R/pitchforks.R

In treestats: Phylogenetic Tree Statistics

#' Number of pitchforks
#' @description
#' Pitchforks are a clade with three tips, as introduced in the phyloTop
#' package.
#' @param input_obj phylo object or ltable
#' @param normalization "none" or "tips", in which case the found number of
#' pitchforks is divided by the expected number.
#' @return number of pitchforks
#' @export
pitchforks <- function(input_obj, normalization = "none") {
  normalization <- check_normalization_key(normalization)

  check_tree(input_obj,
             require_binary = TRUE,
             require_ultrametric = FALSE)

  if (inherits(input_obj, "matrix")) {
    pitch_stat <- pitchforks_ltable_cpp(input_obj)
    if (normalization == "tips" || normalization == TRUE) {
      pitch_stat <- pitch_stat * 3 / length(input_obj[, 1])
    }
    return(pitch_stat)
  }
  if (inherits(input_obj, "phylo")) {
    pitch_stat <- pitchforks_cpp(as.vector(t(input_obj$edge)))
    if (normalization == "tips" || normalization == TRUE) {
      pitch_stat <- pitch_stat * 3 / length(input_obj$tip.label)
    }
    return(pitch_stat)
  }

  stop("input object has to be phylo or ltable")
}