picante

Phylocom integration, community analyses, null-models, traits and evolution in R

About picante

The picante package aims to provide a comprehensive set of tools for analyzing the phylogenetic and trait diversity of ecological communities in R, along with a set of tools for other comparative analyses and manipulations of phenotypic and phylogenetic data.

Package maintainer: Steve Kembel

Developers: Peter Cowan, Matthew Helmus, Steve Kembel

Contributors: David Ackerly, Simon Blomberg, Peter Cowan, Matthew Helmus, Steve Kembel, Cam Webb

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

Current features

• Community phylogenetic and trait similarity measures
• Webb's NRI/NTI and related measures of standardized effect size of community structure
• Mean pairwise distance and mean distance to nearest neighbour among co-occurring species (can be used with any interspecific distance measure)
• Correlations between species co-occurrence and phylogenetic distances
• Phylogenetic diversity measures of Helmus et al. (2007).
• Phylogenetic community-environment regressions of Helmus et al. (2007).
• Phylogenetic signal (Blomberg et al.'s K statistic and P-value based on randomization test)
• Independent contrasts for traits with circular distributions
• Null models for community and phylogeny randomization
• Shuffle taxa labels across tips of phylogeny
• Randomize community co-occurrence data
  • maintaining species occurrence frequency
  • maintaining sample species richness
  • maintaining both species occurrence frequency and sample species richness using independent swap (Gotelli 2000) or trial swap (Miklos and Podani 2004)
• Ives and Godfray's (2006) phylogenetic bipartite linear model.
• Utility functions to read/write data in Phylocom format
• Tree plotting and labelling functions

Obtaining picante

• Version 0.4-0 (stable) is available on CRAN. Simply type install.packages("picante") from within R.
• You can grab the latest nightly build here, or by typing install.packages("picante",repos="http://R-Forge.R-project.org") from within R.

Obtaining help and more information about picante

Visit the project summary page for bug reporting, feature requests, discussions, mailing lists, and access to the source code. If you have problems or questions about the code, please read the function documentation ( help(picante) ), and get in touch with us using one of the above methods.

Release history

• Version 0.4-0: New features and greatly improved speed of community randomizations (randomizeSample). New phylogenetic bipartite linear models functionality added.
• Version 0.3-0: Bugfixes. Added phylogenetic bipartite linear models, phylogenetic community-environment regressions.
• Version 0.2-0: Added new community phylogenetic structure metrics (PSR/PSV/PSC methods of Helmus et al.) and phylogenetic species richness accumulation curves
• Version 0.1-2: Initial public release