Package: caper 1.0.4
caper: Comparative Analyses of Phylogenetics and Evolution in R
Functions for performing phylogenetic comparative analyses.
Authors:
caper_1.0.4.tar.gz
caper_1.0.4.zip(r-4.7)caper_1.0.4.zip(r-4.6)caper_1.0.4.zip(r-4.5)
caper_1.0.4.tgz(r-4.6-any)caper_1.0.4.tgz(r-4.5-any)
caper_1.0.4.tar.gz(r-4.7-any)caper_1.0.4.tar.gz(r-4.6-any)
caper_1.0.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
caper/json (API)
| # Install 'caper' in R: |
| install.packages('caper', repos = c('https://davidorme.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/davidorme/caper/issues
Datasets:
- BayesTraitsMods - Datasets used for benchmarking caper
- benchData - Datasets used for benchmarking caper
- benchTreeDicho - Datasets used for benchmarking caper
- benchTreePoly - Datasets used for benchmarking caper
- BritishBirds.data - Conservation status of British birds
- BritishBirds.tree - Conservation status of British birds
- 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
- 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
- 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
- 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
- perissodactyla.data - Example dataset for the CAIC package
- perissodactyla.tree - Example dataset for the CAIC package
- primates.data - Example dataset for the caper package
- primates.tree - Example dataset for the caper package
- shorebird.data - Example dataset for the caper package
- shorebird.tree - Example dataset for the caper package
- syrphidaeRich - The syrphidae dataset of Katzourakis et al. 2001
- syrphidaeTree - The syrphidae dataset of Katzourakis et al. 2001
- testData - Datasets used for benchmarking caper
- testTree - Datasets used for benchmarking caper
Last updated from:a446e20b7c. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 139 | ||
| source / vignettes | OK | 184 | ||
| linux-release-x86_64 | OK | 127 | ||
| macos-release-arm64 | OK | 137 | ||
| macos-oldrel-arm64 | OK | 143 | ||
| windows-devel | OK | 99 | ||
| windows-release | OK | 80 | ||
| windows-oldrel | OK | 110 | ||
| wasm-release | OK | 132 |
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
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| 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 methods | caic-class |
| Diagnostic tools for independent contrasts models | caic.diagnostics caic.label caic.robust caic.table print.caic.diagnostics |
| Datasets used for benchmarking caper | BayesTraitsMods 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 phylogeny | clade.matrix |
| Identify tips descended from a node | clade.members clade.members.list |
| Comparative dataset creation | as.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 calculations | fuscoBirdData fuscoBirdTree |
| Tree simulation with traits. | as.comparative.data.growTree growTree |
| Example dataset for the caper package | carnivora.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 package | perissodactyla perissodactyla.data perissodactyla.tree |
| Phylogenetic generalized linear models | pgls 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 statistic | phylo.d plot.phylo.d print.phylo.d summary.phylo.d |
| Calculates the phylogenetic D statistic across clades within a phylogeny | phylo.d.subset print.phylo.d.subset summary.phylo.d.subset |
| Diagnostic plots for 'pgls' models. | plot.pgls |
| Example dataset for the caper package | shorebird shorebird.data shorebird.tree |
| Summarize a crunch, brunch or macrocaic analysis | print.caic summary.caic |
| The syrphidae dataset of Katzourakis et al. 2001 | syrphidae syrphidaeRich syrphidaeTree |
| Create a 2D or 3D variance-covariance matrix from a phylogeny | VCV.array |
