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) |
| 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. |
| 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. |
| 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. |
| ed.calc | Calculate and bootstrap phylogenetic diversity measurements. |
| 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 |
| growTree | Tree simulation with traits. |
| IsaacEtAl | Example dataset for the caper package |
| 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 |
| logLik.caic | Anova and model checking methods for independent contrast models. |
| logLik.pgls | Anova and AIC tables for 'pgls' models. |
| 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 |
| na.omit.comparative.data | Comparative dataset creation |
| nobs.pgls | Generic model methods for 'pgls' models. |
| nul | Datasets used for benchmarking caper |
| 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. |
| 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. |
| 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 |
| testData | Datasets used for benchmarking caper |
| testTree | Datasets used for benchmarking caper |
| VCV.array | Create a 2D or 3D variance-covariance matrix from a phylogeny |
| [.comparative.data | Comparative dataset creation |