Integrating Phylogenies and Ecology

Functions for phylocom integration, community analyses, null-models, traits and evolution. Implements numerous ecophylogenetic approaches including measures of community phylogenetic and trait diversity, phylogenetic signal, estimation of trait values for unobserved taxa, null models for community and phylogeny randomizations, and utility functions for data input/output and phylogeny plotting. A full description of package functionality and methods are provided by Kembel et al. (2010) .

R tools for integrating phylogenies and ecology


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.


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


Reference manual

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1.8.2 by Steven W. Kembel, a year ago

Browse source code at

Authors: Steven W. Kembel <[email protected]> , David D. Ackerly <[email protected]> , Simon P. Blomberg <[email protected]> , Will K. Cornwell <[email protected]> , Peter D. Cowan <[email protected]> , Matthew R. Helmus <[email protected]> , Helene Morlon <[email protected]> , Campbell O. Webb <[email protected]>

Documentation:   PDF Manual  

Task views: Phylogenetics, Especially Comparative Methods

GPL-2 license

Depends on ape, vegan, nlme, methods

Suggests brglm, circular, corpcor, quantreg

Imported by DAMOCLES, PCPS, betapart, biosurvey, nodiv, pez, recluster.

Depended on by CommEcol, RPANDA, idar.

Suggested by EcoIndR, RRphylo, Rarefy, cati, ecolottery, enveomics.R, fishtree, microeco, phyr.

See at CRAN