R: Phylogenetics for the Environmental Sciences

# Phylogenetics for the Environmental Sciences

## Documentation for package ‘pez’ version 1.2-5

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS

## Help Pages

A B C D E F G I L P R S T W misc

pez-package | Phylogenetics for the Environmental Sciences

## -- A --

as.data.frame.comparative.comm | Manipulating and examining comparative.comm objects
assemblage.phylogenies | Manipulating and examining comparative.comm objects

## -- B --

bind.replace | Build a novel phylogeny from existing data

## -- C --

cc.manip | Manipulating and examining comparative.comm objects
comm | Manipulating and examining comparative.comm objects
comm.dist | Make co-existence matrices based on phylogeny (and/or) traits, and community or environemntal overlap
comm.dist.comparative.comm | Make co-existence matrices based on phylogeny (and/or) traits, and community or environemntal overlap
comm.dist.matrix | Make co-existence matrices based on phylogeny (and/or) traits, and community or environemntal overlap
comm<- | Manipulating and examining comparative.comm objects
communityPGLMM | Phylogenetic Generalised Linear Mixed Model for Community Data
communityPGLMM.binary | Phylogenetic Generalised Linear Mixed Model for Community Data
communityPGLMM.binary.LRT | Phylogenetic Generalised Linear Mixed Model for Community Data
communityPGLMM.gaussian | Phylogenetic Generalised Linear Mixed Model for Community Data
communityPGLMM.matrix.structure | Phylogenetic Generalised Linear Mixed Model for Community Data
communityPGLMM.predicted.values | Phylogenetic Generalised Linear Mixed Model for Community Data
comparative.comm | Creates a community comparative ecology object, the basis of all functions in pez
ConDivSim | Null models for functional-phylogenetic diversity
congeneric.impute | Build a novel phylogeny from existing data
congeneric.merge | Build a novel phylogeny from existing data

## -- D --

dist.func.default | Make co-existence matrices based on phylogeny (and/or) traits, and community or environemntal overlap
dist.xxx | Make co-existence matrices based on phylogeny (and/or) traits, and community or environemntal overlap
drop_tip | Trim a phylogeny

## -- E --

eco.env.regression | eco.xxx.regression
eco.phy.regression | eco.xxx.regression
eco.scape | eco.space scape simulation with a macro-ecological focus
eco.trait.regression | eco.xxx.regression
eco.xxx.regression | eco.xxx.regression
eco.xxx.regression.list | List of eco.xxx.regressions
edge2phylo | Simulate phylogenies
env | Manipulating and examining comparative.comm objects
env.names | Manipulating and examining comparative.comm objects
env<- | Manipulating and examining comparative.comm objects

## -- F --

fibre.plot | 'fibre.plot' (fibrously) plots a phylogeny
fingerprint.regression | Regress trait evolution against trait ecology (following Cavender-Bares et al. 2004)
funct.phylo.dist | Make co-existence matrices based on phylogeny (and/or) traits, and community or environemntal overlap

## -- G --

generic.metrics | Calculate any metric(s) (and compare with null distributions)
generic.null | Calculate any metric(s) (and compare with null distributions)

## -- I --

invert.traits | Macroinvertebrate samples from the Rio Laja of Mexico
invert.tree | Macroinvertebrate samples from the Rio Laja of Mexico

## -- L --

laja | Macroinvertebrate samples from the Rio Laja of Mexico

## -- P --

package-pez | Phylogenetics for the Environmental Sciences
pez | Phylogenetics for the Environmental Sciences
pez.dispersion | Calculate (phylogenetic) dispersion: examine assemblages in the context of a source pools
pez.dissimilarity | Calculate (phylogenetic) dissimilarity: compare assemblages to one-another
pez.endemism | Calculate (phylogenetic) endemism
pez.evenness | Calculate (phylogenetic) evenness: examine assemblage composition and abundance
pez.metrics | Phylogenetic and functional trait metrics within pez
pez.shape | Calculate (phylogenetic) shape: examine assemblage composition
pglmm | Phylogenetic Generalised Linear Mixed Model for Community Data
phy | Manipulating and examining comparative.comm objects
phy.build | Build a novel phylogeny from existing data
phy.signal | Calculate phylogenetic 'signal'
phy<- | Manipulating and examining comparative.comm objects
phylo.dist | Make co-existence matrices based on phylogeny (and/or) traits, and community or environemntal overlap
phylo.dist.comparative.comm | Make co-existence matrices based on phylogeny (and/or) traits, and community or environemntal overlap
phylo.dist.phylo | Make co-existence matrices based on phylogeny (and/or) traits, and community or environemntal overlap
pianka.dist | Make co-existence matrices based on phylogeny (and/or) traits, and community or environemntal overlap
pianka.dist.comparative.comm | Make co-existence matrices based on phylogeny (and/or) traits, and community or environemntal overlap
pianka.dist.matrix | Make co-existence matrices based on phylogeny (and/or) traits, and community or environemntal overlap
plot.communityPGLMM | Phylogenetic Generalised Linear Mixed Model for Community Data
plot.comparative.comm | Dot-plots of community presence/absence or abundance
plot.eco.xxx.regression | eco.xxx.regression
plot.eco.xxx.regression.list | List of eco.xxx.regressions
plot.fingerprint.regression | Regress trait evolution against trait ecology (following Cavender-Bares et al. 2004)
princompOne | Traitgram for comparative community object
print.communityPGLMM | Phylogenetic Generalised Linear Mixed Model for Community Data
print.comparative.comm | Creates a community comparative ecology object, the basis of all functions in pez
print.eco.xxx.regression | eco.xxx.regression
print.eco.xxx.regression.list | List of eco.xxx.regressions
print.fingerprint.regression | Regress trait evolution against trait ecology (following Cavender-Bares et al. 2004)

