pez v1.2-0

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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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