R/mean_branch_length.R

In treestats: Phylogenetic Tree Statistics

#' Mean branch length of a tree, including extinct branches.
#' @param phy phylo object or Ltable
#' @return mean branch length
#' @export
mean_branch_length <- function(phy) {

  if (inherits(phy, "matrix")) {
    return(calc_mean_branch_length_ltable_cpp(phy))
  }
  if (inherits(phy, "phylo")) {
    return(calc_mean_branch_length_cpp(as.vector(phy$edge.length)))
  }

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

#' Variance of branch lengths of a tree,
#' including extinct branches.
#' @param phy phylo object or Ltable
#' @return variance of branch lengths
#' @export
var_branch_length <- function(phy) {
  if (inherits(phy, "matrix")) {
    phy <- treestats::l_to_phylo(phy)
  }
  if (inherits(phy, "phylo")) {
    return(stats::var(phy$edge.length))
  }

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


#' Variance of internal branch lengths of a tree, e.g. of branches not leading
#' to a tip.
#' @param phy phylo object or Ltable
#' @return variance of internal branch lengths
#' @export
var_branch_length_int <- function(phy) {
  if (inherits(phy, "matrix")) {
    phy <- treestats::l_to_phylo(phy)
  }
  if (inherits(phy, "phylo")) {
    root_no <- min(phy$edge[, 1])

    int_branches <- phy$edge.length[phy$edge[, 2] >= root_no]

    return(stats::var(int_branches))
  }

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

#' Mean length of internal branches of a tree, e.g. of
#' branches not leading to a tip.
#' @param phy phylo object or Ltable
#' @return mean of internal branch lengths
#' @export
mean_branch_length_int <- function(phy) {
  if (inherits(phy, "matrix")) {
    phy <- treestats::l_to_phylo(phy)
  }
  if (inherits(phy, "phylo")) {
    root_no <- min(phy$edge[, 1])

    int_branches <- phy$edge.length[phy$edge[, 2] >= root_no]

    return(mean(int_branches))
  }

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


#' Variance of external branch lengths of a tree, e.g. of
#' branches leading to a tip.
#' @param phy phylo object or Ltable
#' @return variance of external branch lengths
#' @export
var_branch_length_ext <- function(phy) {
  if (inherits(phy, "matrix")) {
    phy <- treestats::l_to_phylo(phy)
  }
  if (inherits(phy, "phylo")) {
    root_no <- min(phy$edge[, 1])

    ext_branches <- phy$edge.length[phy$edge[, 2] < root_no]

    return(stats::var(ext_branches))
  }

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

#' Mean length of external branch lengths of a tree, e.g. of
#' branches leading to a tip.
#' @param phy phylo object or Ltable
#' @return mean of external branch lengths
#' @export
mean_branch_length_ext <- function(phy) {
  if (inherits(phy, "matrix")) {
    phy <- treestats::l_to_phylo(phy)
  }
  if (inherits(phy, "phylo")) {
    root_no <- min(phy$edge[, 1])

    ext_branches <- phy$edge.length[phy$edge[, 2] < root_no]

    return(mean(ext_branches))
  }

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