picante: R tools for integrating phylogenies and ecology
Version 1.6-1

Phylocom integration, community analyses, null-models, traits and evolution in R

AuthorSteven W. Kembel <steve.kembel@gmail.com>, David D. Ackerly <dackerly@berkeley.edu>, Simon P. Blomberg <s.blomberg1@uq.edu.au>, Will K. Cornwell <cornwell@zoology.ubc.ca>, Peter D. Cowan <pdc@berkeley.edu>, Matthew R. Helmus <mrhelmus@wisc.edu>, Helene Morlon <morlon.helene@gmail.com>, Campbell O. Webb <cwebb@oeb.harvard.edu>
Date of publication2013-10-18 01:29:45
MaintainerSteven W. Kembel <steve.kembel@gmail.com>
LicenseGPL-2
Version1.6-1
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("picante", repos="http://R-Forge.R-project.org")

Getting started

Package overview

Popular man pages

color.plot.phylo: Color tip labels based on trait
data.checking: Match taxa in phylogeny and data
mntd: Mean nearest taxon distance
pd: Calculate Faith's Phylogenetic Diversity
randomizeSample: Null models for community data matrix randomization
ses.mntd: Standardized effect size of MNTD
ses.pd: Standardized effect size of PD
See all...

All man pages Function index File listing

Man pages

color.plot.phylo: Color tip labels based on trait
comdist: Calculates inter-community mean pairwise distance
comdistnt: Calculates inter-community mean nearest taxon distance
comm.phylo.cor: Correlations between species co-occurrence and phylogenetic...
comm.phylo.qr: Quantile regression slopes between species co-occurrence and...
cor.table: Table of correlations and P-values
data.checking: Match taxa in phylogeny and data
evol.distinct: Species' evolutionary distinctiveness
expected.pd: Expected PD, PD Variance, and Edge Abundance Distribution of...
IvesGodfray: Host-parasitoid food web data
Kcalc: K statistic of phylogenetic signal
matrix2sample: Convert community data matrix to Phylocom sample
mntd: Mean nearest taxon distance
mpd: Mean pairwise distance
multiPhylosignal: Calculates phylogenetic signal for data.frame of traits
pblm: Phylogenetic Bipartite Linear Model
pcd: Phylogenetic Community Dissimilarity
pd: Calculate Faith's Phylogenetic Diversity
pglmm: Phylogenetic Generalized Linear Mixed Model
phyEstimate: Phylogenetic estimation of traits for unobserved taxa
phylocom: Phylocom default data
phylosignal: Measure phylogenetic signal
phylosor: Phylogenetic index of beta-diversity PhyloSor
phylosor.rnd: Null PhyloSor values of phylogenetic beta-diversity
phylostruct: Permutations to Test for Phylogenetic Signal in Community...
picante-package: picante: R tools for integrating phylogenies and ecology
pruning: Prune tree to match community data or trait data
psd: Phylogenetic Species Diversity Metrics
randomizeSample: Null models for community data matrix randomization
raoD: Rao's quadratic entropy
readsample: Read Phylocom sample
sample2matrix: Convert Phylocom sample to community data matrix
ses.mntd: Standardized effect size of MNTD
ses.mpd: Standardized effect size of MPD
ses.pd: Standardized effect size of PD
specaccum.psr: Phylogenetic Species Richness Sample-Based Rarefaction Curve
species.dist: Species co-occurrence distances
sppregs: Regressions to Separate Phylogenetic Attraction and Repulsion
tax.distinctiveness: Taxonomic distinctiveness sensu Vane-Wright or May
traitgram: Draw phylogeny with nodes at trait positions
unifrac: Unweighted UniFrac distance between communities
utility: Picante utility functions
writesample: Write a Phylocom community sample file
writetraits: Write a Phylocom traits formatted file

