Archive/test.code/test.genind2hierfstat.R

In christianparobek/skeleSim: Genetic Simulation Engine

test.genind2hierfstat <-
function (dat, pop = NULL)
{
  if (!is.genind(dat))
    stop("dat must be a genind object. Exiting")
  if (is.null(pop)) {
    if (is.null(adegenet::pop(dat))) {
      stop("population factor must be defined")
    }
    else {
      pop <- adegenet::pop(dat)
    }
  }
  if (dat@type != "codom")
    stop("data type must be codominant. Exiting")
  ploid <- unique(dat@ploidy)
  if (length(ploid) != 1)
    stop("data must contain only diploids or only haploids. Exiting")
  if (ploid > 2L)
    stop("Data must come from diploids or haploids. Exiting")
  nucleotides <- c("A", "C", "G", "T")
  alleles.name <- toupper(unique(unlist(dat@all.names)))
  x <- genind2df(dat, sep = "", usepop = FALSE)
  x <- if(!all(alleles.name %in% nucleotides)) {
    do.call(cbind, lapply(x, function(x.col) as.numeric(factor(x.col))))
  } else {
    do.call(cbind, lapply(x, function(x.col) {
      x.col <- toupper(x.col)
      as.numeric(factor(x.col, levels = nucleotides))
    }))
  }
  return(data.frame(pop = pop, x))
}