# Comparative Analyses of Phylogenetics and Evolution in R

## Documentation for package ‘caper’ version 1.0.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A B C E F G I K L M N P R S T V misc

caper-package | Comparative analysis of phylogenetics and evolution in R (caper)

## -- A --

anova.caic | Anova and model checking methods for independent contrast models.
anova.caiclist | Anova and model checking methods for independent contrast models.
anova.pgls | Anova and AIC tables for 'pgls' models.
anova.pglslist | Anova and AIC tables for 'pgls' models.
as.comparative.data | Comparative dataset creation
as.comparative.data.growTree | Tree simulation with traits.

## -- B --

BayesTraitsMods | Datasets used for benchmarking caper
benchBayesTraitsOutputs | Datasets used for benchmarking caper
benchBrunchOutputs | Datasets used for benchmarking caper
benchCrunchOutputs | Datasets used for benchmarking caper
benchData | Datasets used for benchmarking caper
benchFuscoOutputs | Datasets used for benchmarking caper
benchMacroCAICOutputs | Datasets used for benchmarking caper
benchMesaOutputs | Datasets used for benchmarking caper
benchTestInputs | Datasets used for benchmarking caper
benchTreeDicho | Datasets used for benchmarking caper
benchTreePoly | Datasets used for benchmarking caper
BritishBirds | Conservation status of British birds (Thomas 2008)
BritishBirds.data | Conservation status of British birds (Thomas 2008)
BritishBirds.tree | Conservation status of British birds (Thomas 2008)
brunch | Comparative analysis using the brunch algorithm.

## -- C --

caic-class | The 'caic' S3 object class and methods
CAIC.BrDi1057 | Datasets used for benchmarking caper
CAIC.BrDi1157 | Datasets used for benchmarking caper
CAIC.BrDi813 | Datasets used for benchmarking caper
CAIC.BrDi913 | Datasets used for benchmarking caper
CAIC.BrPl1057 | Datasets used for benchmarking caper
CAIC.BrPl1157 | Datasets used for benchmarking caper
CAIC.BrPl813 | Datasets used for benchmarking caper
CAIC.BrPl913 | Datasets used for benchmarking caper
CAIC.CrDi213 | Datasets used for benchmarking caper
CAIC.CrDi657 | Datasets used for benchmarking caper
CAIC.CrPl213 | Datasets used for benchmarking caper
CAIC.CrPl413 | Datasets used for benchmarking caper
CAIC.CrPl657 | Datasets used for benchmarking caper
caic.diagnostics | Diagnostic tools for independent contrasts models
caic.label | Diagnostic tools for independent contrasts models
caic.robust | Diagnostic tools for independent contrasts models
caic.table | Diagnostic tools for independent contrasts models
caicStyleArgs | Comparative dataset creation
caper | Comparative analysis of phylogenetics and evolution in R (caper)
caper-benchmarks | Datasets used for benchmarking caper
carnivora.data | Example dataset for the caper package
carnivora.tree | Example dataset for the caper package
chiroptera.data | Example dataset for the caper package
chiroptera.tree | Example dataset for the caper package
clade.matrix | Create a clade matrix from a phylogeny
clade.members | Identify tips descended from a node
clade.members.list | Identify tips descended from a node
coef.caic | Anova and model checking methods for independent contrast models.
coef.pgls | Generic model methods for 'pgls' models.
comparative.data | Comparative dataset creation
contrCalc | Comparative analysis using the crunch algorithm.
crunch | Comparative analysis using the crunch algorithm.

## -- E --

ed.calc | Calculate and bootstrap phylogenetic diversity measurements.

## -- F --

fitted.pgls | Generic model methods for 'pgls' models.
fix | Datasets used for benchmarking caper
fusco.test | Imbalance statistics using Fusco and Cronk's method.
fuscoBirdData | Example dataset for Fusco imbalance calculations
fuscoBirdTree | Example dataset for Fusco imbalance calculations
FuscoDiSpp | Datasets used for benchmarking caper
FuscoDiTax | Datasets used for benchmarking caper
FuscoPolySpp | Datasets used for benchmarking caper
FuscoPolyTax | Datasets used for benchmarking caper

## -- G --

growTree | Tree simulation with traits.

