R/get.corr.R

In pzwiernik/StructuralEM: Structural EM Algorithm for Gaussian Latent Tree Models

#' Get the correlation matrix
#'
#' This function takes the tree (of class 'igraph') with distances between the tips and outputs
#' the corresponding correlation matrix
#'
#' @param T A tree of class igraph
#' @keywords structural EM algorithm
#' @export
#' @examples
#'
#'
get.corr <- function(T) {
  # takes a phylogenetic tree (class "igraph")
  # returns the correlation matrix by taking exp(-dij)
  igraph::E(T)$weight[((igraph::E(T)$weight>-1e-8)*(igraph::E(T)$weight<0))==1] <- 0
  return(exp(-igraph::shortest.paths(T, v=igraph::V(T), to=igraph::V(T))))
}