Uses of Interface
pal.algorithmics.StoppingCriteria
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Packages that use StoppingCriteria Package Description pal.algorithmics pal.treesearch -
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Uses of StoppingCriteria in pal.algorithmics
Methods in pal.algorithmics that return StoppingCriteria Modifier and Type Method Description StoppingCriteria
StoppingCriteria.Factory. newInstance()
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Uses of StoppingCriteria in pal.treesearch
Methods in pal.treesearch with parameters of type StoppingCriteria Modifier and Type Method Description double
GeneralLikelihoodSearcher. optimiseAllFullHeirarchy(StoppingCriteria mainStopper, StoppingCriteria subStopper, MultivariateMinimum rateMinimiser, int fxFracDigits, int xFracDigits, AlgorithmCallback callback, SearchMonitor monitor, MinimiserMonitor rateMonitor)
double
GeneralLikelihoodSearcher. optimiseAllPlusSubstitutionModel(StoppingCriteria stopper, MultivariateMinimum rateMinimiser, MultivariateMinimum substitutionModelMinimiser, int fxFracDigits, int xFracDigits, AlgorithmCallback callback, SearchMonitor monitor, int substitutionModelOptimiseFrequency, MinimiserMonitor substitutionModelMonitor, MinimiserMonitor rateMonitor)
double
GeneralLikelihoodSearcher. optimiseAllSimple(StoppingCriteria stopper, MultivariateMinimum rateMinimiser, int fxFracDigits, int xFracDigits, AlgorithmCallback callback)
double
GeneralLikelihoodSearcher. optimiseAllSimple(StoppingCriteria stopper, MultivariateMinimum rateMinimiser, int fxFracDigits, int xFracDigits, AlgorithmCallback callback, SearchMonitor monitor, MinimiserMonitor rateMonitor)
double
GeneralLikelihoodSearcher. optimiseAllSimple(StoppingCriteria stopper, MultivariateMinimum rateMinimiser, int fxFracDigits, int xFracDigits, AlgorithmCallback callback, SearchMonitor monitor, MinimiserMonitor rateMonitor, int groupOptimistionType)
double
GeneralLikelihoodSearcher. optimiseAllSimpleHeirarchy(StoppingCriteria stopper, MultivariateMinimum rateMinimiser, int fxFracDigits, int xFracDigits, AlgorithmCallback callback, SearchMonitor monitor, MinimiserMonitor rateMonitor)
double
GeneralLikelihoodSearcher. optimiseGeneral(StoppingCriteria stopper, int fracDigits, AlgorithmCallback callback)
double
GeneralLikelihoodSearcher. optimiseGeneral(StoppingCriteria stopper, int fracDigits, AlgorithmCallback callback, SearchMonitor monitor)
double
UnrootedMLSearcher. simpleOptimiseLikelihood(StoppingCriteria stopper, AlgorithmCallback callback)
Optimise the branch lengths of the tree to obtain the maximum likelihood.
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