Package: caper 1.0.3

caper: Comparative Analyses of Phylogenetics and Evolution in R

Functions for performing phylogenetic comparative analyses.

Authors:David Orme [aut, cre], Rob Freckleton [aut], Gavin Thomas [aut], Thomas Petzoldt [aut], Susanne Fritz [aut], Nick Isaac [aut], Will Pearse [aut]

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caper.pdf |caper.html✨
caper/json (API)

# Install 'caper' in R:
install.packages('caper', repos = c('https://davidorme.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/davidorme/caper/issues

Datasets:

On CRAN:

7.37 score 1 stars 5 packages 764 scripts 2.0k downloads 204 mentions 64 exports 7 dependencies

Last updated 1 years agofrom:a6723a4db0. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 15 2024
R-4.5-winNOTENov 15 2024
R-4.5-linuxNOTENov 15 2024
R-4.4-winNOTENov 15 2024
R-4.4-macNOTENov 15 2024
R-4.3-winOKNov 15 2024
R-4.3-macOKNov 15 2024

Exports:[.comparative.dataanova.caicanova.caiclistanova.pglsanova.pglslistas.comparative.dataas.comparative.data.growTreebrunchcaic.diagnosticscaic.labelcaic.robustcaic.tablecaicStyleArgsclade.matrixclade.membersclade.members.listcoef.caiccoef.pglscomparative.datacontrCalccrunched.calcfitted.pglsfusco.testgrowTreelogLik.caiclogLik.pglsmacrocaicna.omit.comparative.datanobs.pglspd.bootstrappd.calcpglspgls.blenTransformpgls.confintpgls.likelihoodpgls.profilephylo.dphylo.d.subsetplot.caicplot.fuscoplot.pglsplot.pgls.profileplot.phylo.dpredict.caicpredict.pglsprint.caicprint.caic.diagnosticsprint.comparative.dataprint.fuscoprint.pglsprint.phylo.dprint.phylo.d.subsetprint.summary.pglsreorder.comparative.dataresiduals.caicresiduals.pglssubset.comparative.datasummary.caicsummary.fuscosummary.pglssummary.phylo.dsummary.phylo.d.subsetVCV.array

Dependencies:apedigestlatticeMASSmvtnormnlmeRcpp

Comparative analysis of phylogenetics and evolution in R

Rendered fromcaper.rnwusingutils::Sweaveon Nov 15 2024.

Last update: 2023-07-03
Started: 2023-06-28

Readme and manuals

Help Manual

Help pageTopics
Comparative analysis of phylogenetics and evolution in R (caper)caper-package caper
Anova and model checking methods for independent contrast models.anova.caic anova.caiclist coef.caic logLik.caic plot.caic predict.caic residuals.caic
Anova and AIC tables for 'pgls' models.anova.pgls anova.pglslist logLik.pgls
Conservation status of British birds (Thomas 2008)BritishBirds BritishBirds.data BritishBirds.tree
Comparative analysis using the brunch algorithm.brunch
The 'caic' S3 object class and methodscaic-class
Diagnostic tools for independent contrasts modelscaic.diagnostics caic.label caic.robust caic.table print.caic.diagnostics
Datasets used for benchmarking caperBayesTraitsMods benchBayesTraitsOutputs benchBrunchOutputs benchCrunchOutputs benchData benchFuscoOutputs benchMacroCAICOutputs benchMesaOutputs benchTestInputs benchTreeDicho benchTreePoly CAIC.BrDi1057 CAIC.BrDi1157 CAIC.BrDi813 CAIC.BrDi913 CAIC.BrPl1057 CAIC.BrPl1157 CAIC.BrPl813 CAIC.BrPl913 CAIC.CrDi213 CAIC.CrDi657 CAIC.CrPl213 CAIC.CrPl413 CAIC.CrPl657 caper-benchmarks fix FuscoDiSpp FuscoDiTax FuscoPolySpp FuscoPolyTax KLD KLd KlD Kld kLD kLd klD kld MacroCAIC.DiSpp23 MacroCAIC.DiSpp67 MacroCAIC.DiTax23 MacroCAIC.DiTax67 MacroCAIC.PolySpp23 MacroCAIC.PolySpp67 MacroCAIC.PolyTax23 MacroCAIC.PolyTax67 MeSA.I nul testData testTree
Create a clade matrix from a phylogenyclade.matrix
Identify tips descended from a nodeclade.members clade.members.list
Comparative dataset creationas.comparative.data caicStyleArgs comparative.data na.omit.comparative.data print.comparative.data reorder.comparative.data subset.comparative.data [.comparative.data
Comparative analysis using the crunch algorithm.contrCalc crunch
Imbalance statistics using Fusco and Cronk's method.fusco.test plot.fusco print.fusco summary.fusco
Example dataset for Fusco imbalance calculationsfuscoBirdData fuscoBirdTree
Tree simulation with traits.as.comparative.data.growTree growTree
Example dataset for the caper packagecarnivora.data carnivora.tree chiroptera.data chiroptera.tree IsaacEtAl marsupialia.data marsupialia.tree primates.data primates.tree
Comparative analysis using independent contrasts on species richness data.macrocaic
Calculate and bootstrap phylogenetic diversity measurements.ed.calc pd.bootstrap pd.calc
Example dataset for the CAIC packageperissodactyla perissodactyla.data perissodactyla.tree
Phylogenetic generalized linear modelspgls pgls.blenTransform pgls.likelihood
Generic model methods for 'pgls' models.coef.pgls fitted.pgls nobs.pgls predict.pgls print.pgls print.summary.pgls residuals.pgls summary.pgls
Likelihood profiles and confidence intervals for 'pgls' models.pgls.confint pgls.profile plot.pgls.profile
Calculates the phylogenetic D statisticphylo.d plot.phylo.d print.phylo.d summary.phylo.d
Calculates the phylogenetic D statistic across clades within a phylogenyphylo.d.subset print.phylo.d.subset summary.phylo.d.subset
Diagnostic plots for 'pgls' models.plot.pgls
Example dataset for the caper packageshorebird shorebird.data shorebird.tree
Summarize a crunch, brunch or macrocaic analysisprint.caic summary.caic
The syrphidae dataset of Katzourakis et al. 2001syrphidae syrphidaeRich syrphidaeTree
Create a 2D or 3D variance-covariance matrix from a phylogenyVCV.array