Uses of Interface
pal.eval.SiteDetails

Packages that use SiteDetails
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   
 

Uses of SiteDetails in pal.eval
 

Methods in pal.eval that return SiteDetails
 SiteDetails MolecularClockLikelihoodModel.External.calculateSiteDetails(double rootHeight, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore)
           
 SiteDetails UnconstrainedLikelihoodModel.External.calculateSiteDetailsRooted(PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore)
          Calculate the conditional probabilities of each pattern for each category
 SiteDetails LHCalculator.External.calculateSiteDetailsRooted(SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore)
          Calculate the conditional probabilities of each pattern for each category
 SiteDetails LHCalculator.AbstractExternal.calculateSiteDetailsRooted(SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore)
           
 SiteDetails UnconstrainedLikelihoodModel.External.calculateSiteDetailsUnrooted(double distance, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore, ConditionalProbabilityStore tempStore)
          Calculate the conditional probabilities of each pattern for each category
 SiteDetails LHCalculator.External.calculateSiteDetailsUnrooted(double distance, SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore, ConditionalProbabilityStore tempStore)
          Calculate the conditional probabilities of each pattern for each category
 SiteDetails LHCalculator.AbstractExternal.calculateSiteDetailsUnrooted(double distance, SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftFlatConditionalProbabilities, ConditionalProbabilityStore rightFlatConditionalProbabilities, ConditionalProbabilityStore tempStore)
           
static SiteDetails SiteDetails.Utils.create(double[][] categoryPatternConditionalProbabilities, boolean isLoggedConditionals, int numberOfPatterns, int[] sitePatternMatchup, int numberOfSites, double[] siteLikelihoods)
          Create a Postriors object with no related substitution model
static 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
RELLTopologyPool(SiteDetails[] topologies, int numberOfSites)
           
 

Uses of SiteDetails in pal.treesearch
 

Methods in pal.treesearch that return SiteDetails
 SiteDetails UnrootedMLSearcher.calculateSiteDetails()
           
 SiteDetails FreeBranch.calculateSiteDetails(UnconstrainedLikelihoodModel.External calculator, GeneralConstructionTool tool)