From: paradis Date: Mon, 12 Jan 2009 14:36:11 +0000 (+0000) Subject: updates for ape 2.2-3 X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=bb09d4ad2968b941d673e6c6279c3b483d80ddeb;p=ape.git updates for ape 2.2-3 git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@58 6e262413-ae40-0410-9e79-b911bd7a66b7 --- diff --git a/DESCRIPTION b/DESCRIPTION index 029c78b..bed4ad4 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: ape Version: 2.2-3 -Date: 2009-01-07 +Date: 2009-01-12 Title: Analyses of Phylogenetics and Evolution Author: Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Sien Cuong, Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel, @@ -9,7 +9,8 @@ Author: Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Sien Cuong, Damien de Vienne Maintainer: Emmanuel Paradis Depends: R (>= 2.6.0) -Suggests: gee, nlme, lattice +Suggests: gee +Imports: gee, nlme, lattice ZipData: no Description: ape provides functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data diff --git a/NAMESPACE b/NAMESPACE index 18ed656..01e3dca 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -1,12 +1,14 @@ useDynLib(ape) -export(as.DNAbin, as.phylo, base.freq, dist.dna, dist.nodes, drop.tip, ltt.plot, nj, rcoal, rtree, rmtree, read.dna, read.nexus, read.tree, vcv.phylo, write.dna, write.nexus, write.tree) +exportPattern(".+") import(gee, nlme) importFrom(lattice, xyplot, panel.lines, panel.points) +importFrom(stats, as.hclust, cophenetic, reorder) S3method(print, phylo) S3method(plot, phylo) +S3method(cophenetic, phylo) S3method(as.hclust, phylo) S3method(reorder, phylo) S3method(print, multiPhylo) diff --git a/R/zzz.R b/R/zzz.R index 943b12f..9ab2b1c 100644 --- a/R/zzz.R +++ b/R/zzz.R @@ -1,15 +1,10 @@ -## zzz.R (2008-02-08) +## zzz.R (2009-01-12) ## Library Loading -## 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. .PlotPhyloEnv <- new.env() - -.First.lib <- function(lib, pkg) { - require(nlme, quietly = TRUE) - library.dynam("ape", pkg, lib) -} diff --git a/man/varcomp.Rd b/man/varcomp.Rd index bf08fe5..8eabec9 100644 --- a/man/varcomp.Rd +++ b/man/varcomp.Rd @@ -26,6 +26,7 @@ varcomp(x, scale = FALSE, cum = FALSE) \seealso{\code{\link[nlme]{lme}}} \examples{ data(carnivora) +library(nlme) m <- lme(log10(SW) ~ 1, random = ~ 1|Order/SuperFamily/Family/Genus, data=carnivora) v <- varcomp(m, TRUE, TRUE) plot(v)