Package | Description |
---|---|
pal.eval |
Classes for evaluating evolutionary hypothesis (chi-square and likelihood
criteria) and estimating model parameters.
|
pal.treesearch |
Modifier and Type | Method and Description |
---|---|
ConditionalProbabilityStore |
MolecularClockLikelihoodModel.Internal.calculateAscendentExtendedConditionals(double topBaseHeight,
double bottomBaseHeight,
PatternInfo centerPattern,
ConditionalProbabilityStore ascendentConditionalProbabilityProbabilties,
ConditionalProbabilityStore otherConditionalProbabilityProbabilties) |
ConditionalProbabilityStore |
MolecularClockLikelihoodModel.Internal.calculateAscendentFlatConditionals(PatternInfo centerPattern,
ConditionalProbabilityStore ascenedentConditionalProbabilityProbabilties,
ConditionalProbabilityStore otherConditionalProbabilityProbabilties) |
ConditionalProbabilityStore |
UnconstrainedLikelihoodModel.Internal.calculateExtended(double distance,
PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilities,
ConditionalProbabilityStore rightConditionalProbabilities) |
ConditionalProbabilityStore |
SimpleUnconstrainedLikelihoodModel.InternalImpl.calculateExtended(double distance,
PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilities,
ConditionalProbabilityStore rightConditionalProbabilities) |
ConditionalProbabilityStore |
LHCalculator.Internal.calculateExtended(double distance,
SubstitutionModel model,
PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilities,
ConditionalProbabilityStore rightConditionalProbabilities,
boolean modelChangedSinceLastCall) |
ConditionalProbabilityStore |
MolecularClockLikelihoodModel.Leaf.calculateExtendedConditionals(double topHeight,
double bottomHeight) |
ConditionalProbabilityStore |
MolecularClockLikelihoodModel.Internal.calculateExtendedConditionals(double topBaseHeight,
double bottomBaseHeight,
PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilityProbabilties,
ConditionalProbabilityStore rightConditionalProbabilityProbabilties) |
ConditionalProbabilityStore |
UnconstrainedLikelihoodModel.Internal.calculateFlat(PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilities,
ConditionalProbabilityStore rightConditionalProbabilities)
calculate flat probability information (not extended over a branch).
|
ConditionalProbabilityStore |
LHCalculator.Internal.calculateFlat(PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilities,
ConditionalProbabilityStore rightConditionalProbabilities)
calculate flat probability information (not extended over a branch).
|
ConditionalProbabilityStore |
SimpleUnconstrainedLikelihoodModel.InternalImpl.calculateFlat(PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilities,
ConditionalProbabilityStore rightConditionalProbabilities) |
ConditionalProbabilityStore |
MolecularClockLikelihoodModel.Leaf.calculateFlatConditionals(double height) |
ConditionalProbabilityStore |
MolecularClockLikelihoodModel.Internal.calculateFlatConditionals(PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilityProbabilties,
ConditionalProbabilityStore rightConditionalProbabilityProbabilties) |
ConditionalProbabilityStore |
LHCalculator.Internal.calculatePostExtendedFlat(double distance,
SubstitutionModel model,
PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilities,
ConditionalProbabilityStore rightConditionalProbabilities,
boolean modelChangedSinceLastCall) |
ConditionalProbabilityStore |
MolecularClockLikelihoodModel.Internal.calculatePostExtendedFlatConditionals(double topBaseHeight,
double bottomBaseHeight,
PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilityProbabilties,
ConditionalProbabilityStore rightConditionalProbabilityProbabilties)
Extends left and right conditionals by type and then calculates flat conditionals
|
ConditionalProbabilityStore |
UnconstrainedLikelihoodModel.Instance.createAppropriateConditionalProbabilityStore(boolean isForLeaf) |
ConditionalProbabilityStore |
LHCalculator.Generator.createAppropriateConditionalProbabilityStore(boolean isForLeaf) |
ConditionalProbabilityStore |
MolecularClockLikelihoodModel.Instance.createAppropriateConditionalProbabilityStore(boolean isForLeaf) |
ConditionalProbabilityStore |
ConditionalProbabilityStore.getCopy()
Cloning
|
ConditionalProbabilityStore |
