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

diff --git a/ChangeLog b/ChangeLog
index ffbca029d4e12518c0b3f326641a93dc80e44e73..3a9c02b524c1387d98fd2ea31c3270c154f78a36 100644 (file)
--- 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 f98af1440d09d75f3698df1a64484ec3c0ea615a..e89a11b1c4d75ae62b5b30aa2316d35a988b38ea 100644 (file)
--- 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 650715e7a9976aacee8225d9456e6ae06bc71850..bee883c9b3e266e9bdda1c8bb4b23526812f31ed 100644 (file)
--- 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 bf681fb326f3f69a3514d2d08b203790313f750e..803d5ef929b9e6015cae8937f88002f6f373fbc0 100644 (file)
--- 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 f63b551078192d53dcc0d3e932a7160d409664d3..6e1f5caa6b1c89534f3d9fcf371774538c2ab30b 100644 (file)
--- 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).
 }