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, 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 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

• A manuscript describing Picante has been published in Bioinformatics.
• Picante 1.3 has been released
  • The phylogenetic community dissimilarity (PCD) of Ives and Helmus (2010) is now included in function pcd
• Lots of changes and new features in version 1.0
  • Calculate Rao's quadratic entropy (alpha and beta diversity taking phylogenetic distinctiveness into account)
  • Added more phylobeta diversity measures (UniFrac, Rao's quadratic entropy)
  • Changed name of randomizeSample to randomizeMatrix for consistency with other functions
  • Added automatic checks to ensure taxa labels in phylogeny and other data sets match

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.
• Rao's quadratic entropy, a measure of diversity within and among communities optionally taking phylogenetic distinctiveness into account.
• 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).
• Taxonomic and evolutionary distinctiveness of taxa for conservation biology.
• Numerous phylogenetic beta diversity measures (PCD, phylosor, UniFrac, betaMPD, betaMNTD, Rao's quadratic entropy).
• 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 1.3-0 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

There is a package vignette with more information about Picante data formats and analysis examples. Download it here, or type vignette("picante-intro") to view within R.

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

If you use our software, please acknowledge our work by citing us:

• S.W. Kembel, P.D. Cowan, M.R. Helmus, W.K. Cornwell, H. Morlon, D.D. Ackerly, S.P. Blomberg, and C.O. Webb. 2010. Picante: R tools for integrating phylogenies and ecology. Bioinformatics 26:1463-1464.

Release history

• Version 1.3: Add function pcd. Fix single-community error in pse.
• Version 1.2: Bugfix release. Fix to evol.distinct function. Kcalc now behaves better with non-ultrametric trees.
• Version 1.1-1: Minor update to address deprecation of evolve.phylo function in ape package; deleted evolve.brownian function and changed example code.
• Version 1.1: Added package vignette, new example data set from Ives & Godfray (2006), function example code. Reinstated "richness" and "frequency" null models for ses.* functions.
• Version 1.0: Added raoD, unifrac, taxonomic and evolutionary distinctiveness functions. Modified phylosor to work with non-ultrametric phylogenies. Changed name of randomizeSample to randomizeMatrix. Added functions for checking taxa label matching between phylogenies and other data.
• 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

Picante: the movie

If you liked the software, you'll love this movie depicting the history of Picante development from version 0.0 to 1.0!