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pez (version 1.0-0)

Phylogenetics for the Environmental Sciences

Description

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 ('shape', 'evenness', 'dispersion', and 'dissimilarity' metrics). Implementation of Cavender-Bares (2004) correlation of phylogenetic and ecological matrices ('fingerprint.regression'). Phylogenetic Generalised Linear Mixed Models (PGLMMs) following ('pglmm') following Ives & Helmus (2011) and Rafferty & Ives (2013). Simulation of null assemblages, traits, and phylogenies ('scape', 'sim.meta.comm').

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Version

Install

install.packages('pez')

Monthly Downloads

393

Version

1.0-0

License

GPL-3

Maintainer

William Pearse

Last Published

February 11th, 2015

Functions in pez (1.0-0)

plot.comparative.comm

Dot-plots of community presence/absence or abundance
dist.xxx

Make co-existence matrices based on phylogeny (and/or) traits, and community or environemntal overlap
phy.signal

Calculate phylogenetic `signal'
comparative.comm

Creates a community comparative ecology object, the basis of all functions in pez
laja

Macroinvertebrate samples from the Rio Laja of Mexico
ConDivSim

Null models for functional-phylogenetic diversity
traitgram.cc

Traitgram for comparative community object
pez-internal

Internal pez Functions
cc.manip

Manipulating and examining comparative.comm objects
eco.xxx.regression

eco.xxx.regression
scape

Simulate phylogenetic community structure across a landscape
evenness

Calculate (phylogenetic) evenness: examine assemblage composition and abundance
sim.phy

Simulate phylogenies
trait.asm

Produces simulated communities based on species attributes
dispersion

Calculate (phylogenetic) dispersion: examine assemblages in the context of a source pools
eco.xxx.regression.list

List of eco.xxx.regressions
shape

Calculate (phylogenetic) shape: examine assemblage composition
phy.build

Build a novel phylogeny from existing data (based on phyloGenerator)
fingerprint.regression

Regress trait evolution against trait ecology (following Cavender-Bares et al. 2004)
dissimilarity

Calculate (phylogenetic) dissimilarity: compare assemblages to one-another
drop_tip

Trim a phylogeny
pglmm

Phylogenetic Generalised Linear Mixed Model for Community Data
pez

Phylogenetics for the Environmental Sciences
sim.meta

Simulate a meta-community (and its phylogeny)