Man pages for cauphy
Trait Evolution on Phylogenies Using the Cauchy Process
| ancestral | Posterior density of a node |
| cauphylm | Phylogenetic Regression using a Cauchy Process |
| checkDuplicates | Check For Duplicated Entries |
| checkTraitTree | Check Matrix Parameter |
| check_tree | Check Binary Tree object |
| compute_vcov | Compute Approximated Variance Covariance Matrix |
| do_optim | NLOPT optimization |
| find_modes | Find modes of a distribution |
| fitCauchy | Model fitting for a Cauchy Process |
| fitCauchy.internal | Maximum Likelihood estimator for a Cauchy model |
| fit_function | Maximum Likelihood estimator for a Cauchy model |
| getBounds | Get bounds |
| getBoundsCauchy | Get bound for a Cauchy process |
| getBoundsLambda | Get bounds for a Cauchy Lambda |
| getParamNames | Get parameter names |
| getStartingValues | Get starting values |
| getStartingValuesCauchy | Get starting values for a Cauchy |
| getStartingValuesLambda | Get starting values for a Cauchy Lambda |
| hdi.ancestralCauchy | Highest (Posterior) Density Interval |
| increment | Posterior density of an increment |
| initDispersionParameter | Initialization of the dispersion parameter. |
| initLambdaParameter | Initialization of the lambda parameter. |
| initPositionParameter | Initialization of the position parameter. |
| lizards | Greater Antillean Anolis lizard dataset |
| logDensityTipsCauchy | Log Density of a Cauchy Process |
| maxLambda | Maximum lambda value |
| minusLikelihoodFixedRoot | Minus Likelihood function for a Cauchy model |
| minusLikelihoodFixedRoot_lm | Minus Likelihood function for a Cauchy model |
| minusLikelihoodFixedRoot_mu | Minus Likelihood function for a Cauchy model |
| minusLikelihoodRandomRoot | Minus Likelihood function for a Cauchy model |
| minusLikelihoodREML | Minus REML function for a Cauchy model |
| plot.ancestralCauchy | Plot for class 'ancestralCauchy' |
| plot_asr | Plot Ancestral States Reconstructions |
| plot.invisible | Invisible Plotting |
| plot.profile.cauphyfit | Plot for class 'profile.cauphyfit' |
| posteriorDensityAncestral | Posterior density of a node |
| posteriorDensityIncrement | Posterior density of an increment |
| printRTreeTest | Print a tree |
| profile.cauphyfit | Method for Profiling 'cauphyfit' Objects |
| reroottip | Re root tree at a tip |
| rTraitCauchy | Cauchy Trait Simulation |
| safe_get | Safely get element of a named vector |
| simulateTipsCauchy | Simulate using the Cauchy Process |
| transformBranchLengths | Transform branch lengths |
| vcov.cauphyfit | Generic Methods for S3 class 'cauphyfit'. |
| vcov.cauphylm | Generic Methods for S3 class 'cauphylm'. |
