Last data update: 2014.03.03
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ape
Package: ape
Version: 3.5
Date: 2016-05-23
Title: Analyses of Phylogenetics and Evolution
Authors@R: c(person("Emmanuel", "Paradis", role = c("aut", "cre", "cph"), email = "Emmanuel.Paradis@ird.fr"),
person("Simon", "Blomberg", role = c("aut", "cph")),
person("Ben", "Bolker", role = c("aut", "cph")),
person("Julien", "Claude", role = c("aut", "cph")),
person("Hoa Sien", "Cuong", role = c("aut", "cph")),
person("Richard", "Desper", role = c("aut", "cph")),
person("Gilles", "Didier", role = c("aut", "cph")),
person("Benoit", "Durand", role = c("aut", "cph")),
person("Julien", "Dutheil", role = c("aut", "cph")),
person("Olivier", "Gascuel", role = c("aut", "cph")),
person("Christoph", "Heibl", role = c("aut", "cph")),
person("Anthony", "Ives", role = c("aut", "cph")),
person("Daniel", "Lawson", role = c("aut", "cph")),
person("Vincent", "Lefort", role = c("aut", "cph")),
person("Pierre", "Legendre", role = c("aut", "cph")),
person("Jim", "Lemon", role = c("aut", "cph")),
person("Rosemary", "McCloskey", role = c("aut", "cph")),
person("Johan", "Nylander", role = c("aut", "cph")),
person("Rainer", "Opgen-Rhein", role = c("aut", "cph")),
person("Andrei-Alin", "Popescu", role = c("aut", "cph")),
person("Manuela", "Royer-Carenzi", role = c("aut", "cph")),
person("Klaus", "Schliep", role = c("aut", "cph")),
person("Korbinian", "Strimmer", role = c("aut", "cph")),
person("Damien", "de Vienne", role = c("aut", "cph")))
Depends: R (>= 3.0.0)
Suggests: gee, expm
Imports: nlme, lattice, graphics, methods, stats, tools, utils,
parallel
ZipData: no
Description: Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from allelic and nucleotide data, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.
License: GPL (>= 2)
URL: http://ape-package.ird.fr/
NeedsCompilation: yes
Packaged: 2016-05-23 07:32:24 UTC; paradis
Author: Emmanuel Paradis [aut, cre, cph],
Simon Blomberg [aut, cph],
Ben Bolker [aut, cph],
Julien Claude [aut, cph],
Hoa Sien Cuong [aut, cph],
Richard Desper [aut, cph],
Gilles Didier [aut, cph],
Benoit Durand [aut, cph],
Julien Dutheil [aut, cph],
Olivier Gascuel [aut, cph],
Christoph Heibl [aut, cph],
Anthony Ives [aut, cph],
Daniel Lawson [aut, cph],
Vincent Lefort [aut, cph],
Pierre Legendre [aut, cph],
Jim Lemon [aut, cph],
Rosemary McCloskey [aut, cph],
Johan Nylander [aut, cph],
Rainer Opgen-Rhein [aut, cph],
Andrei-Alin Popescu [aut, cph],
Manuela Royer-Carenzi [aut, cph],
Klaus Schliep [aut, cph],
Korbinian Strimmer [aut, cph],
Damien de Vienne [aut, cph]
Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>
Repository: CRAN
Date/Publication: 2016-05-24 05:38:54
Install log
* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'ape' ...
** package 'ape' successfully unpacked and MD5 sums checked
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c BIONJ.c -o BIONJ.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c NNI.c -o NNI.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c SPR.c -o SPR.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c TBR.c -o TBR.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c additive.c -o additive.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c ape.c -o ape.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c bNNI.c -o bNNI.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c bionjs.c -o bionjs.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c bipartition.c -o bipartition.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c bitsplits.c -o bitsplits.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c delta_plot.c -o delta_plot.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c dist_dna.c -o dist_dna.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c dist_nodes.c -o dist_nodes.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c ewLasso.c -o ewLasso.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c heap.c -o heap.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c mat_expo.c -o mat_expo.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c me.c -o me.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c me_balanced.c -o me_balanced.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c me_ols.c -o me_ols.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c mvr.c -o mvr.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c mvrs.c -o mvrs.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c nj.c -o nj.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c njs.c -o njs.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c pic.c -o pic.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c plot_phylo.c -o plot_phylo.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c rTrait.c -o rTrait.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c read_dna.c -o read_dna.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c reorder_phylo.c -o reorder_phylo.