Phylogenetics for the Environmental Sciences


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Documentation for package ‘pez’ version 1.0-0

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pez-package Phylogenetics for the Environmental Sciences
assemblage.phylogenies Manipulating and examining comparative.comm objects
bind.replace Build a novel phylogeny from existing data (based on phyloGenerator)
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.merge Build a novel phylogeny from existing data (based on phyloGenerator)
dispersion Calculate (phylogenetic) dispersion: examine assemblages in the context of a source pools
dissimilarity Calculate (phylogenetic) dissimilarity: compare assemblages to one-another
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
eco.env.regression eco.xxx.regression
eco.phy.regression eco.xxx.regression
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
evenness Calculate (phylogenetic) evenness: examine assemblage composition and abundance
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
invert.traits Macroinvertebrate samples from the Rio Laja of Mexico
invert.tree Macroinvertebrate samples from the Rio Laja of Mexico
laja Macroinvertebrate samples from the Rio Laja of Mexico
package-pez Phylogenetics for the Environmental Sciences
pez Phylogenetics for the Environmental Sciences
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 (based on phyloGenerator)
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)
river.env Macroinvertebrate samples from the Rio Laja of Mexico
river.sites Macroinvertebrate samples from the Rio Laja of Mexico
scape Simulate phylogenetic community structure across a landscape
shape Calculate (phylogenetic) shape: examine assemblage composition
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)
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
within.comparative.comm Manipulating and examining comparative.comm objects
[.comparative.comm Manipulating and examining comparative.comm objects