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
 
 
                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
 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,
 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
 
 
 ##   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.
 
 ## 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:
     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?
     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,
 
 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.
 
 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}