Phylogenetics for the Environmental Sciences

Eco-phylogenetic and community phylogenetic analyses. Keeps community ecological and phylogenetic data matched up and comparable using 'comparative.comm' objects. Wrappers for common community phylogenetic indices ('pez.shape', 'pez.evenness', 'pez.dispersion', and 'pez.dissimilarity' metrics). Implementation of Cavender-Bares (2004) correlation of phylogenetic and ecological matrices ('fingerprint.regression'). Phylogenetic Generalised Linear Mixed Models (PGLMMs; 'pglmm') following Ives & Helmus (2011) and Rafferty & Ives (2013). Simulation of null assemblages, traits, and phylogenies ('scape', 'sim.meta.comm').


2019-02-26 Version 1.2-0

  • assemblage.phylogenies - bug in species dropping (affecting IAC and PAE); hat-tip to Carlos Alberto Arnillas
  • pez-pglmm-overview - minor (but very important!) correction to site and species factor creation (hat-tip to Andrew Tanentzap)
  • removed .Random.seed object in laja data
  • added congeneric.impute; fixed regular expression issues in congeneric.merge - hat-tip to Josep Padulles Cubino

2016-01-15 Version 1.1-1

  • eco.scape.R & scape.R - changed return type, stopped crashing bug on certain parameter combinations (hat-tip to Ben Weinstein)
  • metrics.R - more descriptive documentation for .pd (hat-tip to Max Farrell), IMPORTANT change to calculation of .scheiner
  • CITATION - updated now manuscript released
  • pez-pglmm-overview - new overview vignette
  • pglmm.R - corrected mis-specified documentation/code

2015-07-29 Version 1.1-0

  • metric.null.R - added generic metrics, metric null distributions, and changed wrapper naming
  • scale.R - changed return values
  • CITATION - added citation file

2015-02-10 Version 1.0-0

  • pglmm.R - created, examples added to vignette
  • comparative.comm.R - added wrappers
  • shape.R - removed PVR package dependency

Reference manual

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1.2-3 by William D. Pearse, 6 months ago

Browse source code at

Authors: William D. Pearse , Marc W. Cadotte , Jeannine Cavender-Bares , Anthony R. Ives , Caroline Tucker , Steve C. Walker , Matthew R. Helmus

Documentation:   PDF Manual  

GPL-3 license

Imports caper, picante, quantreg, mvtnorm, vegan, ade4, FD, Matrix, methods, animation, phytools

Depends on ape

Suggests knitr, lme4, formatR

Suggested by phyr.

See at CRAN