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picante

R tools for integrating phylogenies and ecology

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 up to version 1.5.

News

There was a bug in the ses.pd function in picante versions <=1.7. Please see this issue for more details.

Bug reports and feature requests

Please use the Github Issues page for picante to submit bug reports and feature requests. Pull requests are welcomed but are more likely to be accepted if you first submit them as an issue.

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Version

Install

install.packages('picante')

Monthly Downloads

5,117

Version

1.8.1

License

GPL-2

Maintainer

Steven W Kembel

Last Published

February 13th, 2020

Functions in picante (1.8.1)

comdist

Calculates inter-community mean pairwise distance
evol.distinct

Species' evolutionary distinctiveness
cor.table

Table of correlations and P-values
match.phylo.data

Match taxa in phylogeny and data
comm.phylo.cor

Correlations between species co-occurrence and phylogenetic distances
comdistnt

Calculates inter-community mean nearest taxon distance
IvesGodfray

Host-parasitoid food web data
pblm

Phylogenetic Bipartite Linear Model
mpd

Mean pairwise distance
comm.phylo.qr

Quantile regression slopes between species co-occurrence and phylogenetic distances
expected.pd

Expected PD, PD Variance, and Edge Abundance Distribution of a phylogeny
color.plot.phylo

Color tip labels based on trait
picante-package

picante: Integrating Phylogenies and Ecology
Kcalc

K statistic of phylogenetic signal
pcd

Phylogenetic Community Dissimilarity
multiPhylosignal

Calculates phylogenetic signal for data.frame of traits
mntd

Mean nearest taxon distance
matrix2sample

Convert community data matrix to Phylocom sample
phyEstimate

Phylogenetic estimation of traits for unobserved taxa
phylocom

Phylocom default data
phylosor.rnd

Null PhyloSor values of phylogenetic beta-diversity
pd

Calculate Faith's Phylogenetic Diversity
phylostruct

Permutations to Test for Phylogenetic Signal in Community Composition
phylosignal

Measure phylogenetic signal
ses.pd

Standardized effect size of PD
ses.mpd

Standardized effect size of MPD
prune.sample

Prune tree to match community data or trait data
unifrac

Unweighted UniFrac distance between communities
psd

Phylogenetic Species Diversity Metrics
randomizeMatrix

Null models for community data matrix randomization
traitgram

Draw phylogeny with nodes at trait positions
sppregs

Regressions to Separate Phylogenetic Attraction and Repulsion
phylosor

Phylogenetic index of beta-diversity PhyloSor
tax.distinctiveness

Taxonomic distinctiveness sensu Vane-Wright or May
ses.mntd

Standardized effect size of MNTD
writesample

Write a Phylocom community sample file
sample2matrix

Convert Phylocom sample to community data matrix
utility

Picante utility functions
readsample

Read Phylocom sample
writetraits

Write a Phylocom traits formatted file
raoD

Rao's quadratic entropy
species.dist

Species co-occurrence distances
specaccum.psr

Phylogenetic Species Richness Sample-Based Rarefaction Curve