A B C D E F G I L P R S T W misc
pez-package | Phylogenetics for the Environmental Sciences |
as.data.frame.comparative.comm | Manipulating and examining comparative.comm objects |
assemblage.phylogenies | Manipulating and examining comparative.comm objects |
bind.replace | Build a novel phylogeny from existing data |
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 |
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.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 |
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 |
generic.metrics | Calculate any metric(s) (and compare with null distributions) |
generic.null | Calculate any metric(s) (and compare with null distributions) |
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 |
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) |
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 |
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 |
.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 |