From: paradis <paradis@6e262413-ae40-0410-9e79-b911bd7a66b7>
Date: Sat, 28 Jun 2008 05:52:48 +0000 (+0000)
Subject: changed check.labels = TRUE in dist.topo() and consensus()
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=155d31f088ad9bd4074e5545c6a2dd48ab178788;p=ape.git

changed check.labels = TRUE in dist.topo() and consensus()

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@38 6e262413-ae40-0410-9e79-b911bd7a66b7
---

diff --git a/Changes b/Changes
index e2ea0af..8d49225 100644
--- a/Changes
+++ b/Changes
@@ -25,6 +25,9 @@ OTHER CHANGES
     o unique.multiPhylo() is faster thanks to a suggestion by Vladimir
       Minin.
 
+    o The option 'check.labels' of consensus() and prop.part() is now
+      TRUE.
+
 
 
 		CHANGES IN APE VERSION 2.2
diff --git a/DESCRIPTION b/DESCRIPTION
index 5f5dcf0..af4d120 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: ape
 Version: 2.2-1
-Date: 2008-06-24
+Date: 2008-06-28
 Title: Analyses of Phylogenetics and Evolution
 Author: Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Sien Cuong,
   Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel,
diff --git a/R/dist.topo.R b/R/dist.topo.R
index cf1899a..88110c5 100644
--- a/R/dist.topo.R
+++ b/R/dist.topo.R
@@ -1,4 +1,4 @@
-## dist.topo.R (2008-05-07)
+## dist.topo.R (2008-06-28)
 
 ##      Topological Distances, Tree Bipartitions,
 ##   Consensus Trees, and Bootstrapping Phylogenies
@@ -78,7 +78,7 @@ dist.topo <- function(x, y, method = "PH85")
     x
 }
 
-prop.part <- function(..., check.labels = FALSE)
+prop.part <- function(..., check.labels = TRUE)
 {
     obj <- list(...)
     if (length(obj) == 1 && class(obj[[1]]) != "phylo")
@@ -198,7 +198,7 @@ boot.phylo <- function(phy, x, FUN, B = 100, block = 1, trees = FALSE)
     ans
 }
 
-consensus <- function(..., p = 1, check.labels = FALSE)
+consensus <- function(..., p = 1, check.labels = TRUE)
 {
     foo <- function(ic, node) {
         ## ic: index of 'pp'
diff --git a/man/boot.phylo.Rd b/man/boot.phylo.Rd
index 5c05fd1..d46e095 100644
--- a/man/boot.phylo.Rd
+++ b/man/boot.phylo.Rd
@@ -8,7 +8,7 @@
 \title{Tree Bipartition and Bootstrapping Phylogenies}
 \usage{
 boot.phylo(phy, x, FUN, B = 100, block = 1, trees = FALSE)
-prop.part(..., check.labels = FALSE)
+prop.part(..., check.labels = TRUE)
 prop.clades(phy, ..., part = NULL)
 \method{print}{prop.part}(x, ...)
 \method{summary}{prop.part}(object, ...)
@@ -30,9 +30,8 @@ prop.clades(phy, ..., part = NULL)
     containing such objects. In the case of \code{plot} further
     arguments for the plot (see details).}
   \item{check.labels}{a logical specifying whether to check the labels
-    of each tree. If \code{FALSE} (the default), it is assumed that all
-    trees have the same tip labels, and that they are in the same order
-    (see details).}
+    of each tree. If \code{FALSE}, it is assumed that all trees have the
+    same tip labels, and that they are in the same order (see details).}
   \item{part}{a list of partitions as returned by \code{prop.part}; if
     this is used then \code{\dots} is ignored.}
   \item{object}{an object of class \code{"prop.part"}.}
@@ -63,11 +62,11 @@ prop.clades(phy, ..., part = NULL)
   be resampled altogether. For instance, if one wants to resample at the
   codon-level, then \code{block = 3} must be used.
 
-  Using (the default) \code{check.labels = FALSE} in \code{prop.part}
-  results in considerable decrease in computing times. This requires that
-  (i) all trees have the same tip labels, \emph{and} (ii) these labels
-  are ordered similarly in all trees (in other words, the element
-  \code{tip.label} are identical in all trees).
+  Using \code{check.labels = FALSE} in \code{prop.part} decreases
+  computing times. This requires that (i) all trees have the same tip
+  labels, \emph{and} (ii) these labels are ordered similarly in all
+  trees (in other words, the element \code{tip.label} are identical in
+  all trees).
 
   The plot function represents a contingency table of the different
   partitions (on the \emph{x}-axis) in the lower panel, and their observed