picante: R tools for integrating phylogenies and ecology

About picante

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, Peter Cowan, Matthew Helmus, Steven Kembel, Helene Morlon, Cam Webb

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

Thanks to Kyle Dexter, Catherine Graham, Nathaniel Hallinan, Nick Matzke, Alain Paquette, Juan Parra, and Marten Winter for feedback and bug reports.

News

• Version 0.7-1 adds the standardized effect size of Faith's PD (ses.pd)
• Several changes and new features in version 0.7
  • Added phylobeta diversity measures (comdist/comdistnt)
  • Abundance-weighted measures of phylogenetic alpha and beta diversity (mpd/mntd/comdist/comdistnt)
  • Added quantile regressions of co-occurrence vs. phylogenetic distance (comm.phylo.qr)
  • Plot continuous trait values as tips of a phylogeny (traitgram)
  • The mnnd and ses.mnnd functions have been renamed to mntd and ses.mntd, respectively, for consistency with naming conventions in Phylocom.
• The pd and phylosor functions in version 0.5 of picante could result in incorrect calculation of phylosor in cases where the supplied phylogeny included taxa not present in any sample, or when pairs of samples collectively contained all taxa in the phylogeny. These functions have been updated in versions of picante >0.5, please see the documentation for more information about how PD and phylosor are calculated.

Current features

• Community phylogenetic and trait diversity
• Faith's PD (phylogenetic diversity) and standardized effect size of PD.
• Webb's NRI/NTI and related measures of standardized effect size of community phylogenetic structure.
• Mean pairwise distance and mean distance to nearest taxon among co-occurring species (can be used with any interspecific distance measure). Distances can be calculated based on presence or abundance in samples.
• Correlations and quantile regressions between species co-occurrence and phylogenetic distances
• Phylogenetic species richness, evenness and variance of Helmus et al. (2007).
• Phylogenetic community-environment regressions of Helmus et al. (2007).
• Phylogenetic beta diversity measures (phylosor, betaMPD, betaMNTD).
• 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 0.7-1 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.

Citing picante

A manuscript describing the software package is in preparation. In the meantime, you can cite picante as:

• S.W. Kembel, D.D. Ackerly, S.P. Blomberg, P.D. Cowan, M.R. Helmus, H. Morlon and C.O. Webb. 2009. picante: R tools for integrating phylogenies and ecology. R package version 0.7-1. http://picante.r-forge.r-project.org

Release history

• Version 0.7-1: Added ses.pd function
• Version 0.7: comm.phylo.qr function (quantile regression of co-occurrence and phylogenetic distance). traitgram function. Changed mnnd terminology to mntd. Added phylogenetic beta diversity measures comdist/comdistnt. Abundance weighting of mpd/mntd.
• Version 0.6: Bugfix release. Changes to pd and phylosor functions.
• Version 0.5: Phylogenetic beta diversity measures (phylosor) with randomization testing.
• Version 0.4: New features and greatly improved speed of community randomizations (randomizeSample). New phylogenetic bipartite linear models functionality added.
• Version 0.3: Bugfixes. Added phylogenetic bipartite linear models, phylogenetic community-environment regressions.
• Version 0.2: Added new community phylogenetic structure metrics (PSR/PSV/PSC methods of Helmus et al.) and phylogenetic species richness accumulation curves
• Version 0.1: Initial public release