R/disCharToProb.R

In ndukler/phyloGLM: Tests for signals of variable rates of evolution between gene classes and lineages for probabalistic alleles

#' Discrete characters to probabailites
#'
#' Converts discrete characters labels at each site to probabailites
#' @param x either a matrix or a data.frame of allele values with each column being a species and each row being a site
#' @param levels a vector of all possible values of the discrete allele label
#' @name disCharToProb
#' @return a list of allele probabilities with one matrix per species
#' @export
disCharToProb <- function(x, charLevels) {
  if (is.null(colnames(x)) || length(unique(colnames(x))) != ncol(x)) {
    colnames(x) <- 1:ncol(x)
    warning("Columns of x do not have unique column names.")
  }
  aData <- lapply(split(t(x), f = colnames(x)), function(y) {
    z <- matrix(0, nrow = length(y), ncol = length(charLevels))
    yConv <- as.numeric(factor(y, levels = charLevels))
    if (any(is.na(yConv))) {
      stop("Invalid character level present in data")
    }
    for (k in 1:length(yConv)) {
      z[k, yConv[k]] <- 1
    }
    return(z)
  })
  return(aData)
}