pez: Phylogenetics for the Environmental Sciences

Eco-phylogenetic and community phylogenetic analyses. Keeps community ecological and phylogenetic data matched up and comparable using 'comparative.comm' objects. Wrappers for common community phylogenetic indices ('pez.shape', 'pez.evenness', 'pez.dispersion', and 'pez.dissimilarity' metrics). Implementation of Cavender-Bares (2004) correlation of phylogenetic and ecological matrices ('fingerprint.regression'). Phylogenetic Generalised Linear Mixed Models (PGLMMs; 'pglmm') following Ives & Helmus (2011) and Rafferty & Ives (2013). Simulation of null assemblages, traits, and phylogenies ('scape', 'sim.meta.comm').

AuthorWilliam D. Pearse, Marc W. Cadotte, Jeannine Cavender-Bares, Anthony R. Ives, Caroline Tucker, Steve C. Walker, Matthew R. Helmus
Date of publication2016-01-15 17:59:25
MaintainerWilliam D. Pearse <will.pearse@gmail.com>
LicenseGPL-3
Version1.1-1

View on CRAN

Man pages

cc.manip: Manipulating and examining comparative.comm objects

comparative.comm: Creates a community comparative ecology object, the basis of...

ConDivSim: Null models for functional-phylogenetic diversity

dist.xxx: Make co-existence matrices based on phylogeny (and/or)...

drop_tip: Trim a phylogeny

eco.scape: eco.space scape simulation with a macro-ecological focus

eco.xxx.regression: eco.xxx.regression

eco.xxx.regression.list: List of eco.xxx.regressions

fingerprint.regression: Regress trait evolution against trait ecology (following...

generic.metrics: Calculate any metric(s) (and compare with null distributions)

laja: Macroinvertebrate samples from the Rio Laja of Mexico

pez: Phylogenetics for the Environmental Sciences

pez.dispersion: Calculate (phylogenetic) dispersion: examine assemblages in...

pez.dissimilarity: Calculate (phylogenetic) dissimilarity: compare assemblages...

pez.evenness: Calculate (phylogenetic) evenness: examine assemblage...

pez-internal: Internal pez Functions

pez.metrics: Phylogenetic and functional trait metrics within pez

pez.shape: Calculate (phylogenetic) shape: examine assemblage...

pglmm: Phylogenetic Generalised Linear Mixed Model for Community...

phy.build: Build a novel phylogeny from existing data (based on...

phy.signal: Calculate phylogenetic 'signal'

plot.comparative.comm: Dot-plots of community presence/absence or abundance

scape: Simulate phylogenetic community structure across a landscape

sim.meta: Simulate a meta-community (and its phylogeny)

sim.phy: Simulate phylogenies

trait.asm: Produces simulated communities based on species attributes

traitgram.cc: Traitgram for comparative community object

Functions

.aed Man page
as.data.frame.comparative.comm Man page
assemblage.phylogenies Man page
bind.replace Man page
cc.manip Man page
.colless Man page
.comdist Man page
comm Man page
comm<- Man page
comm.dist Man page
comm.dist.comparative.comm Man page
comm.dist.matrix Man page
communityPGLMM Man page
communityPGLMM.binary Man page
communityPGLMM.binary.LRT Man page
communityPGLMM.gaussian Man page
communityPGLMM.matrix.structure Man page
communityPGLMM.predicted.values Man page
[.comparative.comm Man page
comparative.comm Man page
ConDivSim Man page
congeneric.merge Man page
.d Man page
.delta Man page
.dist.fd Man page
dist.func.default Man page
dist.xxx Man page
drop_tip Man page
.eaed Man page
eco.env.regression Man page
.eco.evo.clade.regression Man page
.eco.evo.regression Man page
.eco.null Man page
.eco.phy.regression Man page
eco.phy.regression Man page
eco.scape Man page
eco.trait.regression Man page
eco.xxx.regression Man page
eco.xxx.regression.list Man page
edge2phylo Man page
.eed Man page
.eigen.sum Man page
env Man page
env<- Man page
env.names Man page
fingerprint.regression Man page
funct.phylo.dist Man page
.gamma Man page
generic.metrics Man page
generic.null Man page
.haed Man page
.hed Man page
.iac Man page
.innd Man page
invert.traits Man page
invert.tree Man page
.kappa Man page
laja Man page
.lambda Man page
.metric.null Man page
.mipd Man page
.mntd Man page
.mpd Man page
package-pez Man page
.pae Man page
.pcd Man page
.pd Man page
pez Man page
pez.dispersion Man page
pez.dissimilarity Man page
pez.evenness Man page
pez.metrics Man page
pez-package Man page
pez.shape Man page
pglmm Man page
phy Man page
phy<- Man page
phy.build Man page
phylo.dist Man page
phylo.dist.comparative.comm Man page
phylo.dist.phylo Man page
.phylo.entropy Man page
.phylosor Man page
phy.signal Man page
pianka.dist Man page
pianka.dist.comparative.comm Man page
pianka.dist.matrix Man page
plot.communityPGLMM Man page
plot.comparative.comm Man page
plot.eco.xxx.regression Man page
plot.eco.xxx.regression.list Man page
plot.fingerprint.regression Man page
.plot.regression Man page
.prepare.regression.output Man page
princompOne Man page
print.comparative.comm Man page
print.eco.xxx.regression Man page
print.eco.xxx.regression.list Man page
print.fingerprint.regression Man page
.pse Man page
.psr Man page
.psv Man page
.Random.seed Man page
.rao Man page
.removeErrors Man page
river.env Man page
river.sites Man page
scape Man page
.scheiner Man page
.ses Man page
.ses.innd Man page
.ses.mipd Man page
.ses.mntd Man page
.ses.mpd Man page
sim.bd.phy Man page
sim.bd.tr.phy Man page
sim.meta Man page
sim.meta.comm Man page
sim.meta.phy.comm Man page
sim.phy Man page
.simpson.phylogenetic Man page
sites Man page
sites<- Man page
species Man page
species<- Man page
.sqrt.phy Man page
summary.communityPGLMM Man page
summary.eco.xxx.regression Man page
summary.eco.xxx.regression.list Man page
summary.fingerprint.regression Man page
summary.phy.structure Man page
.summary.regression Man page
.taxon Man page
trait.asm Man page
traitgram.cc Man page
trait.names Man page
traits Man page
traits<- Man page
traits.dist Man page
traits.dist.comparative.comm Man page
traits.dist.data.frame Man page
traits.dist.default Man page
tree Man page
tree<- Man page
.unifrac Man page
within.comparative.comm Man page

