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

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

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