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caper (version 0.5.1)
Comparative Analyses of Phylogenetics and Evolution in R
Description
Functions for performing phylogenetic comparative analyses.
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Install
install.packages('caper')
Monthly Downloads
1,762
Version
0.5.1
License
GPL (>= 2)
Maintainer
David Orme
Last Published
November 29th, 2013
Functions in caper (0.5.1)
Search functions
IsaacEtAl
Example dataset for the caper package
fusco.test
Imbalance statistics using Fusco and Cronk's method.
anova.caic
Anova and model checking methods for independent contrast models.
clade.members
Identify tips descended from a node
caper-benchmarks
Datasets used for benchmarking caper
clade.matrix
Create a clade matrix from a phylogeny
perissodactyla
Example dataset for the CAIC package
shorebird
Example dataset for the caper package
caper-package
Comparative analysis of phylogenetics and evolution in R (caper)
brunch
Comparative analysis using the brunch algorithm.
plot.pgls
Diagnostic plots for 'pgls' models.
pgls
Phylogenetic generalized linear models
growTree
Tree simulation with traits.
VCV.array
Create a 2D or 3D variance-covariance matrix from a phylogeny
phylo.d
Calculates the phylogenetic D statistic
summary.caic
Summarize a crunch, brunch or macrocaic analysis
crunch
Comparative analysis using the crunch algorithm.
macrocaic
Comparative analysis using independent contrasts on species richness data.
phylo.d.subset
Calculates the phylogenetic D statistic across clades within a phylogeny
pgls-methods
Generic model methods for 'pgls' models.
anova.pgls
Anova and AIC tables for 'pgls' models.
syrphidae
The syrphidae dataset of Katzourakis et al. 2001
pgls.profile
Likelihood profiles and confidence intervals for 'pgls' models.
pd.calc
Calculate and bootstrap phylogenetic diversity measurements.
caic-class
The 'caic' S3 object class and methods
fuscoData
Example dataset for Fusco imbalance calculations
BritishBirds
Conservation status of British birds (Thomas 2008)
comparative.data
Comparative dataset creation
caic.diagnostics
Diagnostic tools for independent contrasts models