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

Files in this package

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.

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