Uses of Interface
pal.eval.SiteDetails
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Packages that use SiteDetails Package Description pal.eval Classes for evaluating evolutionary hypothesis (chi-square and likelihood criteria) and estimating model parameters.pal.statistics 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.)pal.treesearch -
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Uses of SiteDetails in pal.eval
Methods in pal.eval that return SiteDetails Modifier and Type Method Description SiteDetailsMolecularClockLikelihoodModel.External. calculateSiteDetails(double rootHeight, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore)SiteDetailsLHCalculator.AbstractExternal. calculateSiteDetailsRooted(SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore)SiteDetailsLHCalculator.External. calculateSiteDetailsRooted(SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore)Calculate the conditional probabilities of each pattern for each categorySiteDetailsUnconstrainedLikelihoodModel.External. calculateSiteDetailsRooted(PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore)Calculate the conditional probabilities of each pattern for each categorySiteDetailsLHCalculator.AbstractExternal. calculateSiteDetailsUnrooted(double distance, SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftFlatConditionalProbabilities, ConditionalProbabilityStore rightFlatConditionalProbabilities, ConditionalProbabilityStore tempStore)SiteDetailsLHCalculator.External. calculateSiteDetailsUnrooted(double distance, SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore, ConditionalProbabilityStore tempStore)Calculate the conditional probabilities of each pattern for each categorySiteDetailsUnconstrainedLikelihoodModel.External. calculateSiteDetailsUnrooted(double distance, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore, ConditionalProbabilityStore tempStore)Calculate the conditional probabilities of each pattern for each categorystatic SiteDetailsSiteDetails.Utils. create(double[][] categoryPatternConditionalProbabilities, boolean isLoggedConditionals, int numberOfPatterns, int[] sitePatternMatchup, int numberOfSites, double[] siteLikelihoods)Create a Postriors object with no related substitution modelstatic 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 Constructor Description RELLTopologyPool(SiteDetails[] topologies, int numberOfSites) -
Uses of SiteDetails in pal.treesearch
Methods in pal.treesearch that return SiteDetails Modifier and Type Method Description SiteDetailsFreeBranch. calculateSiteDetails(UnconstrainedLikelihoodModel.External calculator, GeneralConstructionTool tool)SiteDetailsUnrootedMLSearcher. calculateSiteDetails()
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