R/gl2sfs.R

In dartR: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

#'Converts a genlight object into a sfs input file
#'
#'The output of this function is suitable for analysis in fastsimcoal2 or dada.
#'
#'It saves a derived sfs, assuming that the reference allele is the ancestral,
#'and a MAF sfs.
#'
#'At this stage this function caters only for diploid organisms, for samples
#'from one population only, and for genotypes without missing data. Note that
#'sfs uses frequencies considered \bold{independent}, data are assumed to be
#'from independent (i.e. not linked) loci. This means that only one site per tag
#'should be considered 9i.e. secondaries should be removed). If no monomorphic
#'site estimates is provided (with \code{n.invariant.tags}), the sfs will only
#'include the number of monomorphic sites in the data (but this will be a biased
#'estimates as it doesn't take into account the invariant tags that have not
#'been included. This will affect parameter estimates in the analyses). Note
#'that the number of invariant tags can be estimated with
#'\code{gl.report.secondaries}. In a limited number of cases, ascertainment bias
#'can be explicitly modelled in fastsimcoal2. See fastsimcoal2 manual for
#'details.
#'
#'
#'It expects a dartR formatted genlight object, but it should also  work with
#'other genlight objects.
#' @param x Name of the genlight object containing the SNP data [required].
#' @param n.invariant.tags Number of invariant sites[default 0].
#' @param outfile_root The root of the name of the output file [default "gl2sfs"].
#' @param outpath Path where to save the output file [default tempdir()].
#' @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, unless specified using gl.set.verbosity].
#'@return Deprecated. Please use gl.sfs instead.
#'@author Custodian: Carlo Pacioni (Post to
#'  \url{https://groups.google.com/d/forum/dartr})
#'@seealso \code{\link{gl.report.heterozygosity}},
#'  \code{\link{gl.report.secondaries}}, \code{\link{utils.n.var.invariant}}
#'@export
#'@references Excoffier L., Dupanloup I., Huerta-Sánchez E., Sousa V. C. and
#'  Foll M. (2013) Robust demographic inference from genomic and SNP data. PLoS
#'  genetics 9(10)

gl2sfs <- function(x,
                   n.invariant.tags = 0,
                   outfile_root = "gl2sfs",
                   outpath = tempdir(),
                   verbose = NULL) {
  cat(warn("Deprecated. Use gl.sfs instead.\n"))
}