From 34f56710584c96664cbdcc2f9586af02b6e849bd Mon Sep 17 00:00:00 2001 From: paradis Date: Mon, 19 Jan 2009 09:48:04 +0000 Subject: [PATCH] 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 --- ChangeLog | 14 ++++++++++++++ DESCRIPTION | 4 ++-- R/read.nexus.R | 6 +++--- Thanks | 4 ++-- man/ape-package.Rd | 37 +++++++++++++++++++++++++++++++++++++ 5 files changed, 58 insertions(+), 7 deletions(-) create mode 100644 man/ape-package.Rd diff --git a/ChangeLog b/ChangeLog index 5aab9bd..6e2f4f1 100644 --- 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 bed4ad4..538343c 100644 --- 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 01aec64..b8a17d8 100644 --- 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 9c705ef..8f93403 100644 --- 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 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 +} +\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} -- 2.39.2