All functions
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CollectBootstrapResults()
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Collect the results from a parametric bootstrap MGPM fit |
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DefaultArgsConfigOptim()
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Specify arguments for PCMFit during calls to PCMFitMixed. |
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.cacheEnv
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Internally used cache environment. |
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GuessInitVecParams()
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A heuristic-based guess of the optimal parameters of a model |
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HashCodes()
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Generate hash codes. |
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is.PCMFit()
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Check if an object is a PCMFit. |
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is.PCMFitModelMappings()
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Check if an object is a PCMFitModelMappings. |
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JitterModelParams()
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Add random white noise to the parameters of a model. |
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LookupFit()
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Lookup a fit vector for a given tree and model mapping in a data.table of
previously run fits. |
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MatchModelMapping()
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Match a model mapping vector against a vector of model types |
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PCMFit()
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Fitting a PCM model |
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PCMFitDemoObjects
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Demo objects for the PCMFit package |
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PCMFitMixed()
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Search for an optimal mixed Gaussian phylogenetic model, given a tree, trait
measurements at its tips and a score function. |
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PCMIteratorMapping()
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Iterator over combinations with repetions of a given set of modelTypes |
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PCMNextMapping()
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Generate the next mapping of model-types chosen from regime-specific sets of possible model-types. |
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RetrieveBestFitScore()
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Retrieve the best fit from a PCMFitMappings object. |
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RetrieveBestModel()
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Retrieve the optimal PCM model from a PCMFit object |
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RetrieveFittedModelsFromFitVectors()
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Retrieve the ML fits from the fitVectors column in a table of fits. |
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RunOptim()
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Calling optim a number of times |