new is.monophyletic() + various changes/fixes

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

diff --git a/R/drop.tip.R b/R/drop.tip.R
index efa429af446223f5838cfe58930d9bed17fc2395..a4a3d030207f2baa34d5a63ef535826fd11bce27 100644 (file)
--- a/R/drop.tip.R
+++ b/R/drop.tip.R
@@ -96,24 +96,23 @@ drop.tip <-
     ## find the tips to drop:
     if (is.character(tip))
         tip <- which(phy$tip.label %in% tip)
-    trms <- edge2 <= Ntip
     ## delete the terminal edges given by `tip':
     keep[match(tip, edge2)] <- FALSE
 
     if (trim.internal) {
-        ## delete the internal edges that do not have descendants
-        ## anymore (ie, they are in the 2nd column of `edge' but
+        internals <- edge2 <= Ntip
+        ## delete the internal edges that do not have anymore
+        ## descendants (ie, they are in the 2nd col of `edge' but
         ## not in the 1st one)
         repeat {
-            sel <- !(edge2 %in% edge1[keep]) & !trms & keep
+            sel <- !(edge2 %in% edge1[keep]) & internals & keep
             if (!sum(sel)) break
             keep[sel] <- FALSE
         }
         if (subtree) {
             ## keep the subtending edge(s):
             subt <- edge1 %in% edge1[keep] & edge1 %in% edge1[!keep]
-            ## <FIXME> 'if (... ' needed below?
-            if (any(subt)) keep[which(subt)] <- TRUE
+            keep[subt] <- TRUE
         }
         if (root.edge && wbl) {
             degree <- tabulate(edge1[keep])