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Picante: R tools for integrating phylogenies and ecology

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A lightning talk presented at the iEvoBio meeting

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Picante: R tools for integrating phylogenies and ecology

  1. 1. Picante R tools for integrating phylogenies and ecology Steven Kembel David Ackerly Simon Blomberg Will Cornwell Peter Cowan Matthew Helmus Helene Morlon Cam Webb
  2. 2. Image courtesy Brian O’Meara http://treetapper-dev.blogspot.com
  3. 3. Phylogenies and ecology   Rapid growth in the use of phylogenetic information in ecology   phylogenetic diversity   conservation prioritization   Barriers to the use of phylogenetic information in ecology include   lack of open-source implementations of methods   methods implemented in different software packages
  4. 4. Picante   R package for analyzing phylogenetic and ecological data   Phylogenetic diversity   Phylogenetic signal   Open source, collaborative   Heavy lifting in C   Leverages methods already available in the R language and environment   >2430 R packages!   CRAN Task Views for Phylogenetics and Ecology
  5. 5. Phylogenetic data Visualization Community vegan Picante data Statistical analysis Trait data API
  6. 6. Phylogenetic diversity   Phylogenetic relatedness within and among ecological communities   Faith’s PD   Mean pairwise distance   Mean nearest taxon distance   Phylogenetic distance – species co-occurrence regressions   Phylogenetic species richness/variance/evenness   Rao’s quadratic entropy   Taxonomic distinctness index   PhyloSor   UniFrac
  7. 7. Phylogenetic signal   K statistic   Phylogenetic signal relative to Brownian motion   Phylogenetic bipartite model   Phylogenetic signal in species associations   Plants and pollinators   Predators and prey Miscellany   Independent contrasts for traits with circular distributions   Community data randomization and null models   Traitgrams
  8. 8. Picante http://picante.r-forge.r-project.org Kembel et al. 2010. Bioinformatics 26:1463-1464.

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