pez: Phylogenetics for the Environmental Sciences

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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').

Author
William D. Pearse, Marc W. Cadotte, Jeannine Cavender-Bares, Anthony R. Ives, Caroline Tucker, Steve C. Walker, Matthew R. Helmus
Date of publication
2016-01-15 17:59:25
Maintainer
William D. Pearse <will.pearse@gmail.com>
License
GPL-3
Version
1.1-1

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

Files in this package

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