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 029c78b707d1422514f2d401bf87f3f45a042499..bed4ad4c339165126a963f86ebb4b6a59fc3c02a 100644 (file)
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: ape
 Version: 2.2-3
 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,
 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 <Emmanuel.Paradis@ird.fr>
 Depends: R (>= 2.6.0)
   Damien de Vienne
 Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>
 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
 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 18ed656695aad2e6021e9dea95ced3255d94fc9e..01e3dcaf55a448ba34a5d9881d56ddcd9bdd5c44 100644 (file)
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,12 +1,14 @@
 useDynLib(ape)
 
 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)
 
 import(gee, nlme)
 importFrom(lattice, xyplot, panel.lines, panel.points)

+importFrom(stats, as.hclust, cophenetic, reorder)

 
 S3method(print, phylo)
 S3method(plot, phylo)
 
 S3method(print, phylo)
 S3method(plot, phylo)

+S3method(cophenetic, phylo)

 S3method(as.hclust, phylo)
 S3method(reorder, phylo)
 S3method(print, multiPhylo)
 S3method(as.hclust, phylo)
 S3method(reorder, phylo)
 S3method(print, multiPhylo)

diff --git a/R/zzz.R b/R/zzz.R
index 943b12fbf6ef541be2283145a5c9cfeb47430ce3..9ab2b1cb161771912e67941fa962429c7b09503f 100644 (file)
--- a/R/zzz.R
+++ b/R/zzz.R
@@ -1,15 +1,10 @@
-## zzz.R (2008-02-08)
+## zzz.R (2009-01-12)

 
 ##   Library Loading
 
 
 ##   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()
 
 ## 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 bf08fe56a7c640f618a963b535d7309ba0ed515c..8eabec9c779ce46b4271a3e17412ac4e14005223 100644 (file)
--- 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)
 \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)
 m <- lme(log10(SW) ~ 1, random = ~ 1|Order/SuperFamily/Family/Genus, data=carnivora)
 v <- varcomp(m, TRUE, TRUE)
 plot(v)