R/phy2dist.R

In boydorr/RDiversity: Measurement and Partitioning of Similarity-Sensitive Biodiversity

#' Phylogenetic pairwise tip distance matrix
#'
#' Converts any \code{phylo} object to a matrix of pairwise tip-to-tip distances.
#'
#' @param tree object of class \code{phylo}.
#' @param precompute_dist object of class \code{logical} or \code{numeric}.
#' When TRUE (by default) a distance matrix is generated and stored in slot
#' \code{distance}, when FALSE no distance matrix is generated, and when numeric
#' a distance matrix is generated until the number of species exceeds the
#' defined value.
#'
#' @return \code{phy2sim(x)} returns an object of class \code{distance}
#' containing a \code{matrix} of pairwise tip-to-tip distances.
#' @export
#'
phy2dist <- function(tree, precompute_dist = TRUE) {
  dist <- stats::cophenetic(tree)

  new("distance",
      distance = dist,
      dat_id = "phylogenetic")
}