pez: 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').

Version:	1.2-5
Depends:	ape (≥ 3.1-4)
Imports:	caper (≥ 0.5-2), picante (≥ 1.6-2), quantreg (≥ 5.05), mvtnorm (≥ 1.0-0), vegan (≥ 2.0-10), ade4 (≥ 1.6-2), FD (≥ 1.0-12), Matrix (≥ 1.1-4), methods (≥ 3.1.0), animation (≥ 2.4-0), phytools (≥ 0.6-60)
Suggests:	knitr (≥ 1.6), lme4 (≥ 1.1-7), formatR (≥ 1.7)
Published:	2025-08-28
DOI:	10.32614/CRAN.package.pez
Author:	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]
Maintainer:	William D. Pearse <will.pearse at gmail.com>
License:	GPL-3
NeedsCompilation:	no
Citation:	pez citation info
Materials:	NEWS
In views:	MixedModels
CRAN checks:	pez results

Documentation:

Reference manual:	pez.html , pez.pdf
Vignettes:	pez-intro (source, R code) pez-pglmm-overview (source, R code)

Downloads:

Package source:	pez_1.2-5.tar.gz
Windows binaries:	r-devel: pez_1.2-5.zip, r-release: pez_1.2-5.zip, r-oldrel: pez_1.2-5.zip
macOS binaries:	r-release (arm64): pez_1.2-5.tgz, r-oldrel (arm64): pez_1.2-5.tgz, r-release (x86_64): pez_1.2-5.tgz, r-oldrel (x86_64): pez_1.2-5.tgz
Old sources:	pez archive

Reverse dependencies:

Reverse suggests:

phyr

Linking:

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