caper: Comparative Analyses of Phylogenetics and Evolution in R

Functions for performing phylogenetic comparative analyses.

AuthorDavid Orme, Rob Freckleton, Gavin Thomas, Thomas Petzoldt, Susanne Fritz, Nick Isaac, Will Pearse
Date of publication2013-11-29 17:25:36
MaintainerDavid Orme <d.orme@imperial.ac.uk>
LicenseGPL (>= 2)
Version0.5.2

View on CRAN

Man pages

anova.pglm: Anova and AIC tables for 'pgls' models.

benchmarkDatasets: Datasets used for benchmarking caper

BritishBirds: Conservation status of British birds (Thomas 2008)

brunch: Comparative analysis using the brunch algorithm.

caic-class: The 'caic' S3 object class and methods

caic.diagnostics: Diagnostic tools for independent contrasts models

caic-methods: Anova and model checking methods for independent contrast...

caper-package: Comparative analysis of phylogenetics and evolution in R...

clade.matrix: Create a clade matrix from a phylogeny

clade.members: Identify tips descended from a node

comparative.data: Comparative dataset creation

crunch: Comparative analysis using the crunch algorithm.

fuscoData: Example dataset for Fusco imbalance calculations

fusco.test: Imbalance statistics using Fusco and Cronk's method.

growTree: Tree simulation with traits.

IsaacEtAl: Example dataset for the caper package

macrocaic: Comparative analysis using independent contrasts on species...

pd.calc: Calculate and bootstrap phylogenetic diversity measurements.

perrisodactyla: Example dataset for the CAIC package

pgls: Phylogenetic generalized linear models

pgls-methods: Generic model methods for 'pgls' models.

pgls.profile: Likelihood profiles and confidence intervals for 'pgls'...

phylo.d: Calculates the phylogenetic D statistic

phylo.d.subset: Calculates the phylogenetic D statistic across clades within...

plot.pglm: Diagnostic plots for 'pgls' models.

shorebird: Example dataset for the caper package

summary.caic: Summarize a crunch, brunch or macrocaic analysis

syrphidae: The syrphidae dataset of Katzourakis et al. 2001

vcv.array: Create a 2D or 3D variance-covariance matrix from a phylogeny

Functions

anova.caic Man page
anova.caiclist Man page
anova.pgls Man page
anova.pglslist Man page
as.comparative.data Man page
as.comparative.data.growTree Man page
BayesTraitsMods Man page
benchBayesTraitsOutputs Man page
benchBrunchOutputs Man page
benchCrunchOutputs Man page
benchData Man page
benchFuscoOutputs Man page
benchMacroCAICOutputs Man page
benchMesaOutputs Man page
benchTestInputs Man page
benchTreeDicho Man page
benchTreePoly Man page
BritishBirds Man page
BritishBirds.data Man page
BritishBirds.tree Man page
brunch Man page
CAIC.BrDi1057 Man page
CAIC.BrDi1157 Man page
CAIC.BrDi813 Man page
CAIC.BrDi913 Man page
CAIC.BrPl1057 Man page
CAIC.BrPl1157 Man page
CAIC.BrPl813 Man page
CAIC.BrPl913 Man page
caic-class Man page
CAIC.CrDi213 Man page
CAIC.CrDi657 Man page
CAIC.CrPl213 Man page
CAIC.CrPl413 Man page
CAIC.CrPl657 Man page
caic.diagnostics Man page
caic.label Man page
caic.robust Man page
caicStyleArgs Man page
caic.table Man page
caper Man page
caper-benchmarks Man page
caper-package Man page
carnivora.data Man page
carnivora.tree Man page
chiroptera.data Man page
chiroptera.tree Man page
clade.matrix Man page
clade.members Man page
clade.members.list Man page
coef.caic Man page
coef.pgls Man page
[.comparative.data Man page
comparative.data Man page
contrCalc Man page
crunch Man page
ed.calc Man page
fitted.pgls Man page
fix Man page
fuscoBirdData Man page
fuscoBirdTree Man page
FuscoDiSpp Man page
FuscoDiTax Man page
FuscoPolySpp Man page
FuscoPolyTax Man page
fusco.test Man page
growTree Man page
IsaacEtAl Man page
kld Man page
klD Man page
kLd Man page
kLD Man page
Kld Man page
KlD Man page
KLd Man page
KLD Man page
logLik.caic Man page
logLik.pgls Man page
macrocaic Man page
MacroCAIC.DiSpp23 Man page
MacroCAIC.DiSpp67 Man page
MacroCAIC.DiTax23 Man page
MacroCAIC.DiTax67 Man page
MacroCAIC.PolySpp23 Man page
MacroCAIC.PolySpp67 Man page
MacroCAIC.PolyTax23 Man page
MacroCAIC.PolyTax67 Man page
marsupialia.data Man page
marsupialia.tree Man page
MeSA.I Man page
na.omit.comparative.data Man page
nobs.pgls Man page
nul Man page
pd.bootstrap Man page
pd.calc Man page
perissodactyla Man page
perissodactyla.data Man page
perissodactyla.tree Man page
pgls Man page
pgls.blenTransform Man page
pgls.likelihood Man page
pgls.profile Man page
phylo.d Man page
phylo.d.subset Man page
plot.caic Man page
plot.fusco Man page
plot.pgls Man page
plot.pgls.profile Man page
plot.phylo.d Man page
predict.caic Man page
predict.pgls Man page
primates.data Man page
primates.tree Man page
print.caic Man page
print.caic.diagnostics Man page
print.comparative.data Man page
print.fusco Man page
print.pgls Man page
print.phylo.d Man page
print.phylo.d.subset Man page
print.summary.pgls Man page
reorder.comparative.data Man page
residuals.caic Man page
residuals.pgls Man page
shorebird Man page
shorebird.data Man page
shorebird.tree Man page
subset.comparative.data Man page
summary.caic Man page
summary.fusco Man page
summary.pgls Man page
summary.phylo.d Man page
summary.phylo.d.subset Man page
syrphidae Man page
syrphidaeRich Man page
syrphidaeTree Man page
testData Man page
testTree Man page
VCV.array Man page

