Arthur Georges -- Post to
#' \url{https://groups.google.com/d/forum/dartr}
#' @examples
#' result <- gl.make.recode.ind(testset.gl, out.recode.file ='Emmac_recode_ind.csv',outpath=tempdir())

gl.make.recode.ind <- function(x,
                               out.recode.file = "default_recode_ind.csv",
                               outpath = tempdir(),
                               verbose = NULL) {
    # SET VERBOSITY
    verbose <- gl.check.verbosity(verbose)
    
    # FLAG SCRIPT START
    funname <- match.call()[[1]]
    utils.flag.start(func = funname,
                     build = "Jody",
                     verbosity = verbose)
    
    # CHECK DATATYPE
    datatype <- utils.check.datatype(x, verbose = verbose)
    
    outfilespec <- file.path(outpath, out.recode.file)
    
    # DO THE JOB
    
    # if (verbose >= 2) {cat(report(' Creating draft lookup table\n'))}
    mat <- cbind(indNames(x), indNames(x))
    if (verbose >= 2) {
        cat(report(
            "  Writing draft lookup table to",
            outfilespec,
            ". Edit before use\n"
        ))
    }
    write.table(
        mat,
        file = outfilespec,
        sep = ",",
        row.names = FALSE,
        col.names = FALSE
    )
    
    # FLAG SCRIPT END
    
    if (verbose > 0) {
        cat(report("Completed:", funname, "\n"))
    }
    
    return(NULL)
}
green-striped-gecko/dartR documentation built on Jan. 31, 2024, 10:14 a.m.