Phylogenetics for the Environmental Sciences

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Documentation for package ‘pez’ version 1.2-4

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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.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