## -- R --

river.env | Macroinvertebrate samples from the Rio Laja of Mexico
river.sites | Macroinvertebrate samples from the Rio Laja of Mexico

## -- S --

scape | Simulate phylogenetic community structure across a landscape
sim.bd.phy | Simulate phylogenies
sim.bd.tr.phy | Simulate phylogenies
sim.meta | Simulate a meta-community (and its phylogeny)
sim.meta.comm | Simulate a meta-community (and its phylogeny)
sim.meta.phy.comm | Simulate a meta-community (and its phylogeny)
sim.phy | Simulate phylogenies
sites | Manipulating and examining comparative.comm objects
sites<- | Manipulating and examining comparative.comm objects
species | Manipulating and examining comparative.comm objects
species<- | Manipulating and examining comparative.comm objects
summary.communityPGLMM | Phylogenetic Generalised Linear Mixed Model for Community Data
summary.eco.xxx.regression | eco.xxx.regression
summary.eco.xxx.regression.list | List of eco.xxx.regressions
summary.fingerprint.regression | Regress trait evolution against trait ecology (following Cavender-Bares et al. 2004)

## -- T --

trait.asm | Produces simulated communities based on species attributes
trait.names | Manipulating and examining comparative.comm objects
traitgram.cc | Traitgram for comparative community object
traits | Manipulating and examining comparative.comm objects
traits.dist | Make co-existence matrices based on phylogeny (and/or) traits, and community or environemntal overlap
traits.dist.comparative.comm | Make co-existence matrices based on phylogeny (and/or) traits, and community or environemntal overlap
traits.dist.data.frame | Make co-existence matrices based on phylogeny (and/or) traits, and community or environemntal overlap
traits.dist.default | Make co-existence matrices based on phylogeny (and/or) traits, and community or environemntal overlap
traits<- | Manipulating and examining comparative.comm objects
tree | Manipulating and examining comparative.comm objects
tree<- | Manipulating and examining comparative.comm objects

## -- W --

within.comparative.comm | Manipulating and examining comparative.comm objects

## -- misc --

.aed | Phylogenetic and functional trait metrics within pez
.bed | Phylogenetic and functional trait metrics within pez
.comdist | Phylogenetic and functional trait metrics within pez
.d | Phylogenetic and functional trait metrics within pez
.delta | Phylogenetic and functional trait metrics within pez
.dist.fd | Phylogenetic and functional trait metrics within pez
.eaed | Phylogenetic and functional trait metrics within pez
.eed | Phylogenetic and functional trait metrics within pez
.eigen.sum | Phylogenetic and functional trait metrics within pez
.gamma | Phylogenetic and functional trait metrics within pez
.haed | Phylogenetic and functional trait metrics within pez
.hed | Phylogenetic and functional trait metrics within pez
.iac | Phylogenetic and functional trait metrics within pez
.innd | Phylogenetic and functional trait metrics within pez
.kappa | Phylogenetic and functional trait metrics within pez
.lambda | Phylogenetic and functional trait metrics within pez
.metric.null | Calculate any metric(s) (and compare with null distributions)
.mipd | Phylogenetic and functional trait metrics within pez
.mntd | Phylogenetic and functional trait metrics within pez
.mpd | Phylogenetic and functional trait metrics within pez
.pae | Phylogenetic and functional trait metrics within pez
.pcd | Phylogenetic and functional trait metrics within pez
.pd | Phylogenetic and functional trait metrics within pez
.pe | Phylogenetic and functional trait metrics within pez
.phylo.entropy | Phylogenetic and functional trait metrics within pez
.phylosor | Phylogenetic and functional trait metrics within pez
.pse | Phylogenetic and functional trait metrics within pez
.psr | Phylogenetic and functional trait metrics within pez
.psv | Phylogenetic and functional trait metrics within pez
.rao | Phylogenetic and functional trait metrics within pez
.scheiner | Phylogenetic and functional trait metrics within pez
.ses | Calculate any metric(s) (and compare with null distributions)
.ses.innd | Phylogenetic and functional trait metrics within pez
.ses.mipd | Phylogenetic and functional trait metrics within pez
.ses.mntd | Phylogenetic and functional trait metrics within pez
.ses.mpd | Phylogenetic and functional trait metrics within pez
.ses.vntd | Phylogenetic and functional trait metrics within pez
.ses.vpd | Phylogenetic and functional trait metrics within pez
.simpson.phylogenetic | Phylogenetic and functional trait metrics within pez
.sqrt.phy | Phylogenetic and functional trait metrics within pez
.taxon | Phylogenetic and functional trait metrics within pez
.unifrac | Phylogenetic and functional trait metrics within pez
.vntd | Phylogenetic and functional trait metrics within pez
.vpd | Phylogenetic and functional trait metrics within pez
[.comparative.comm | Manipulating and examining comparative.comm objects
_PACKAGE | Phylogenetics for the Environmental Sciences