Files

caper
caper/inst
caper/inst/doc
caper/inst/doc/caper.pdf
caper/inst/doc/caper.rnw
caper/inst/doc/caper-benchmarks.rnw
caper/inst/doc/caper-benchmarks.R
caper/inst/doc/caper-benchmarks.pdf
caper/NAMESPACE
caper/data
caper/data/fuscoData.rda
caper/data/benchBayesTraitsOutputs.rda
caper/data/benchFuscoOutputs.rda
caper/data/pglsBenchmarks.rda
caper/data/benchCrunchOutputs.rda
caper/data/BritishBirds.rda
caper/data/syrphidae.rda
caper/data/benchMacroCAICOutputs.rda
caper/data/shorebird.rda
caper/data/IsaacEtAl.rda
caper/data/benchBrunchOutputs.rda
caper/data/benchMesaOutputs.rda
caper/data/benchTestInputs.rda
caper/data/perissodactyla.rda
caper/R
caper/R/phylo.d.R caper/R/contrCalc.R caper/R/caic.diagnostics.R caper/R/brunch.R caper/R/growTree.R caper/R/macrocaic.R caper/R/fusco.R caper/R/clade.matrix.R caper/R/comparative.data.R caper/R/vcv.array.R caper/R/crunch.R caper/R/pd.calc.R caper/R/pgls.R caper/R/caic.methods.R caper/R/clade.members.R caper/R/phylo.d.subset.R
caper/vignettes
caper/vignettes/caper.rnw
caper/vignettes/caper-benchmarks.rnw
caper/vignettes/caper_refs.bib
caper/MD5
caper/README
caper/build
caper/build/vignette.rds
caper/DESCRIPTION
caper/man
caper/man/pd.calc.Rd caper/man/vcv.array.Rd caper/man/growTree.Rd caper/man/fusco.test.Rd caper/man/clade.matrix.Rd caper/man/caic-methods.Rd caper/man/BritishBirds.Rd caper/man/perrisodactyla.Rd caper/man/brunch.Rd caper/man/caper-package.Rd caper/man/caic-class.Rd caper/man/crunch.Rd caper/man/syrphidae.Rd caper/man/shorebird.Rd caper/man/fuscoData.Rd caper/man/phylo.d.subset.Rd caper/man/caic.diagnostics.Rd caper/man/macrocaic.Rd caper/man/pgls.profile.Rd caper/man/plot.pglm.Rd caper/man/benchmarkDatasets.Rd caper/man/anova.pglm.Rd caper/man/IsaacEtAl.Rd caper/man/summary.caic.Rd caper/man/clade.members.Rd caper/man/phylo.d.Rd caper/man/pgls.Rd caper/man/pgls-methods.Rd caper/man/comparative.data.Rd
caper/CHANGES

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.