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 SiteDetails
LHCalculator.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 SiteDetails
LHCalculator.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 SiteDetails
SiteDetails.Utils.create
(double[][] categoryPatternConditionalProbabilities, boolean isLoggedConditionals, int numberOfPatterns, int[] sitePatternMatchup, int numberOfSites, double[] siteLikelihoods) Create a Postriors object with no related substitution modelstatic final SiteDetails
SiteDetails.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()