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picante

R tools for integrating phylogenies and ecology

http://picante.r-forge.r-project.org/

About

The Picante package provides tools for Phylocom integration, community analyses, null-models, traits and evolution in R.

The package includes functions for analyzing the phylogenetic and trait diversity of ecological communities, comparative analyses, and the display and manipulation of phenotypic and phylogenetic data.

Package maintainer: Steven Kembel

Developers: Peter Cowan, Matthew Helmus, Steven Kembel

Contributors: David Ackerly, Simon Blomberg, Will Cornwell, Peter Cowan, Matthew Helmus, Steven Kembel, Helene Morlon, Cam Webb

Development of picante has been supported by NSERC, NESCent, the Google Summer of Code, and the Gordon and Betty Moore Foundation.

Thanks to Jonathan Davies, Kyle Dexter, Catherine Graham, Nathaniel Hallinan, Nick Matzke, Alain Paquette, Emmanuel Paradis, Juan Parra, Dan Rabosky, and Marten Winter for feedback and bug reports. Thanks to R-Forge for hosting the project.

News

From version 1.6 onwards, development of picante will primarily happen on Github

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Version

Install

install.packages('picante')

Monthly Downloads

6,187

Version

1.6-2

License

GPL-2

Maintainer

Steven W Kembel

Last Published

March 5th, 2014

Functions in picante (1.6-2)

comdistnt

Calculates inter-community mean nearest taxon distance
comm.phylo.qr

Quantile regression slopes between species co-occurrence and phylogenetic distances
IvesGodfray

Host-parasitoid food web data
color.plot.phylo

Color tip labels based on trait
ses.pd

Standardized effect size of PD
phyEstimate

Phylogenetic estimation of traits for unobserved taxa
comdist

Calculates inter-community mean pairwise distance
expected.pd

Expected PD, PD Variance, and Edge Abundance Distribution of a phylogeny
Kcalc

K statistic of phylogenetic signal
cor.table

Table of correlations and P-values
pd

Calculate Faith's Phylogenetic Diversity
ses.mpd

Standardized effect size of MPD
traitgram

Draw phylogeny with nodes at trait positions
match.phylo.data

Match taxa in phylogeny and data
writetraits

Write a Phylocom traits formatted file
utility

Picante utility functions
mpd

Mean pairwise distance
prune.sample

Prune tree to match community data or trait data
readsample

Read Phylocom sample
comm.phylo.cor

Correlations between species co-occurrence and phylogenetic distances
psd

Phylogenetic Species Diversity Metrics
evol.distinct

Species' evolutionary distinctiveness
specaccum.psr

Phylogenetic Species Richness Sample-Based Rarefaction Curve
sample2matrix

Convert Phylocom sample to community data matrix
phylostruct

Permutations to Test for Phylogenetic Signal in Community Composition
picante-package

picante: R tools for integrating phylogenies and ecology
writesample

Write a Phylocom community sample file
pblm

Phylogenetic Bipartite Linear Model
phylosor

Phylogenetic index of beta-diversity PhyloSor
raoD

Rao's quadratic entropy
tax.distinctiveness

Taxonomic distinctiveness sensu Vane-Wright or May
mntd

Mean nearest taxon distance
sppregs

Regressions to Separate Phylogenetic Attraction and Repulsion
species.dist

Species co-occurrence distances
pcd

Phylogenetic Community Dissimilarity
phylosor.rnd

Null PhyloSor values of phylogenetic beta-diversity
ses.mntd

Standardized effect size of MNTD
matrix2sample

Convert community data matrix to Phylocom sample
multiPhylosignal

Calculates phylogenetic signal for data.frame of traits
randomizeMatrix

Null models for community data matrix randomization
phylocom

Phylocom default data
unifrac

Unweighted UniFrac distance between communities
phylosignal

Measure phylogenetic signal