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c treePop.c -o treePop.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tree_build.c -o tree_build.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tree_phylo.c -o tree_phylo.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c triangMtd.c -o triangMtd.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c triangMtds.c -o triangMtds.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c ultrametric.c -o ultrametric.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o ape.so BIONJ.o NNI.o SPR.o TBR.o additive.o ape.o bNNI.o bionjs.o bipartition.o bitsplits.o delta_plot.o dist_dna.o dist_nodes.o ewLasso.o heap.o mat_expo.o me.o me_balanced.o me_ols.o mvr.o mvrs.o nj.o njs.o pic.o plot_phylo.o rTrait.o read_dna.o reorder_phylo.o treePop.o tree_build.o tree_phylo.o triangMtd.o triangMtds.o ultrametric.o -L/home/ddbj/local/lib64/R/lib -lRlapack -L/home/ddbj/local/lib64/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/ape/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'ape'
finding HTML links ... done
AAbin html
Rd warning: /tmp/RtmpmsMIyB/R.INSTALL4a6460786de1/ape/man/AAbin.Rd:78: missing file link 'dist.ml'
CADM.global html
DNAbin html
DNAbin2indel html
Initialize.corPhyl html
LTT html
MPR html
MoranI html
SDM html
ace html
add.scale.bar html
additive html
alex html
all.equal.phylo html
alview html
ape-internal html
ape-package html
as.alignment html
as.bitsplits html
as.matching html
as.phylo html
as.phylo.formula html
axisPhylo html
balance html
base.freq html
bd.ext html
bd.time html
binaryPGLMM html
bind.tree html
bionj html
bird.families html
bird.orders html
birthdeath html
boot.phylo html
branching.times html
c.phylo html
carnivora html
checkAlignment html
checkValidPhylo html
cherry html
chiroptera html
chronoMPL html
chronopl html
chronos html
clustal html
coalescent.intervals html
collapse.singles html
collapsed.intervals html
compar.cheverud html
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Rd warning: /tmp/RtmpmsMIyB/R.INSTALL4a6460786de1/ape/man/compar.gee.Rd:105: missing file link 'drop1'
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consensus html
cophenetic.phylo html
cophyloplot html
corBlomberg html
corBrownian html
corClasses html
corGrafen html
corMartins html
corPagel html
corphylo html
correlogram.formula html
cynipids html
dbd html
def html
del.gaps html
delta.plot html
dist.dna html
dist.gene html
dist.topo html
diversi.gof html
diversi.time html
diversity.contrast.test html
drop.tip html
edges html
evonet html
Rd warning: /tmp/RtmpmsMIyB/R.INSTALL4a6460786de1/ape/man/evonet.Rd:62: missing file link 'as.networx'
ewLasso html
fastme html
gammaStat html
hivtree html
howmanytrees html
identify.phylo html
image.DNAbin html
Rd warning: /tmp/RtmpmsMIyB/R.INSTALL4a6460786de1/ape/man/image.DNAbin.Rd:31: missing file link 'image.default'
is.binary.tree html
is.compatible html
is.monophyletic html
is.ultrametric html
Rd warning: /tmp/RtmpmsMIyB/R.INSTALL4a6460786de1/ape/man/is.ultrametric.Rd:27: missing file link '.Machine'
kronoviz html
label2table html
ladderize html
landplants html
lmorigin html
ltt.plot html
makeLabel html
makeNodeLabel html
mantel.test html
mat3 html
mat5M3ID html
mat5Mrand html
matexpo html
mcconwaysims.test html
mcmc.popsize html
mixedFontLabel html
mrca html
mst html
multi2di html
multiphylo html
mvr html
nj html
njs html
node.depth html
nodelabels html
nodepath html
opsin html
parafit html
pcoa html
phydataplot html
Rd warning: /tmp/RtmpmsMIyB/R.INSTALL4a6460786de1/ape/man/phydataplot.Rd:47: missing file link 'rainbow'
phymltest html
pic html
pic.ortho html
plot.correlogram html
plot.phylo html
plot.phyloExtra html
plot.varcomp html
print.phylo html
rTraitCont html
rTraitDisc html
rTraitMult html
read.GenBank html
read.caic html
read.dna html
read.nexus html
read.nexus.data html
read.tree html
reconstruct html
reorder.phylo html
Rd warning: /tmp/RtmpmsMIyB/R.INSTALL4a6460786de1/ape/man/reorder.phylo.Rd:51: missing file link 'reorder'
richness.yule.test html
rlineage html
root html
rotate html
rtree html
rtt html
seg.sites html
skyline html
skylineplot html
slowinskiguyer.test html
speciesTree html
stree html
subtreeplot html
subtrees html
summary.phylo html
trans html
treePop html
trex html
triangMtd html
unique.multiPhylo html
varCompPhylip html
varcomp html
vcv.phylo html
vcv2phylo html
weight.taxo html
where html
which.edge html
woodmouse html
write.dna html
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write.tree html
yule html
yule.cov html
yule.time html
zoom html
Rd warning: /tmp/RtmpmsMIyB/R.INSTALL4a6460786de1/ape/man/zoom.Rd:37: missing file link 'rainbow'
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Rd warning: /tmp/RtmpmsMIyB/R.INSTALL4a6460786de1/ape/man/zoom.Rd:44: missing file link 'grey'
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ape)
Making 'packages.html' ... done
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