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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 |