inst/phytools/nodeHeights.r

In sckott/treeshape: treeshape fxns

nodeHeights <- function (tree) 
{
  if (attr(tree, "order") != "cladewise" || is.null(attr(tree, 
                                                         "order"))) 
    t <- reorder(tree)
  else t <- tree
  root <- length(t$tip) + 1
  X <- matrix(NA, nrow(t$edge), 2)
  for (i in 1:nrow(t$edge)) {
    if (t$edge[i, 1] == root) {
      X[i, 1] <- 0
      X[i, 2] <- t$edge.length[i]
    }
    else {
      X[i, 1] <- X[match(t$edge[i, 1], t$edge[, 2]), 2]
      X[i, 2] <- X[i, 1] + t$edge.length[i]
    }
  }
  if (attr(tree, "order") != "cladewise" || is.null(attr(tree, 
                                                         "order"))) 
    o <- apply(matrix(tree$edge[, 2]), 1, function(x, y) which(x == 
      y), y = t$edge[, 2])
  else o <- 1:nrow(t$edge)
  return(X[o, ])
}