R/vector.to.equidistant.tree.R

In TML: Tropical Geometry Tools for Machine Learning

#' Vector to equidistant tree
#'
#' A vector of pairwise distances is used to reconstruct the corresponding equidistant tree
#' @param vec vector of pairwise distances in R^(m choose 2), where m is the number of leaves
#' @return equidistant phylogenetic tree
#' @author Georgios Aliatimis \email{g.aliatimis@lancaster.ac.uk}
#' @references Aliatimis, Georgios, Ruriko Yoshida, Burak Boyaci and James A. Grant (2023). Tropical Logistic Regression on Space of Phylogenetic Trees
#' @export
#' @examples
#' vec = c(1/3,1,1,1,1,1/3)
#' tree = vector.to.equidistant.tree(vec)
#' plot(tree)

vector.to.equidistant.tree <- function(vec){
  e = length(vec)
  m = (1+sqrt(1+8*e))/2 # so that m choose 2 = e
  pairs = names(vec)
  if(is.null(pairs)){
    labels = 1:m
  } else {
    labels = sort(unique(unlist(strsplit(pairs,"-"))))
  }
  if(length(labels) != m) stop("There are more leaf labels than there should be.")
  dist_mat = matrix(0,nrow=m,ncol=m,dimnames = list(labels,labels))
  dist_mat[lower.tri(dist_mat)]= vec
  dist_mat = dist_mat + t(dist_mat)
  u = hclust(as.dist(dist_mat),method="complete")
  u = as.phylo(u)
  return(u)
}