some changes for ape 3.0-6

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

diff --git a/R/drop.tip.R b/R/drop.tip.R
index e59b59b957a06ebf2a350b5d68d10741e3e3fbc4..e9bd5c037364f4f8e20604ac3aff8ae6755a7b16 100644 (file)
--- a/R/drop.tip.R
+++ b/R/drop.tip.R
@@ -1,8 +1,8 @@
-## drop.tip.R (2010-02-11)
+## drop.tip.R (2012-10-06)
 
 ##   Remove Tips in a Phylogenetic Tree
 
-## Copyright 2003-2010 Emmanuel Paradis
+## Copyright 2003-2012 Emmanuel Paradis
 
 ## This file is part of the R-package `ape'.
 ## See the file ../COPYING for licensing issues.
@@ -54,7 +54,11 @@ extract.clade <- function(phy, node, root.edge = 0, interactive = FALSE)
     if (wbl) phy$edge.length <- phy$edge.length[keep]
     TIPS <- phy$edge[, 2] <= Ntip
     tip <- phy$edge[TIPS, 2]
-    phy$tip.label <- phy$tip.label[tip]
+    ## Fix by Ludovic Mallet and Mahendra Mariadassou (2011-11-21):
+    name <- vector("character", length(tip))
+    name[order(tip)] <- phy$tip.label[tip]
+    phy$tip.label <- name
+    ## End of fix
     ## keep the ordering so no need to reorder tip.label:
     phy$edge[TIPS, 2] <- order(tip)
     if (!is.null(phy$node.label))
@@ -79,6 +83,7 @@ drop.tip <-
 {
     if (!inherits(phy, "phylo"))
         stop('object "phy" is not of class "phylo"')
+    if (!length(tip)) return(phy)
 
     Ntip <- length(phy$tip.label)
     ## find the tips to drop:
@@ -96,6 +101,8 @@ drop.tip <-
         if (is.character(tip))
             tip <- which(phy$tip.label %in% tip)
     }
+    if (any(tip > Ntip))
+        warning("some tip numbers were higher than the number of tips")
 
     if (!rooted && subtree) {
         phy <- root(phy, (1:Ntip)[-tip][1])
@@ -119,15 +126,6 @@ drop.tip <-
     edge2 <- phy$edge[, 2] #
     keep <- !logical(Nedge)
 
-    ## find the tips to drop:
-    if (is.character(tip))
-        tip <- which(phy$tip.label %in% tip)
-
-    if (!rooted && subtree) {
-        phy <- root(phy, (1:Ntip)[-tip][1])
-        root.edge <- 0
-    }
-
     ## delete the terminal edges given by `tip':
     keep[match(tip, edge2)] <- FALSE
 
@@ -179,21 +177,27 @@ drop.tip <-
     ## get the old No. of the nodes and tips that become tips:
     oldNo.ofNewTips <- phy$edge[TERMS, 2]
 
+    ## in case some tips are dropped but kept because of 'subtree = TRUE':
+    if (subtree) {
+        i <- which(tip %in% oldNo.ofNewTips)
+        if (length(i)) {
+            phy$tip.label[tip[i]] <- "[1_tip]"
+            tip <- tip[-i]
+        }
+    }
+
     n <- length(oldNo.ofNewTips) # the new number of tips in the tree
 
-    ## the tips may not be sorted in increasing order of their
-    ## in the 2nd col of edge, so no need to reorder $tip.label
+    ## the tips may not be sorted in increasing order in the
+    ## 2nd col of edge, so no need to reorder $tip.label
     phy$edge[TERMS, 2] <- rank(phy$edge[TERMS, 2])
+    phy$tip.label <- phy$tip.label[-tip]
 
     ## make new tip labels if necessary:
     if (subtree || !trim.internal) {
-        ## get the logical indices of the tips that are kept within 'oldNo.ofNewTips':
-        tips.kept <- oldNo.ofNewTips <= Ntip & !(oldNo.ofNewTips %in% tip)
-        new.tip.label <- character(n)
-        new.tip.label[tips.kept] <- phy$tip.label[-tip]
         ## get the numbers of the nodes that become tips:
-        node2tip <- oldNo.ofNewTips[!tips.kept]
-        new.tip.label[!tips.kept] <- if (subtree) {
+        node2tip <- oldNo.ofNewTips[oldNo.ofNewTips > Ntip]
+        new.tip.label <- if (subtree) {
             paste("[", N[node2tip], "_tips]", sep = "")
         } else {
             if (is.null(phy$node.label)) rep("NA", length(node2tip))
@@ -201,17 +205,13 @@ drop.tip <-
         }
         if (!is.null(phy$node.label))
             phy$node.label <- phy$node.label[-(node2tip - Ntip)]
-        phy$tip.label <- new.tip.label
-    } else phy$tip.label <- phy$tip.label[-tip]
-
-    ## update node.label if needed:
-    if (!is.null(phy$node.label))
-        phy$node.label <- phy$node.label[sort(unique(phy$edge[, 1])) - Ntip]
+        phy$tip.label <- c(phy$tip.label, new.tip.label)
+    }
 
     phy$Nnode <- dim(phy$edge)[1] - n + 1L # update phy$Nnode
 
     ## The block below renumbers the nodes so that they conform
-    ## to the "phylo" format -- same as in root()
+    ## to the "phylo" format, same as in root()
     newNb <- integer(n + phy$Nnode)
     newNb[NEWROOT] <- n + 1L
     sndcol <- phy$edge[, 2] > n
@@ -220,5 +220,10 @@ 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])]
+    }
     collapse.singles(phy)
 }
+