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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 takes place on Github.

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

4,043

Version

1.8

License

GPL-2

Maintainer

Steven W Kembel

Last Published

March 21st, 2019

Functions in picante (1.8)

mntd

Mean nearest taxon distance
psd

Phylogenetic Species Diversity Metrics
pblm

Phylogenetic Bipartite Linear Model
multiPhylosignal

Calculates phylogenetic signal for data.frame of traits
phylosor.rnd

Null PhyloSor values of phylogenetic beta-diversity
utility

Picante utility functions
writesample

Write a Phylocom community sample file
unifrac

Unweighted UniFrac distance between communities
phylostruct

Permutations to Test for Phylogenetic Signal in Community Composition
traitgram

Draw phylogeny with nodes at trait positions
comm.phylo.cor

Correlations between species co-occurrence and phylogenetic distances
phyEstimate

Phylogenetic estimation of traits for unobserved taxa
mpd

Mean pairwise distance
tax.distinctiveness

Taxonomic distinctiveness sensu Vane-Wright or May
phylosignal

Measure phylogenetic signal
phylosor

Phylogenetic index of beta-diversity PhyloSor
sppregs

Regressions to Separate Phylogenetic Attraction and Repulsion
phylocom

Phylocom default data
pcd

Phylogenetic Community Dissimilarity
ses.mntd

Standardized effect size of MNTD
randomizeMatrix

Null models for community data matrix randomization
sample2matrix

Convert Phylocom sample to community data matrix
writetraits

Write a Phylocom traits formatted file
prune.sample

Prune tree to match community data or trait data
picante-package

picante: Integrating Phylogenies and Ecology
matrix2sample

Convert community data matrix to Phylocom sample
expected.pd

Expected PD, PD Variance, and Edge Abundance Distribution of a phylogeny
ses.mpd

Standardized effect size of MPD
ses.pd

Standardized effect size of PD
pd

Calculate Faith's Phylogenetic Diversity
raoD

Rao's quadratic entropy
readsample

Read Phylocom sample
specaccum.psr

Phylogenetic Species Richness Sample-Based Rarefaction Curve
species.dist

Species co-occurrence distances
match.phylo.data

Match taxa in phylogeny and data
comdistnt

Calculates inter-community mean nearest taxon distance
evol.distinct

Species' evolutionary distinctiveness
comm.phylo.qr

Quantile regression slopes between species co-occurrence and phylogenetic distances
cor.table

Table of correlations and P-values
color.plot.phylo

Color tip labels based on trait
IvesGodfray

Host-parasitoid food web data
Kcalc

K statistic of phylogenetic signal
comdist

Calculates inter-community mean pairwise distance