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pez (version 1.2-4)

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

482

Version

1.2-4

License

GPL-3

Maintainer

William Pearse

Last Published

August 31st, 2022

Functions in pez (1.2-4)

fibre.plot

fibre.plot (fibrously) plots a phylogeny
drop_tip

Trim a phylogeny
fingerprint.regression

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

Null models for functional-phylogenetic diversity
cc.manip

Manipulating and examining comparative.comm objects
comparative.comm

Creates a community comparative ecology object, the basis of all functions in pez
dist.xxx

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

eco.space scape simulation with a macro-ecological focus
eco.xxx.regression.list

List of eco.xxx.regressions
eco.xxx.regression

eco.xxx.regression
laja

Macroinvertebrate samples from the Rio Laja of Mexico
pez.endemism

Calculate (phylogenetic) endemism
pez

Phylogenetics for the Environmental Sciences
generic.metrics

Calculate any metric(s) (and compare with null distributions)
pez.evenness

Calculate (phylogenetic) evenness: examine assemblage composition and abundance
pez.metrics

Phylogenetic and functional trait metrics within pez
pez-internal

Internal pez Functions
pez.shape

Calculate (phylogenetic) shape: examine assemblage composition
pez.dissimilarity

Calculate (phylogenetic) dissimilarity: compare assemblages to one-another
pez.dispersion

Calculate (phylogenetic) dispersion: examine assemblages in the context of a source pools
traitgram.cc

Traitgram for comparative community object
scape

Simulate phylogenetic community structure across a landscape
plot.comparative.comm

Dot-plots of community presence/absence or abundance
sim.meta

Simulate a meta-community (and its phylogeny)
phy.signal

Calculate phylogenetic `signal'
sim.phy

Simulate phylogenies
trait.asm

Produces simulated communities based on species attributes
pglmm

Phylogenetic Generalised Linear Mixed Model for Community Data
phy.build

Build a novel phylogeny from existing data