All functions

CollectBootstrapResults()

Collect the results from a parametric bootstrap MGPM fit

DefaultArgsConfigOptim()

Specify arguments for PCMFit during calls to PCMFitMixed.

GuessInitVecParams()

A heuristic-based guess of the optimal parameters of a model

HashCodes()

Generate hash codes.

JitterModelParams()

Add random white noise to the parameters of a model.

LookupFit()

Lookup a fit vector for a given tree and model mapping in a data.table of previously run fits.

MatchModelMapping()

Match a model mapping vector against a vector of model types

PCMFit()

Fitting a PCM model

PCMFitDemoObjects

Demo objects for the PCMFit package

PCMFitMixed()

Search for an optimal mixed Gaussian phylogenetic model, given a tree, trait measurements at its tips and a score function.

PCMIteratorMapping()

Iterator over combinations with repetions of a given set of modelTypes

PCMNextMapping()

Generate the next mapping of model-types chosen from regime-specific sets of possible model-types.

RetrieveBestFitScore()

Retrieve the best fit from a PCMFitMappings object.

RetrieveBestModel()

Retrieve the optimal PCM model from a PCMFit object

RetrieveFittedModelsFromFitVectors()

Retrieve the ML fits from the fitVectors column in a table of fits.

RunOptim()

Calling optim a number of times

.cacheEnv

Internally used cache environment.

is.PCMFit()

Check if an object is a PCMFit.

is.PCMFitModelMappings()

Check if an object is a PCMFitModelMappings.