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 |