caper: Comparative Analyses of Phylogenetics and Evolution in R

Functions for performing phylogenetic comparative analyses.

AuthorDavid Orme, Rob Freckleton, Gavin Thomas, Thomas Petzoldt, Susanne Fritz, Nick Isaac, Will Pearse
Date of publication2013-11-29 17:25:36
MaintainerDavid Orme <d.orme@imperial.ac.uk>
LicenseGPL (>= 2)
Version0.5.2

View on CRAN

Man pages

anova.pglm: Anova and AIC tables for 'pgls' models.

benchmarkDatasets: Datasets used for benchmarking caper

BritishBirds: Conservation status of British birds (Thomas 2008)

brunch: Comparative analysis using the brunch algorithm.

caic-class: The 'caic' S3 object class and methods

caic.diagnostics: Diagnostic tools for independent contrasts models

caic-methods: Anova and model checking methods for independent contrast...

caper-package: Comparative analysis of phylogenetics and evolution in R...

clade.matrix: Create a clade matrix from a phylogeny

clade.members: Identify tips descended from a node

comparative.data: Comparative dataset creation

crunch: Comparative analysis using the crunch algorithm.

fuscoData: Example dataset for Fusco imbalance calculations

fusco.test: Imbalance statistics using Fusco and Cronk's method.

growTree: Tree simulation with traits.

IsaacEtAl: Example dataset for the caper package

macrocaic: Comparative analysis using independent contrasts on species...

pd.calc: Calculate and bootstrap phylogenetic diversity measurements.

perrisodactyla: Example dataset for the CAIC package

pgls: Phylogenetic generalized linear models

pgls-methods: Generic model methods for 'pgls' models.

pgls.profile: Likelihood profiles and confidence intervals for 'pgls'...

phylo.d: Calculates the phylogenetic D statistic

phylo.d.subset: Calculates the phylogenetic D statistic across clades within...

plot.pglm: Diagnostic plots for 'pgls' models.

shorebird: Example dataset for the caper package

summary.caic: Summarize a crunch, brunch or macrocaic analysis

syrphidae: The syrphidae dataset of Katzourakis et al. 2001

vcv.array: Create a 2D or 3D variance-covariance matrix from a phylogeny

Files in this package

caper
caper/inst
caper/inst/doc
caper/inst/doc/caper.pdf
caper/inst/doc/caper.rnw
caper/inst/doc/caper-benchmarks.rnw
caper/inst/doc/caper-benchmarks.R
caper/inst/doc/caper-benchmarks.pdf
caper/NAMESPACE
caper/data
caper/data/fuscoData.rda
caper/data/benchBayesTraitsOutputs.rda
caper/data/benchFuscoOutputs.rda
caper/data/pglsBenchmarks.rda
caper/data/benchCrunchOutputs.rda
caper/data/BritishBirds.rda
caper/data/syrphidae.rda
caper/data/benchMacroCAICOutputs.rda
caper/data/shorebird.rda
caper/data/IsaacEtAl.rda
caper/data/benchBrunchOutputs.rda
caper/data/benchMesaOutputs.rda
caper/data/benchTestInputs.rda
caper/data/perissodactyla.rda
caper/R
caper/R/phylo.d.R caper/R/contrCalc.R caper/R/caic.diagnostics.R caper/R/brunch.R caper/R/growTree.R caper/R/macrocaic.R caper/R/fusco.R caper/R/clade.matrix.R caper/R/comparative.data.R caper/R/vcv.array.R caper/R/crunch.R caper/R/pd.calc.R caper/R/pgls.R caper/R/caic.methods.R caper/R/clade.members.R caper/R/phylo.d.subset.R
caper/vignettes
caper/vignettes/caper.rnw
caper/vignettes/caper-benchmarks.rnw
caper/vignettes/caper_refs.bib
caper/MD5
caper/README
caper/build
caper/build/vignette.rds
caper/DESCRIPTION
caper/man
caper/man/pd.calc.Rd caper/man/vcv.array.Rd caper/man/growTree.Rd caper/man/fusco.test.Rd caper/man/clade.matrix.Rd caper/man/caic-methods.Rd caper/man/BritishBirds.Rd caper/man/perrisodactyla.Rd caper/man/brunch.Rd caper/man/caper-package.Rd caper/man/caic-class.Rd caper/man/crunch.Rd caper/man/syrphidae.Rd caper/man/shorebird.Rd caper/man/fuscoData.Rd caper/man/phylo.d.subset.Rd caper/man/caic.diagnostics.Rd caper/man/macrocaic.Rd caper/man/pgls.profile.Rd caper/man/plot.pglm.Rd caper/man/benchmarkDatasets.Rd caper/man/anova.pglm.Rd caper/man/IsaacEtAl.Rd caper/man/summary.caic.Rd caper/man/clade.members.Rd caper/man/phylo.d.Rd caper/man/pgls.Rd caper/man/pgls-methods.Rd caper/man/comparative.data.Rd
caper/CHANGES

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