pez v1.2-0

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by William Pearse View Source

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').

Functions in pez

Name	Description
comparative.comm	Creates a community comparative ecology object, the basis of all functions in pez
drop_tip	Trim a phylogeny
pez.shape	Calculate (phylogenetic) shape: examine assemblage composition
fingerprint.regression	Regress trait evolution against trait ecology (following Cavender-Bares et al. 2004)
pez.dispersion	Calculate (phylogenetic) dispersion: examine assemblages in the context of a source pools
pez.metrics	Phylogenetic and functional trait metrics within pez
eco.scape	eco.space scape simulation with a macro-ecological focus
dist.xxx	Make co-existence matrices based on phylogeny (and/or) traits, and community or environemntal overlap
pez.dissimilarity	Calculate (phylogenetic) dissimilarity: compare assemblages to one-another
sim.meta	Simulate a meta-community (and its phylogeny)
scape	Simulate phylogenetic community structure across a landscape
pez-internal	Internal pez Functions
pez	Phylogenetics for the Environmental Sciences
trait.asm	Produces simulated communities based on species attributes
sim.phy	Simulate phylogenies
phy.build	Build a novel phylogeny from existing data
pglmm	Phylogenetic Generalised Linear Mixed Model for Community Data
cc.manip	Manipulating and examining comparative.comm objects
generic.metrics	Calculate any metric(s) (and compare with null distributions)
laja	Macroinvertebrate samples from the Rio Laja of Mexico
traitgram.cc	Traitgram for comparative community object
ConDivSim	Null models for functional-phylogenetic diversity
eco.xxx.regression.list	List of eco.xxx.regressions
eco.xxx.regression	eco.xxx.regression
fibre.plot	fibre.plot (fibrously) plots a phylogeny
pez.endemism	Calculate (phylogenetic) endemism
pez.evenness	Calculate (phylogenetic) evenness: examine assemblage composition and abundance
phy.signal	Calculate phylogenetic `signal'
plot.comparative.comm	Dot-plots of community presence/absence or abundance
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Vignettes of pez

Name
fingerprint_regression.png
pez-intro.Rnw
pez-pglmm-overview.Rnw
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Details

Type	Package
License	GPL-3
VignetteBuilder	knitr
RoxygenNote	6.1.1
NeedsCompilation	no
Packaged	2019-02-27 05:07:47 UTC; will
Repository	CRAN
Date/Publication	2019-02-27 05:40:03 UTC

imports	ade4 (>= 1.6-2) , animation (>= 2.4-0) , apTreeshape (>= 1.4-5) , caper (>= 0.5-2) , FD (>= 1.0-12) , Matrix (>= 1.1-4) , methods (>= 3.1.0) , mvtnorm (>= 1.0-0) , phytools (>= 0.6-60) , picante (>= 1.6-2) , quantreg (>= 5.05) , vegan (>= 2.0-10)
depends	ape (>= 3.1-4)
suggests	knitr (>= 1.6) , lme4 (>= 1.1-7)
Contributors	Anthony Ives, William Pearse, Marc Cadotte, Jeannine Cavender-Bares, Caroline Tucker, Steve Walker, Matthew Helmus