Functions

IvesGodfray Man page
Kcalc Man page Source code
PCD Man page
binomial.pd Source code
color.plot.phylo Man page
comdist Man page Source code
comdistnn Man page
comdistnt Man page Source code
comm.phylo.cor Man page
comm.phylo.qr Man page
cor.table Man page Source code
df2vec Man page
ead Man page Source code
edge.children.var Source code
edge.children.var.ub Source code
evol.distinct Man page Source code
expected.pd Man page Source code
extract.clade.noreord Source code
get.nodes Source code
internal2tips Man page
match.comm.dist Man page Source code
match.phylo.comm Man page Source code
match.phylo.data Man page Source code
matrix2sample Man page
mnnd Man page
mntd Man page Source code
mpd Man page Source code
multiPhylosignal Man page Source code
node.age Man page
node.desc Source code
node.number Source code
pblm Man page Source code
pblmpredict Man page Source code
pcd Man page Source code
pd Man page Source code
pglmm Man page
pglmm.data Man page Source code
pglmm.fit Man page Source code
pglmm.sim Man page Source code
phyEstimate Man page Source code
phyEstimateDisc Man page Source code
phylocom Man page
phylosignal Man page Source code
phylosor Man page Source code
phylosor.richness Source code
phylosor.rnd Man page Source code
phylosor.taxaShuffle Source code
phylostruct Man page Source code
pic.variance Man page Source code
picante Man page
picante-package Man page
prune.missing Man page
prune.sample Man page
psc Man page Source code
psd Man page Source code
pse Man page Source code
psr Man page Source code
psv Man page Source code
psv.spp Man page Source code
randomizeMatrix Man page
raoD Man page Source code
readsample Man page
sample2matrix Man page
ses.mnnd Man page
ses.mntd Man page
ses.mpd Man page
ses.pd Man page
sortColumns Man page
sortRows Man page
specaccum.psr Man page Source code
species.dist Man page
sppregs Man page Source code
sppregs.plot Man page Source code
tax.distinctiveness Man page Source code
taxaShuffle Man page
tipShuffle Man page
traitgram Man page Source code
unifrac Man page Source code
var.pd Source code
var.pd.ub Source code
variance.pd Man page Source code
writesample Man page
writetraits Man page

Files

DESCRIPTION
NAMESPACE
R
R/color.plot.phylo.R
R/cor.table.R
R/data.checking.R
R/evol.distinct.R
R/evolve.trait.R
R/expected.pd.R
R/get.nodes.R
R/node.desc.R
R/node.number.R
R/pblm.R
R/pblmpredict.R
R/pcd.R
R/pglmm.R
R/phyEstimate.R
R/phylobeta.R
R/phylocom.R
R/phylodiversity.R
R/phylosignal.R
R/phylosor.R
R/phylostruct.R
R/pruning.R
R/randomizeSample.R
R/raoD.R
R/specaccum.psr.R
R/species.dist.R
R/sppregs.R
R/tax.distinctiveness.R
R/traitgram.R
R/utility.R
build
build/vignette.rds
data
data/IvesGodfray.rda
data/phylocom.rda
inst
inst/CITATION
inst/doc
inst/doc/picante-intro.R
inst/doc/picante-intro.Rnw
inst/doc/picante-intro.pdf
man
man/IvesGodfray.Rd
man/Kcalc.Rd
man/color.plot.phylo.Rd
man/comdist.Rd
man/comdistnt.Rd
man/comm.phylo.cor.Rd
man/comm.phylo.qr.Rd
man/cor.table.Rd
man/data.checking.Rd
man/evol.distinct.Rd
man/expected.pd.Rd
man/matrix2sample.Rd
man/mntd.Rd
man/mpd.Rd
man/multiPhylosignal.Rd
man/pblm.Rd
man/pcd.Rd
man/pd.Rd
man/pglmm.Rd
man/phyEstimate.Rd
man/phylocom.Rd
man/phylosignal.Rd
man/phylosor.Rd
man/phylosor.rnd.Rd
man/phylostruct.Rd
man/picante-package.Rd
man/pruning.Rd
man/psd.Rd
man/randomizeSample.Rd
man/raoD.Rd
man/readsample.Rd
man/sample2matrix.Rd
man/ses.mntd.Rd
man/ses.mpd.Rd
man/ses.pd.Rd
man/specaccum.psr.Rd
man/species.dist.Rd
man/sppregs.Rd
man/tax.distinctiveness.Rd
man/traitgram.Rd
man/unifrac.Rd
man/utility.Rd
man/writesample.Rd
man/writetraits.Rd
src
src/picante.c
picante documentation built on May 21, 2017, 3:55 a.m.

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