caper: Comparative Analyses of Phylogenetics and Evolution in R

Functions for performing phylogenetic comparative analyses.

Author
David Orme, Rob Freckleton, Gavin Thomas, Thomas Petzoldt, Susanne Fritz, Nick Isaac, Will Pearse
Date of publication
2013-11-29 17:25:36
Maintainer
David Orme <d.orme@imperial.ac.uk>
License
GPL (>= 2)
Version
0.5.2

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