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 |
Modifier and Type | Method | Description |
---|---|---|
SiteDetails |
MolecularClockLikelihoodModel.External.calculateSiteDetails(double rootHeight,
PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilitiesStore,
ConditionalProbabilityStore rightConditionalProbabilitiesStore) |
|
SiteDetails |
LHCalculator.AbstractExternal.calculateSiteDetailsRooted(SubstitutionModel model,
PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilitiesStore,
ConditionalProbabilityStore rightConditionalProbabilitiesStore) |
|
SiteDetails |
LHCalculator.External.calculateSiteDetailsRooted(SubstitutionModel model,
PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilitiesStore,
ConditionalProbabilityStore rightConditionalProbabilitiesStore) |
Calculate the conditional probabilities of each pattern for each category
|
SiteDetails |
UnconstrainedLikelihoodModel.External.calculateSiteDetailsRooted(PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilitiesStore,
ConditionalProbabilityStore rightConditionalProbabilitiesStore) |
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) |
|
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 |
UnconstrainedLikelihoodModel.External.calculateSiteDetailsUnrooted(double distance,
PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilitiesStore,
ConditionalProbabilityStore rightConditionalProbabilitiesStore,
ConditionalProbabilityStore tempStore) |
Calculate the conditional probabilities of each pattern for each category
|
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
|
Constructor | Description |
---|---|
RELLTopologyPool(SiteDetails[] topologies,
int numberOfSites) |
Modifier and Type | Method | Description |
---|---|---|
SiteDetails |
FreeBranch.calculateSiteDetails(UnconstrainedLikelihoodModel.External calculator,
GeneralConstructionTool tool) |
|
SiteDetails |
UnrootedMLSearcher.calculateSiteDetails() |