From 2196f258796ca3294a8e134a04db83af9183a248 Mon Sep 17 00:00:00 2001
From: paradis <paradis@6e262413-ae40-0410-9e79-b911bd7a66b7>
Date: Wed, 1 Apr 2009 07:35:31 +0000
Subject: [PATCH] fix on dist.gene + a few man pages corrections

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@70 6e262413-ae40-0410-9e79-b911bd7a66b7
---
 ChangeLog          | 10 ++++++++++
 DESCRIPTION        |  4 ++--
 R/dist.gene.R      |  6 +++---
 man/ape-package.Rd |  9 +++++----
 man/consensus.Rd   |  6 +++---
 5 files changed, 23 insertions(+), 12 deletions(-)

diff --git a/ChangeLog b/ChangeLog
index ffbca02..3a9c02b 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,13 @@
+		CHANGES IN APE VERSION 2.3-1
+
+
+BUG FIXES
+
+    o dist.gene() failed on most occasions with the default
+      pairwise.deletion = FALSE.
+
+
+
 		CHANGES IN APE VERSION 2.3
 
 
diff --git a/DESCRIPTION b/DESCRIPTION
index f98af14..e89a11b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: ape
-Version: 2.3
-Date: 2009-03-29
+Version: 2.3-1
+Date: 2009-04-31
 Title: Analyses of Phylogenetics and Evolution
 Author: Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Sien Cuong, Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel, Gangolf Jobb, Christoph Heibl, Daniel Lawson, Vincent Lefort, Pierre Legendre, Jim Lemon, Yvonnick Noel, Johan Nylander, Rainer Opgen-Rhein, Korbinian Strimmer, Damien de Vienne
 Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>
diff --git a/R/dist.gene.R b/R/dist.gene.R
index 650715e..bee883c 100644
--- a/R/dist.gene.R
+++ b/R/dist.gene.R
@@ -1,8 +1,8 @@
-## dist.gene.R (2008-07-18)
+## dist.gene.R (2009-04-01)
 
 ##   Pairwise Distances from Genetic Data
 
-## Copyright 2002-2008 Emmanuel Paradis
+## Copyright 2002-2009 Emmanuel Paradis
 
 ## This file is part of the R-package `ape'.
 ## See the file ../COPYING for licensing issues.
@@ -18,7 +18,7 @@ dist.gene <-
     if (!pairwise.deletion) {
         ## delete the columns with at least one NA:
         del <- apply(x, 2, function(xx) any(is.na(xx)))
-        x <- x[, -del]
+        x <- x[, !del]
     }
     n <- dim(x)
     L <- n[2]
diff --git a/man/ape-package.Rd b/man/ape-package.Rd
index bf681fb..803d5ef 100644
--- a/man/ape-package.Rd
+++ b/man/ape-package.Rd
@@ -13,16 +13,17 @@ Analyses of Phylogenetics and Evolution
   provided for programming new phylogenetic methods.
 
   The complete list of functions can be displayed with
-  \code{library(help = "splines")}.
+  \code{library(help = ape)}.
 
-  More information on \pkg{ape} can be at \url{http://ape.mpl.ird.fr/}.
+  More information on \pkg{ape} can be found at \url{http://ape.mpl.ird.fr/}.
 }
 
 \author{
   Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Sien Cuong, Richard
   Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel, Gangolf Jobb,
-  Christoph Heibl, Vincent Lefort, Jim Lemon, Yvonnick Noel, Johan
-  Nylander, Rainer Opgen-Rhein, Korbinian Strimmer, Damien de Vienne
+  Christoph Heibl, Daniel Lawson, Vincent Lefort, Pierre Legendre, Jim
+  Lemon, Yvonnick Noel, Johan Nylander, Rainer Opgen-Rhein, Korbinian
+  Strimmer, Damien de Vienne
 
   Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>
 }
diff --git a/man/consensus.Rd b/man/consensus.Rd
index f63b551..6e1f5ca 100644
--- a/man/consensus.Rd
+++ b/man/consensus.Rd
@@ -22,9 +22,9 @@ consensus(..., p = 1, check.labels = TRUE)
   0.5 and 1 can be used.
 }
 \details{
-  Using (the default) \code{check.labels = FALSE} results in
-  considerable decrease in computing times. This requires that (i) all
-  trees have the same tip labels, \emph{and} (ii) these labels are
+  Using \code{check.labels = FALSE} results in
+  considerable decrease in computing times. This requires that all
+  trees have the same tip labels, \emph{and} these labels are
   ordered similarly in all trees (in other words, the element
   \code{tip.label} are identical in all trees).
 }
-- 
2.39.5