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').


Reference manual

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install.packages("pez")

1.2-5 by William D. Pearse, a year ago


Browse source code at https://github.com/cran/pez


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


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