change nlm to nlminb in ace() + new makeNodeLabel + fixed drop.tip

[ape.git] / R / drop.tip.R

diff --git a/R/drop.tip.R b/R/drop.tip.R
index 69c957629e6533598488d0f7b3c4ede773faede7..c0bda8bc15042186f101ac7f548e7fc1fb20dd34 100644 (file)
--- a/R/drop.tip.R
+++ b/R/drop.tip.R
@@ -1,4 +1,4 @@
-## drop.tip.R (2009-03-04)
+## drop.tip.R (2009-03-22)
 
 ##   Remove Tips in a Phylogenetic Tree
 
@@ -76,6 +76,7 @@ drop.tip <-
 {
     if (class(phy) != "phylo")
         stop('object "phy" is not of class "phylo"')
+    phy <- reorder(phy)
     Ntip <- length(phy$tip.label)
     NEWROOT <- ROOT <- Ntip + 1
     Nnode <- phy$Nnode
@@ -145,7 +146,10 @@ drop.tip <-
     TIPS <- phy$edge[, 2] <= Ntip
     ## keep the ordering so no need to reorder tip.label:
     phy$edge[TIPS, 2] <- rank(phy$edge[TIPS, 2])
-    Ntip <- length(phy$tip.label) # update Ntip
+    ## 3) update node.label if needed
+    if (!is.null(phy$node.label))
+        phy$node.label <- phy$node.label[sort(unique(phy$edge[, 1])) - Ntip]
+    Ntip <- length(phy$tip.label) # 4) update Ntip
 
     ## make new tip labels if necessary
     if (subtree || !trim.internal) {