bug fix in read.nexus + new ?ape man page

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@60 6e262413-ae40-0410-9e79-b911bd7a66b7

diff --git a/ChangeLog b/ChangeLog
index 5aab9bdf0da3824e12300e0419b913fc164b8fb4..6e2f4f15ac1ac7ee4619f2f18504019c1227f0b3 100644 (file)
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,17 @@
+               CHANGES IN APE VERSION 2.2-4
+
+BUG FIXES
+
+    o The bug fix in read.nexus() in version 2.2-3 was wrong: this is
+      now fixed. (thanks to Peter Wragg for the fix!)
+
+
+OTHER CHANGES
+
+    o There is now a general help page displayed with '?ape' 
+
+
+
                CHANGES IN APE VERSION 2.2-3
 
 

diff --git a/DESCRIPTION b/DESCRIPTION
index bed4ad4c339165126a963f86ebb4b6a59fc3c02a..538343c95ec3e17000fd09dee32a704a2b971712 100644 (file)
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: ape
-Version: 2.2-3
-Date: 2009-01-12
+Version: 2.2-4
+Date: 2009-01-19
 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/read.nexus.R b/R/read.nexus.R
index 01aec6495d560e7dc5ef15386f062941ad0e2af0..b8a17d8ee798ae16a9fca148f5353ed82c52ded6 100644 (file)
--- a/R/read.nexus.R
+++ b/R/read.nexus.R
@@ -1,8 +1,8 @@
-## read.nexus.R (2008-11-24)
+## read.nexus.R (2009-01-19)
 
 ##   Read Tree File in Nexus Format
 
-## Copyright 2003-2008 Emmanuel Paradis
+## Copyright 2003-2009 Emmanuel Paradis
 
 ## This file is part of the R-package `ape'.
 ## See the file ../COPYING for licensing issues.
@@ -154,7 +154,7 @@ read.nexus <- function(file, tree.names = NULL)
     rm(X)
     tree <- gsub("^.*= *", "", tree)
     ## check whether there are empty lines from the above manips:
-    tree <- tree[tree == ""]
+    tree <- tree[tree != ""]
     semico <- grep(";", tree)
     Ntree <- length(semico)
     ## are some trees on several lines?

diff --git a/Thanks b/Thanks
index 9c705efc7a9748920f339cf20bf4fd2eb627bf4a..8f93403e4748d0fc9b8329e11b75a3381835ba65 100644 (file)
--- a/Thanks
+++ b/Thanks
@@ -6,8 +6,8 @@ comments, or bug reports: thanks to all of you!
 
 Significant bug fixes were provided by Cécile Ané, James Bullard,
 Éric Durand, Olivier François, Bret Larget, Nick Matzke,
-Elizabeth Purdom, Klaus Schliep, Li-San Wang, and Yan Wong. Contact
-me if I forgot someone.
+Elizabeth Purdom, Klaus Schliep, Li-San Wang, Yan Wong, and Peter
+Wragg. Contact me if I forgot someone.
 
 Kurt Hornik, of the R Core Team, helped in several occasions to
 fix some problems and bugs.

diff --git a/man/ape-package.Rd b/man/ape-package.Rd
new file mode 100644 (file)
index 0000000..bf681fb
--- /dev/null
+++ b/man/ape-package.Rd
@@ -0,0 +1,37 @@
+\name{ape-package}
+\alias{ape-package}
+\alias{ape}
+\docType{package}
+\title{
+Analyses of Phylogenetics and Evolution
+}
+\description{
+  \pkg{ape} provides functions for reading and manipulating phylogenetic
+  trees and DNA sequences, computing DNA distances, estimating trees
+  with distance-based methods, and a range of methods for comparative
+  analyses and analysis of diversification. Functionalities are also
+  provided for programming new phylogenetic methods.
+
+  The complete list of functions can be displayed with
+  \code{library(help = "splines")}.
+
+  More information on \pkg{ape} can be 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
+
+  Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>
+}
+\references{
+  Paradis, E. (2006) \emph{Analyses of Phylogenetics and Evolution with
+    R}. Springer, New York.
+
+  Paradis, E., Claude, J. and Strimmer, K. (2004) APE: analyses of
+  phylogenetics and evolution in R language. \emph{Bioinformatics},
+  \bold{20}, 289--290.
+}
+\keyword{package}