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caper (version 1.0.3)

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

1,834

Version

1.0.3

License

GPL (>= 2)

Maintainer

David Orme

Last Published

September 26th, 2023

Functions in caper (1.0.3)

clade.members

Identify tips descended from a node
perissodactyla

Example dataset for the CAIC package
macrocaic

Comparative analysis using independent contrasts on species richness data.
crunch

Comparative analysis using the crunch algorithm.
fusco.test

Imbalance statistics using Fusco and Cronk's method.
pd.calc

Calculate and bootstrap phylogenetic diversity measurements.
fuscoData

Example dataset for Fusco imbalance calculations
phylo.d

Calculates the phylogenetic D statistic
phylo.d.subset

Calculates the phylogenetic D statistic across clades within a phylogeny
comparative.data

Comparative dataset creation
growTree

Tree simulation with traits.
pgls

Phylogenetic generalized linear models
syrphidae

The syrphidae dataset of Katzourakis et al. 2001
summary.caic

Summarize a crunch, brunch or macrocaic analysis
pgls-methods

Generic model methods for 'pgls' models.
pgls.profile

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

Diagnostic plots for 'pgls' models.
shorebird

Example dataset for the caper package
VCV.array

Create a 2D or 3D variance-covariance matrix from a phylogeny
anova.caic

Anova and model checking methods for independent contrast models.
caper-benchmarks

Datasets used for benchmarking caper
BritishBirds

Conservation status of British birds (Thomas 2008)
IsaacEtAl

Example dataset for the caper package
anova.pgls

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

Diagnostic tools for independent contrasts models
caper-package

Comparative analysis of phylogenetics and evolution in R (caper)
clade.matrix

Create a clade matrix from a phylogeny
caic-class

The 'caic' S3 object class and methods
brunch

Comparative analysis using the brunch algorithm.