Comparative Analyses of Phylogenetics and Evolution in R

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Documentation for package ‘caper’ version 1.0.3

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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