fix in drop.tip() and new option in pic()

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

diff --git a/R/drop.tip.R b/R/drop.tip.R
index a720a7ca1561be9b9ab0cd166509df4109834771..f1b413f8fe9eba18cf57c896aabcf73ec6fb353f 100644 (file)
--- a/R/drop.tip.R
+++ b/R/drop.tip.R
@@ -1,4 +1,4 @@
-## drop.tip.R (2012-10-20)
+## drop.tip.R (2012-11-22)
 
 ##   Remove Tips in a Phylogenetic Tree
 
@@ -213,7 +213,7 @@ drop.tip <-
 
     ## The block below renumbers the nodes so that they conform
     ## to the "phylo" format, same as in root()
-    newNb <- integer(n + phy$Nnode)
+    newNb <- integer(Ntip + Nnode)
     newNb[NEWROOT] <- n + 1L
     sndcol <- phy$edge[, 2] > n
     ## executed from right to left, so newNb is modified before phy$edge:
@@ -221,10 +221,8 @@ drop.tip <-
         (n + 2):(n + phy$Nnode)
     phy$edge[, 1] <- newNb[phy$edge[, 1]]
     storage.mode(phy$edge) <- "integer"
-    if (!is.null(phy$node.label)) { # update node.label if needed
-        newNb[is.na(newNb)] <- 0L
-        phy$node.label <- phy$node.label[order(newNb[newNb > 0])]
-    }
+    if (!is.null(phy$node.label)) # update node.label if needed
+        phy$node.label <- phy$node.label[which(newNb > 0) - Ntip]
     collapse.singles(phy)
 }