Files

pez
pez/inst
pez/inst/CITATION
pez/inst/tests
pez/inst/tests/test_scape.R
pez/inst/tests/test_eco.phy.regression.R
pez/inst/tests/test_metrics.R
pez/inst/tests/test_traits.R
pez/inst/tests/test_eco.trait.regression.R
pez/inst/tests/test_metapop.sim.R
pez/inst/tests/test_phy.signal.R
pez/inst/tests/test_eco.env.regression.R
pez/inst/tests/test_metric_wrappers.R
pez/inst/tests/test_comparative.comm.R
pez/inst/tests/test_plots.R
pez/inst/tests/test_dist.R
pez/inst/tests/test_fingerprint.regression.R
pez/inst/tests/test_phy.build.R
pez/inst/tests/test_phy.sim.R
pez/inst/tests/test_pglmm.R
pez/inst/doc
pez/inst/doc/pez-pglmm-overview.R
pez/inst/doc/pez-pglmm-overview.Rnw
pez/inst/doc/pez-intro.Rnw
pez/inst/doc/pez-intro.R
pez/inst/doc/pez-intro.pdf
pez/inst/doc/pez-pglmm-overview.pdf
pez/NAMESPACE
pez/NEWS
pez/data
pez/data/laja.RData
pez/R
pez/R/fingerprint.regression.R pez/R/dispersion.R pez/R/phy.signal.R pez/R/eco.env.regression.R pez/R/eco.trait.regression.R pez/R/plotting.R pez/R/dissimilarity.R pez/R/pglmm.R pez/R/eco.scape.R pez/R/pez-package.R pez/R/dist.matrix.R pez/R/metrics.R pez/R/laja.R pez/R/shape.R pez/R/utility.R pez/R/traits.R pez/R/comparative.comm.R pez/R/phy.build.R pez/R/phy.sim.R pez/R/eco.phy.regression.R pez/R/metric.null.R pez/R/metapop.sim.R pez/R/scape.R pez/R/evenness.R
pez/vignettes
pez/vignettes/fingerprint_regression.png
pez/vignettes/pez-pglmm-overview.Rnw
pez/vignettes/pez-intro.Rnw
pez/MD5
pez/build
pez/build/vignette.rds
pez/DESCRIPTION
pez/man
pez/man/pez.metrics.Rd pez/man/laja.Rd pez/man/pez-internal.Rd pez/man/pez.dispersion.Rd pez/man/pez.shape.Rd pez/man/dist.xxx.Rd pez/man/trait.asm.Rd pez/man/fingerprint.regression.Rd pez/man/eco.xxx.regression.list.Rd pez/man/scape.Rd pez/man/cc.manip.Rd pez/man/sim.meta.Rd pez/man/ConDivSim.Rd pez/man/pez.dissimilarity.Rd pez/man/phy.signal.Rd pez/man/eco.xxx.regression.Rd pez/man/drop_tip.Rd pez/man/eco.scape.Rd pez/man/pglmm.Rd pez/man/pez.evenness.Rd pez/man/pez.Rd pez/man/traitgram.cc.Rd pez/man/plot.comparative.comm.Rd pez/man/comparative.comm.Rd pez/man/generic.metrics.Rd pez/man/sim.phy.Rd pez/man/phy.build.Rd

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