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caper (version 1.0.4)

Comparative Analyses of Phylogenetics and Evolution in R

Description

Functions for performing phylogenetic comparative analyses.

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Version

Install

install.packages('caper')

Monthly Downloads

1,290

Version

1.0.4

License

GPL (>= 2)

Maintainer

David Orme

Last Published

August 28th, 2025

Functions in caper (1.0.4)

pd.calc

Calculate and bootstrap phylogenetic diversity measurements.
fuscoData

Example dataset for Fusco imbalance calculations
comparative.data

Comparative dataset creation
perissodactyla

Example dataset for the CAIC package
growTree

Tree simulation with traits.
clade.members

Identify tips descended from a node
pgls-methods

Generic model methods for 'pgls' models.
fusco.test

Imbalance statistics using Fusco and Cronk's method.
summary.caic

Summarize a crunch, brunch or macrocaic analysis
pgls

Phylogenetic generalized linear models
crunch

Comparative analysis using the crunch algorithm.
shorebird

Example dataset for the caper package
pgls.profile

Likelihood profiles and confidence intervals for 'pgls' models.
plot.pgls

Diagnostic plots for 'pgls' models.
phylo.d

Calculates the phylogenetic D statistic
macrocaic

Comparative analysis using independent contrasts on species richness data.
syrphidae

The syrphidae dataset of Katzourakis et al. 2001
phylo.d.subset

Calculates the phylogenetic D statistic across clades within a phylogeny
VCV.array

Create a 2D or 3D variance-covariance matrix from a phylogeny
caper-package

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

Datasets used for benchmarking caper
BritishBirds

Conservation status of British birds (Thomas 2008)
IsaacEtAl

Example dataset for the caper package
anova.caic

Anova and model checking methods for independent contrast models.
clade.matrix

Create a clade matrix from a phylogeny
anova.pgls

Anova and AIC tables for 'pgls' models.
caic.diagnostics

Diagnostic tools for independent contrasts models
caic-class

The 'caic' S3 object class and methods
brunch

Comparative analysis using the brunch algorithm.