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pez (version 1.2-0)

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 ('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').

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Version

Install

install.packages('pez')

Monthly Downloads

439

Version

1.2-0

License

GPL-3

Maintainer

William Pearse

Last Published

February 27th, 2019

Functions in pez (1.2-0)

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