R/terminalSisters.R

In ips: Interfaces to Phylogenetic Software in R

## This code is part of the ips package
## Written by C. Heibl 2014 (last update 2025-09-14)

#' @title Find Pairs of Sister Species
#' @description Finds pairs of sister species in
#' a phylogenetic tree.
#' @param phy An object of class \code{\link[ape:read.tree]{phylo}}.
#' @param labels Logical, indicating whether to return tip labels or tip numbers.
#' @return A list of which each element contains the tip labels
#' of a sister species pair.
#' @examples
#' set.seed(1234)
#' tr <- rtree(12)
#' plot(tr)
#' terminalSisters(tr)
#' @export

terminalSisters <- function(phy, labels = TRUE) {

  obj <- unique(
    lapply(1:Ntip(phy), function(x) sort(c(x, sister(x, phy = phy))))
  )
  is.nested <- function(x, y){
    identical(sort(union(x, y)), x)
  }
  id <- vapply(seq_along(obj), function(i) 
    !any(vapply(obj[-i], is.nested, x = obj[[i]], logical(1))),
    logical(1))
  obj <- obj[id]
  if (labels) obj <- lapply(obj, function(phy, x) phy$tip.label[x], phy = phy)
  obj
}