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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

1.7

License

GPL-2

Maintainer

Steven W Kembel

Last Published

May 14th, 2018

Functions in picante (1.7)

phylosor

Phylogenetic index of beta-diversity PhyloSor
cor.table

Table of correlations and P-values
mntd

Mean nearest taxon distance
comm.phylo.qr

Quantile regression slopes between species co-occurrence and phylogenetic distances
color.plot.phylo

Color tip labels based on trait
phylosor.rnd

Null PhyloSor values of phylogenetic beta-diversity
mpd

Mean pairwise distance
ses.mntd

Standardized effect size of MNTD
utility

Picante utility functions
sample2matrix

Convert Phylocom sample to community data matrix
Kcalc

K statistic of phylogenetic signal
writetraits

Write a Phylocom traits formatted file
ses.mpd

Standardized effect size of MPD
evol.distinct

Species' evolutionary distinctiveness
pcd

Phylogenetic Community Dissimilarity
match.phylo.data

Match taxa in phylogeny and data
randomizeMatrix

Null models for community data matrix randomization
phylostruct

Permutations to Test for Phylogenetic Signal in Community Composition
psd

Phylogenetic Species Diversity Metrics
unifrac

Unweighted UniFrac distance between communities
traitgram

Draw phylogeny with nodes at trait positions
ses.pd

Standardized effect size of PD
multiPhylosignal

Calculates phylogenetic signal for data.frame of traits
writesample

Write a Phylocom community sample file
readsample

Read Phylocom sample
pblm

Phylogenetic Bipartite Linear Model
sppregs

Regressions to Separate Phylogenetic Attraction and Repulsion
raoD

Rao's quadratic entropy
tax.distinctiveness

Taxonomic distinctiveness sensu Vane-Wright or May
expected.pd

Expected PD, PD Variance, and Edge Abundance Distribution of a phylogeny
matrix2sample

Convert community data matrix to Phylocom sample
picante-package

picante: Integrating Phylogenies and Ecology
specaccum.psr

Phylogenetic Species Richness Sample-Based Rarefaction Curve
species.dist

Species co-occurrence distances
pd

Calculate Faith's Phylogenetic Diversity
comdist

Calculates inter-community mean pairwise distance
phylosignal

Measure phylogenetic signal
prune.sample

Prune tree to match community data or trait 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
phylocom

Phylocom default data
phyEstimate

Phylogenetic estimation of traits for unobserved taxa