caper: Comparative Analyses of Phylogenetics and Evolution in R
Version 0.5.2

Functions for performing phylogenetic comparative analyses.

Browse man pages Browse package API and functions Browse package files

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
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("caper")

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

Functions

BayesTraitsMods Man page
BritishBirds Man page
BritishBirds.data Man page
BritishBirds.tree Man page
CAIC.BrDi1057 Man page
CAIC.BrDi1157 Man page
CAIC.BrDi813 Man page
CAIC.BrDi913 Man page
CAIC.BrPl1057 Man page
CAIC.BrPl1157 Man page
CAIC.BrPl813 Man page
CAIC.BrPl913 Man page
CAIC.CrDi213 Man page
CAIC.CrDi657 Man page
CAIC.CrPl213 Man page
CAIC.CrPl413 Man page
CAIC.CrPl657 Man page
FuscoDiSpp Man page
FuscoDiTax Man page
FuscoPolySpp Man page
FuscoPolyTax Man page
IsaacEtAl Man page
KLD Man page
KLd Man page
KlD Man page
Kld Man page
MacroCAIC.DiSpp23 Man page
MacroCAIC.DiSpp67 Man page
MacroCAIC.DiTax23 Man page
MacroCAIC.DiTax67 Man page
MacroCAIC.PolySpp23 Man page
MacroCAIC.PolySpp67 Man page
MacroCAIC.PolyTax23 Man page
MacroCAIC.PolyTax67 Man page
MeSA.I Man page
VCV.array Man page Source code
[.comparative.data Man page
anova.caic Man page Source code
anova.caiclist Man page Source code
anova.pgls Man page Source code
anova.pglslist Man page Source code
as.comparative.data Man page Source code Source code
as.comparative.data.growTree Man page Source code Source code
benchBayesTraitsOutputs Man page
benchBrunchOutputs Man page
benchCrunchOutputs Man page
benchData Man page
benchFuscoOutputs Man page
benchMacroCAICOutputs Man page
benchMesaOutputs Man page
benchTestInputs Man page
benchTreeDicho Man page
benchTreePoly Man page
brunch Man page Source code
caic-class Man page
caic.diagnostics Man page Source code
caic.label Man page Source code
caic.robust Man page Source code
caic.table Man page Source code
caicStyleArgs Man page Source code
caper Man page
caper-benchmarks Man page
caper-package Man page
carnivora.data Man page
carnivora.tree Man page
chiroptera.data Man page
chiroptera.tree Man page
clade.matrix Man page
clade.members Man page
clade.members.list Man page
coef.caic Man page Source code
coef.pgls Man page Source code
comparative.data Man page Source code
contrCalc Man page Source code
crunch Man page Source code
ed.calc Man page Source code
fitted.pgls Man page Source code
fix Man page
fusco.test Man page Source code
fuscoBirdData Man page
fuscoBirdTree Man page
growTree Man page Source code
kLD Man page
kLd Man page
klD Man page
kld Man page
logLik.caic Man page Source code
logLik.pgls Man page Source code
macrocaic Man page Source code
marsupialia.data Man page
marsupialia.tree Man page
na.omit.comparative.data Man page Source code
nobs.pgls Man page Source code
nul Man page
pd.bootstrap Man page
pd.calc Man page
perissodactyla Man page
perissodactyla.data Man page
perissodactyla.tree Man page
pgls Man page Source code
pgls.blenTransform Man page Source code
pgls.confint Source code
pgls.likelihood Man page Source code
pgls.profile Man page Source code
phylo.d Man page Source code
phylo.d.subset Man page Source code
plot.caic Man page Source code
plot.fusco Man page Source code
plot.pgls Man page Source code
plot.pgls.profile Man page Source code
plot.phylo.d Man page Source code
predict.caic Man page Source code
predict.pgls Man page Source code
primates.data Man page
primates.tree Man page
print.caic Man page Source code
print.caic.diagnostics Man page Source code
print.comparative.data Man page Source code
print.fusco Man page Source code
print.pgls Man page Source code
print.phylo.d Man page Source code
print.phylo.d.subset Man page Source code
print.summary.pgls Man page Source code
reorder.comparative.data Man page Source code
residuals.caic Man page Source code
residuals.pgls Man page Source code
shorebird Man page
shorebird.data Man page
shorebird.tree Man page
subset.comparative.data Man page Source code
summary.caic Man page Source code
summary.fusco Man page Source code
summary.pgls Man page Source code
summary.phylo.d Man page Source code
summary.phylo.d.subset Man page Source code
syrphidae Man page
syrphidaeRich Man page
syrphidaeTree Man page
testData Man page
testTree Man page

Files

inst
inst/doc
inst/doc/caper.pdf
inst/doc/caper.rnw
inst/doc/caper-benchmarks.rnw
inst/doc/caper-benchmarks.R
inst/doc/caper-benchmarks.pdf
NAMESPACE
data
data/fuscoData.rda
data/benchBayesTraitsOutputs.rda
data/benchFuscoOutputs.rda
data/pglsBenchmarks.rda
data/benchCrunchOutputs.rda
data/BritishBirds.rda
data/syrphidae.rda
data/benchMacroCAICOutputs.rda
data/shorebird.rda
data/IsaacEtAl.rda
data/benchBrunchOutputs.rda
data/benchMesaOutputs.rda
data/benchTestInputs.rda
data/perissodactyla.rda
R
R/phylo.d.R
R/contrCalc.R
R/caic.diagnostics.R
R/brunch.R
R/growTree.R
R/macrocaic.R
R/fusco.R
R/clade.matrix.R
R/comparative.data.R
R/vcv.array.R
R/crunch.R
R/pd.calc.R
R/pgls.R
R/caic.methods.R
R/clade.members.R
R/phylo.d.subset.R
vignettes
vignettes/caper.rnw
vignettes/caper-benchmarks.rnw
vignettes/caper_refs.bib
MD5
README
build
build/vignette.rds
DESCRIPTION
man
man/pd.calc.Rd
man/vcv.array.Rd
man/growTree.Rd
man/fusco.test.Rd
man/clade.matrix.Rd
man/caic-methods.Rd
man/BritishBirds.Rd
man/perrisodactyla.Rd
man/brunch.Rd
man/caper-package.Rd
man/caic-class.Rd
man/crunch.Rd
man/syrphidae.Rd
man/shorebird.Rd
man/fuscoData.Rd
man/phylo.d.subset.Rd
man/caic.diagnostics.Rd
man/macrocaic.Rd
man/pgls.profile.Rd
man/plot.pglm.Rd
man/benchmarkDatasets.Rd
man/anova.pglm.Rd
man/IsaacEtAl.Rd
man/summary.caic.Rd
man/clade.members.Rd
man/phylo.d.Rd
man/pgls.Rd
man/pgls-methods.Rd
man/comparative.data.Rd
CHANGES
caper documentation built on May 19, 2017, 11:23 a.m.