R/contr.deg2.R

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

#'  Contract degree two nodes
#'
#' This is an internal function that is used in the M-step to output a binary tree. It contracts degree two nodes
#' that do not correspond to observed variables.
#' @param T a tree
#' @keywords Gaussian phylogenetic trees, Chow-Liu algortihm
#' @export
#' @examples
contr.deg2 <- function(T){
  # contracts all degree two red nodes
  igraph::E(T)$weight[((igraph::E(T)$weight>-1e-8)*(igraph::E(T)$weight<0))==1] <- 0
  while (is.binary(T)==0) {
    v <- as.vector(igraph::V(T)[((igraph::degree(T)==2)*(igraph::V(T)$color=="red"))==1])[1]
    u <- as.vector(T[[v,]][[1]][1])
    w <- as.vector(T[[v,]][[1]][2])
    T[u,w] <- T[u,v]+T[v,w]
    T <- igraph::delete.vertices(T,v)
  }
  return(T)
}