picante: R tools for integrating phylogenies and ecology

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 publication2014-03-05 21:51:49
MaintainerSteven W. Kembel <steve.kembel@gmail.com>
LicenseGPL-2
Version1.6-2

View on CRAN

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

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

color.plot.phylo Man page
comdist Man page
comdistnn Man page
comdistnt Man page
comm.phylo.cor Man page
comm.phylo.qr Man page
cor.table Man page
df2vec Man page
ead Man page
evol.distinct Man page
expected.pd Man page
internal2tips Man page
IvesGodfray Man page
Kcalc Man page
match.comm.dist Man page
match.phylo.comm Man page
match.phylo.data Man page
matrix2sample Man page
mnnd Man page
mntd Man page
mpd Man page
multiPhylosignal Man page
node.age Man page
pblm Man page
pblmpredict Man page
pcd Man page
PCD Man page
pd Man page
phyEstimate Man page
phyEstimateDisc Man page
phylocom Man page
phylosignal Man page
phylosor Man page
phylosor.rnd Man page
phylostruct Man page
picante Man page
picante-package Man page
pic.variance Man page
prune.missing Man page
prune.sample Man page
psc Man page
psd Man page
pse Man page
psr Man page
psv Man page
psv.spp Man page
randomizeMatrix Man page
raoD Man page
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
species.dist Man page
sppregs Man page
sppregs.plot Man page
taxaShuffle Man page
tax.distinctiveness Man page
tipShuffle Man page
traitgram Man page
unifrac Man page
variance.pd Man page
writesample Man page
writetraits Man page

Files

picante
picante/inst
picante/inst/CITATION
picante/inst/doc
picante/inst/doc/picante-intro.R
picante/inst/doc/picante-intro.Rnw
picante/inst/doc/picante-intro.pdf
picante/src
picante/src/picante.c
picante/NAMESPACE
picante/data
picante/data/phylocom.rda
picante/data/IvesGodfray.rda
picante/R
picante/R/tax.distinctiveness.R picante/R/sppregs.R picante/R/randomizeSample.R picante/R/evol.distinct.R picante/R/phylosignal.R picante/R/pcd.R picante/R/species.dist.R picante/R/pblm.R picante/R/phylobeta.R picante/R/phylocom.R picante/R/pblmpredict.R picante/R/pruning.R picante/R/utility.R picante/R/traitgram.R picante/R/node.desc.R picante/R/phyEstimate.R picante/R/data.checking.R picante/R/cor.table.R picante/R/phylodiversity.R picante/R/raoD.R picante/R/phylosor.R picante/R/phylostruct.R picante/R/color.plot.phylo.R picante/R/specaccum.psr.R picante/R/evolve.trait.R picante/R/get.nodes.R picante/R/node.number.R picante/R/expected.pd.R
picante/vignettes
picante/vignettes/picante-intro.Rnw
picante/README.md
picante/MD5
picante/build
picante/build/vignette.rds
picante/DESCRIPTION
picante/man
picante/man/pruning.Rd picante/man/comm.phylo.cor.Rd picante/man/comm.phylo.qr.Rd picante/man/traitgram.Rd picante/man/evol.distinct.Rd picante/man/utility.Rd picante/man/color.plot.phylo.Rd picante/man/expected.pd.Rd picante/man/ses.mpd.Rd picante/man/specaccum.psr.Rd picante/man/raoD.Rd picante/man/phylocom.Rd picante/man/picante-package.Rd picante/man/comdist.Rd picante/man/sample2matrix.Rd picante/man/ses.mntd.Rd picante/man/phyEstimate.Rd picante/man/pblm.Rd picante/man/phylosor.rnd.Rd picante/man/psd.Rd picante/man/sppregs.Rd picante/man/phylosignal.Rd picante/man/comdistnt.Rd picante/man/mntd.Rd picante/man/phylostruct.Rd picante/man/ses.pd.Rd picante/man/mpd.Rd picante/man/data.checking.Rd picante/man/unifrac.Rd picante/man/tax.distinctiveness.Rd picante/man/pcd.Rd picante/man/species.dist.Rd picante/man/multiPhylosignal.Rd picante/man/phylosor.Rd picante/man/Kcalc.Rd picante/man/matrix2sample.Rd picante/man/readsample.Rd picante/man/writesample.Rd picante/man/cor.table.Rd picante/man/randomizeSample.Rd picante/man/writetraits.Rd picante/man/pd.Rd picante/man/IvesGodfray.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.