## -- I --

IsaacEtAl | Example dataset for the caper package

## -- K --

KLD | Datasets used for benchmarking caper
KLd | Datasets used for benchmarking caper
KlD | Datasets used for benchmarking caper
Kld | Datasets used for benchmarking caper
kLD | Datasets used for benchmarking caper
kLd | Datasets used for benchmarking caper
klD | Datasets used for benchmarking caper
kld | Datasets used for benchmarking caper

## -- L --

logLik.caic | Anova and model checking methods for independent contrast models.
logLik.pgls | Anova and AIC tables for 'pgls' models.

## -- M --

macrocaic | Comparative analysis using independent contrasts on species richness data.
MacroCAIC.DiSpp23 | Datasets used for benchmarking caper
MacroCAIC.DiSpp67 | Datasets used for benchmarking caper
MacroCAIC.DiTax23 | Datasets used for benchmarking caper
MacroCAIC.DiTax67 | Datasets used for benchmarking caper
MacroCAIC.PolySpp23 | Datasets used for benchmarking caper
MacroCAIC.PolySpp67 | Datasets used for benchmarking caper
MacroCAIC.PolyTax23 | Datasets used for benchmarking caper
MacroCAIC.PolyTax67 | Datasets used for benchmarking caper
marsupialia.data | Example dataset for the caper package
marsupialia.tree | Example dataset for the caper package
MeSA.I | Datasets used for benchmarking caper

## -- N --

na.omit.comparative.data | Comparative dataset creation
nobs.pgls | Generic model methods for 'pgls' models.
nul | Datasets used for benchmarking caper

## -- P --

pd.bootstrap | Calculate and bootstrap phylogenetic diversity measurements.
pd.calc | Calculate and bootstrap phylogenetic diversity measurements.
perissodactyla | Example dataset for the CAIC package
perissodactyla.data | Example dataset for the CAIC package
perissodactyla.tree | Example dataset for the CAIC package
pgls | Phylogenetic generalized linear models
pgls.blenTransform | Phylogenetic generalized linear models
pgls.confint | Likelihood profiles and confidence intervals for 'pgls' models.
pgls.likelihood | Phylogenetic generalized linear models
pgls.profile | Likelihood profiles and confidence intervals for 'pgls' models.
phylo.d | Calculates the phylogenetic D statistic
phylo.d.subset | Calculates the phylogenetic D statistic across clades within a phylogeny
plot.caic | Anova and model checking methods for independent contrast models.
plot.fusco | Imbalance statistics using Fusco and Cronk's method.
plot.pgls | Diagnostic plots for 'pgls' models.
plot.pgls.profile | Likelihood profiles and confidence intervals for 'pgls' models.
plot.phylo.d | Calculates the phylogenetic D statistic
predict.caic | Anova and model checking methods for independent contrast models.
predict.pgls | Generic model methods for 'pgls' models.
primates.data | Example dataset for the caper package
primates.tree | Example dataset for the caper package
print.caic | Summarize a crunch, brunch or macrocaic analysis
print.caic.diagnostics | Diagnostic tools for independent contrasts models
print.comparative.data | Comparative dataset creation
print.fusco | Imbalance statistics using Fusco and Cronk's method.
print.pgls | Generic model methods for 'pgls' models.
print.phylo.d | Calculates the phylogenetic D statistic
print.phylo.d.subset | Calculates the phylogenetic D statistic across clades within a phylogeny
print.summary.pgls | Generic model methods for 'pgls' models.

## -- R --

reorder.comparative.data | Comparative dataset creation
residuals.caic | Anova and model checking methods for independent contrast models.
residuals.pgls | Generic model methods for 'pgls' models.

## -- S --

shorebird | Example dataset for the caper package
shorebird.data | Example dataset for the caper package
shorebird.tree | Example dataset for the caper package
subset.comparative.data | Comparative dataset creation
summary.caic | Summarize a crunch, brunch or macrocaic analysis
summary.fusco | Imbalance statistics using Fusco and Cronk's method.
summary.pgls | Generic model methods for 'pgls' models.
summary.phylo.d | Calculates the phylogenetic D statistic
summary.phylo.d.subset | Calculates the phylogenetic D statistic across clades within a phylogeny
syrphidae | The syrphidae dataset of Katzourakis et al. 2001
syrphidaeRich | The syrphidae dataset of Katzourakis et al. 2001
syrphidaeTree | The syrphidae dataset of Katzourakis et al. 2001

## -- T --

testData | Datasets used for benchmarking caper
testTree | Datasets used for benchmarking caper

## -- V --

VCV.array | Create a 2D or 3D variance-covariance matrix from a phylogeny

## -- misc --

[.comparative.data | Comparative dataset creation