Uses of Interface
pal.eval.SiteDetails
Packages that use SiteDetails
Package
Description
Classes for evaluating evolutionary hypothesis (chi-square and likelihood
criteria) and estimating model parameters.
Classes with useful for statistics (normal distribution,
Gamma distribution, chi-square distribution, exponential distribution,
likelihood-ratio test, chi-square test, descriptive statistics, bootstrap estimators etc.)
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Uses of SiteDetails in pal.eval
Methods in pal.eval that return SiteDetailsModifier and TypeMethodDescriptionMolecularClockLikelihoodModel.External.calculateSiteDetails(double rootHeight, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore) final SiteDetailsLHCalculator.AbstractExternal.calculateSiteDetailsRooted(SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore) LHCalculator.External.calculateSiteDetailsRooted(SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore) Calculate the conditional probabilities of each pattern for each categoryUnconstrainedLikelihoodModel.External.calculateSiteDetailsRooted(PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore) Calculate the conditional probabilities of each pattern for each categoryfinal SiteDetailsLHCalculator.AbstractExternal.calculateSiteDetailsUnrooted(double distance, SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftFlatConditionalProbabilities, ConditionalProbabilityStore rightFlatConditionalProbabilities, ConditionalProbabilityStore tempStore) LHCalculator.External.calculateSiteDetailsUnrooted(double distance, SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore, ConditionalProbabilityStore tempStore) Calculate the conditional probabilities of each pattern for each categoryUnconstrainedLikelihoodModel.External.calculateSiteDetailsUnrooted(double distance, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore, ConditionalProbabilityStore tempStore) Calculate the conditional probabilities of each pattern for each categorystatic final SiteDetailsSiteDetails.Utils.create(double[][] categoryPatternConditionalProbabilities, boolean isLoggedConditionals, int numberOfPatterns, int[] sitePatternMatchup, int numberOfSites, double[] siteLikelihoods) Create a Postriors object with no related substitution modelstatic final SiteDetailsSiteDetails.Utils.create(double[][] categoryPatternConditionalProbabilities, boolean isLoggedConditionals, SubstitutionModel model, int numberOfPatterns, int[] sitePatternMatchup, int numberOfSites, double[] siteLikelihoods) Create a Postriors object -
Uses of SiteDetails in pal.statistics
Constructors in pal.statistics with parameters of type SiteDetails -
Uses of SiteDetails in pal.treesearch
Methods in pal.treesearch that return SiteDetailsModifier and TypeMethodDescriptionFreeBranch.calculateSiteDetails(UnconstrainedLikelihoodModel.External calculator, GeneralConstructionTool tool) UnrootedMLSearcher.calculateSiteDetails()