R/weighL1dist.R

Defines functions weighL1dist

Documented in weighL1dist

#' Calculation of weighted l1 distance index for rooted binary trees
#'
#' This function calculates the weighted l1 distance index \eqn{D_{l1}(T)}{Dl1(T)} for a
#' given rooted binary tree \eqn{T}. \eqn{D_{l1}(T)}{Dl1(T)} is defined as
#' \deqn{D_{l1}(T)=\sum_{z=2}^n z \cdot |f_n(z)-p_n(z)|}{Dl1(T)= \sum z*|f_n(z)-p_n(z)|
#' over all possible sizes 2<=z<=n} in which \eqn{n} denotes the
#' number of leaves of \eqn{T}, \eqn{f_n(z)} denotes the frequency of pending subtrees
#' of size \eqn{z} in \eqn{T} and \eqn{p_n(z)} is the expected number of
#' pending subtrees of size \eqn{z} under the Yule model, i.e. \eqn{p_n(z)=\frac{1}{n-1}}{p_n(z)=1/(n-1)}
#' if \eqn{z=n} and otherwise \eqn{\frac{n}{n-1}\cdot\frac{2}{z\cdot(z+1)}}{n/(n-1)*2/(z*(z+1))}.\cr\cr
#' For \eqn{n=1} the function returns \eqn{D_{l1}(T)=0}{Dl1(T)=0}.
#'
#' @param tree A rooted binary tree in phylo format.
#'
#' @return \code{weighL1distI} returns the weighted l1 distance index of the given tree.
#'
#' @author Sophie Kersting
#'
#' @references M. G. Blum and O. Fran├žois. On statistical tests of phylogenetic tree imbalance: The Sackin and other indices revisited. Mathematical Biosciences, 195(2):141-153, 2005. doi: 10.1016/j.mbs.2005.03.003.
#'
#' @examples
#' tree <- ape::read.tree(text="((((,),),(,)),(((,),),(,)));")
#' weighL1dist(tree)
#'
#'@export
weighL1dist <- function(tree)
{
  #Check for errors in input
  if (!is_binary(tree)) stop("The input tree must be binary.")

  n <- length(tree$tip.label)
  if(n == 1) {return(0)}

  # get the size of each subtree
  sub.size <- get.subtreesize(tree=tree)
  # summarise over all subtree sizes
  wL1d_val <- 0
  for(z in 2:n)
  {
    f_z <- sum(sub.size==z) / tree$Nnode
    if(z == n) {
      p_z <- 1/(n-1)
    } else {
      p_z <- n/(n-1)*2/(z*(z+1))
    }
    wL1d_val <- wL1d_val + z*abs(f_z-p_z)
  }
  return (wL1d_val)
}

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treebalance documentation built on Oct. 17, 2021, 5:06 p.m.