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Picante
R tools for integrating phylogenies and ecology
                 Steven Kembel
                 David Ackerly
                Simon Blomberg
                 Will Cornwell
                  Peter Cowan
                Matthew Helmus
                 Helene Morlon
                   Cam Webb
Image courtesy Brian O’Meara
http://treetapper-dev.blogspot.com
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
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
Phylogenetic
    data


                                 Visualization

Community      vegan   Picante
   data



                                  Statistical
                                   analysis
 Trait data



                         API
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
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
Picante
http://picante.r-forge.r-project.org
     Kembel et al. 2010. Bioinformatics 26:1463-1464.

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Picante: R tools for integrating phylogenies and ecology

  • 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. Image courtesy Brian O’Meara http://treetapper-dev.blogspot.com
  • 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. 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. Phylogenetic data Visualization Community vegan Picante data Statistical analysis Trait data API
  • 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. 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. Picante http://picante.r-forge.r-project.org Kembel et al. 2010. Bioinformatics 26:1463-1464.