a collection of bug fixes

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

diff --git a/R/drop.tip.R b/R/drop.tip.R
index 6e497cb9c0245dd66e39bbd79d291bd484cab0af..2d2a8f0165847347777db326584b10c1811543f1 100644 (file)
--- a/R/drop.tip.R
+++ b/R/drop.tip.R
@@ -1,4 +1,4 @@
-## drop.tip.R (2009-06-23)
+## drop.tip.R (2009-09-09)
 
 ##   Remove Tips in a Phylogenetic Tree
 
@@ -29,7 +29,7 @@ extract.clade <- function(phy, node, root.edge = 0)
     root.node <- which(phy$edge[, 2] == node)
     start <- root.node + 1 # start of the clade looked for
     anc <- phy$edge[root.node, 1] # the ancestor of 'node'
-    next.anc <- which(phy$edge[-(1:start), 1] == anc) # find the next occurence of 'anc'
+    next.anc <- which(phy$edge[-(1:start), 1] <= anc) # find the next occurence of 'anc' or an 'older' node
 
     keep <- if (length(next.anc)) start + 0:(next.anc[1] - 1) else start:Nedge
 
@@ -167,8 +167,9 @@ drop.tip <-
 
     n <- length(oldNo.ofNewTips) # the new number of tips in the tree
 
-    ## assumes that the ordering of tips is unchanged:
-    phy$edge[TERMS, 2] <- 1:n
+    ## the tips may not be sorted in increasing order of their
+    ## in the 2nd col of edge, so no need to reorder $tip.label
+    phy$edge[TERMS, 2] <- rank(phy$edge[TERMS, 2])
 
     ## make new tip labels if necessary:
     if (subtree || !trim.internal) {