From 5090ae602c33e1cd3bbdbd2429a43daa8188b8c3 Mon Sep 17 00:00:00 2001
From: paradis <paradis@6e262413-ae40-0410-9e79-b911bd7a66b7>
Date: Sat, 9 Feb 2013 12:43:50 +0000
Subject: [PATCH] fix bug in prop.clades

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@207 6e262413-ae40-0410-9e79-b911bd7a66b7
---
 NEWS              |  4 ++++
 R/dist.topo.R     | 13 +++++++++++--
 man/boot.phylo.Rd |  4 ++--
 3 files changed, 17 insertions(+), 4 deletions(-)

diff --git a/NEWS b/NEWS
index 5f1d758..59c6fed 100644
--- a/NEWS
+++ b/NEWS
@@ -11,6 +11,10 @@ BUG FIXES
 
     o read.dna(, "fasta") may add '\r' in labels: this is fixed.
 
+    o prop.clades() returned wrong numbers when the tip labels of
+      'phy' are not in the same order than the list of trees (thanks
+      to Rupert Collins for the report).
+
 
 
 		CHANGES IN APE VERSION 3.0-7
diff --git a/R/dist.topo.R b/R/dist.topo.R
index 230f009..fa7edf8 100644
--- a/R/dist.topo.R
+++ b/R/dist.topo.R
@@ -1,9 +1,9 @@
-## dist.topo.R (2012-12-12)
+## dist.topo.R (2013-02-09)
 
 ##      Topological Distances, Tree Bipartitions,
 ##   Consensus Trees, and Bootstrapping Phylogenies
 
-## Copyright 2005-2012 Emmanuel Paradis
+## Copyright 2005-2013 Emmanuel Paradis
 
 ## This file is part of the R-package `ape'.
 ## See the file ../COPYING for licensing issues.
@@ -87,6 +87,7 @@ dist.topo <- function(x, y, method = "PH85")
         y$tip.label <- NULL
         y
     }
+    x <- unclass(x) # another killer improvement by Tucson's hackathon (1/2/2013)
     x <- lapply(x, relabel)
     attr(x, "TipLabel") <- ref
     class(x) <- "multiPhylo"
@@ -165,6 +166,14 @@ prop.clades <- function(phy, ..., part = NULL, rooted = FALSE)
         part <- prop.part(obj, check.labels = TRUE)
     }
 
+    ## until ape 3.0-7 it was assumed implicitly that the labels in phy
+    ## are in the same order than in 'part' (bug report by Rupert Collins)
+    if (!identical(phy$tip.label, attr(part, "labels"))) {
+        i <- match(phy$tip.label, attr(part, "labels"))
+        j <- match(seq_len(Ntip(phy)), phy$edge[, 2])
+        phy$edge[j, 2] <- i
+        phy$tip.label <- attr(part, "labels")
+    }
     bp <- prop.part(phy)
     if (!rooted) {
         bp <- postprocess.prop.part(bp)
diff --git a/man/boot.phylo.Rd b/man/boot.phylo.Rd
index 8ac8668..2e16665 100644
--- a/man/boot.phylo.Rd
+++ b/man/boot.phylo.Rd
@@ -133,11 +133,11 @@ tr <- f(woodmouse)
 for (i in 1:5)
   print(boot.phylo(tr, woodmouse, f, quiet = TRUE))
 ### How many partitions in 100 random trees of 10 labels?...
-TR <- replicate(100, rtree(10), FALSE)
+TR <- rmtree(100, 10)
 pp10 <- prop.part(TR)
 length(pp10)
 ### ... and in 100 random trees of 20 labels?
-TR <- replicate(100, rtree(20), FALSE)
+TR <- rmtree(100, 20)
 pp20 <- prop.part(TR)
 length(pp20)
 plot(pp10, pch = "x", col = 2)
-- 
2.39.2