@@ -1319,27 +1319,36 @@ edge2vec <- function(tr) {

 }

-extract_inode_hclust_item <- function(h, i, ev) {

-  j <- h$merge[i,]

-  if (any(j < 0)) {

-    j2 <- j[j < 0][1]

-    res <- ev[abs(j2)]

-  } else {

-    res <- ev[extract_inode_hclust_item(h, j, ev)]

-  }

-  return(res)

-}

-

-

-

 # tr is converted from h via ape::as.phylo

 update_edge_hclust <- function(tr, h) {

   ev <- edge2vec(tr)

+

+  #extract_inode_hclust_item <- function(h, i, ev) {

+  #  j <- h$merge[i,]

+  #  if (any(j < 0)) {

+  #    j2 <- j[j < 0][1]

+  #    res <- ev[abs(j2)]

+  #  } else {

+  #    res <- ev[extract_inode_hclust_item(h, j, ev)]

+  #  }

+  #  return(res)

+  #}

+

+  #nodes <- vapply(seq_along(h$height), function(i) {

+  #  extract_inode_hclust_item(h, i, ev)

+  #}, numeric(1))

-  nodes <- vapply(seq_along(h$height), function(i) {

-    extract_inode_hclust_item(h, i, ev)

-  }, numeric(1))

-  

+  nodes <- integer(length(h$height))

+  for (i in seq_along(nodes)) {

+    j <- h$merge[i,]

+    if (any(j < 0)) {

+      j2 <- j[j < 0][1]

+      nodes[i] <- ev[abs(j2)]

+    } else {

+      nodes[i] <- ev[nodes[j[1]]]

+    }

+  }

+

   len <- numeric(max(tr$edge))

   len[nodes] <- h$height

   pn <- ev[nodes]

@@ -1350,3 +1359,5 @@ update_edge_hclust <- function(tr, h) {

   tr$edge.length <- len[tr$edge[,2]]

   return(tr)

 }

+

+