UnconstrainedLikelihoodModel.Leaf.getExtendedConditionalProbabilities(double distance) |
ConditionalProbabilityStore |
SimpleUnconstrainedLikelihoodModel.LeafImpl.getExtendedConditionalProbabilities(double distance) |
ConditionalProbabilityStore |
SimpleLeafCalculator.getExtendedConditionalProbabilities(double distance,
SubstitutionModel model,
boolean modelChanged) |
ConditionalProbabilityStore |
LHCalculator.Leaf.getExtendedConditionalProbabilities(double distance,
SubstitutionModel model,
boolean modelChanged) |
ConditionalProbabilityStore |
UnconstrainedLikelihoodModel.Leaf.getFlatConditionalProbabilities() |
ConditionalProbabilityStore |
SimpleLeafCalculator.getFlatConditionalProbabilities() |
ConditionalProbabilityStore |
LHCalculator.Leaf.getFlatConditionalProbabilities() |
ConditionalProbabilityStore |
SimpleUnconstrainedLikelihoodModel.LeafImpl.getFlatConditionalProbabilities() |
Modifier and Type | Method and Description |
---|---|
ConditionalProbabilityStore |
MolecularClockLikelihoodModel.Internal.calculateAscendentExtendedConditionals(double topBaseHeight,
double bottomBaseHeight,
PatternInfo centerPattern,
ConditionalProbabilityStore ascendentConditionalProbabilityProbabilties,
ConditionalProbabilityStore otherConditionalProbabilityProbabilties) |
ConditionalProbabilityStore |
MolecularClockLikelihoodModel.Internal.calculateAscendentFlatConditionals(PatternInfo centerPattern,
ConditionalProbabilityStore ascenedentConditionalProbabilityProbabilties,
ConditionalProbabilityStore otherConditionalProbabilityProbabilties) |
protected abstract void |
LHCalculator.AbstractExternal.calculateCategoryPatternProbabilities(double distance,
SubstitutionModel model,
PatternInfo centerPattern,
ConditionalProbabilityStore leftFlatConditionalProbabilities,
ConditionalProbabilityStore rightFlatConditionalProbabilities,
ConditionalProbabilityStore tempStore,
double[][] categoryPatternLogLikelihoodStore) |
protected abstract void |
LHCalculator.AbstractExternal.calculateCategoryPatternProbabilities(SubstitutionModel model,
PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilities,
ConditionalProbabilityStore rightConditionalProbabilities,
double[][] categoryPatternLikelihoodStore) |
ConditionalProbabilityStore |
UnconstrainedLikelihoodModel.Internal.calculateExtended(double distance,
PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilities,
ConditionalProbabilityStore rightConditionalProbabilities) |
ConditionalProbabilityStore |
SimpleUnconstrainedLikelihoodModel.InternalImpl.calculateExtended(double distance,
PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilities,
ConditionalProbabilityStore rightConditionalProbabilities) |
void |
UnconstrainedLikelihoodModel.External.calculateExtended(double distance,
PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilities,
ConditionalProbabilityStore rightConditionalProbabilities,
ConditionalProbabilityStore resultStore) |
ConditionalProbabilityStore |
LHCalculator.Internal.calculateExtended(double distance,
SubstitutionModel model,
PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilities,
ConditionalProbabilityStore rightConditionalProbabilities,
boolean modelChangedSinceLastCall) |
void |
LHCalculator.External.calculateExtended(double distance,
SubstitutionModel model,
PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilities,
ConditionalProbabilityStore rightConditionalProbabilities,
ConditionalProbabilityStore resultStore) |
ConditionalProbabilityStore |
MolecularClockLikelihoodModel.Internal.calculateExtendedConditionals(double topBaseHeight,
double bottomBaseHeight,
PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilityProbabilties,
ConditionalProbabilityStore rightConditionalProbabilityProbabilties) |
void |
MolecularClockLikelihoodModel.External.calculateExtendedConditionals(double topBaseHeight,
double bottomBaseHeight,
PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilities,
ConditionalProbabilityStore rightConditionalProbabilities,
ConditionalProbabilityStore resultStore) |
ConditionalProbabilityStore |
UnconstrainedLikelihoodModel.Internal.calculateFlat(PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilities,
ConditionalProbabilityStore rightConditionalProbabilities)
calculate flat probability information (not extended over a branch).
|
ConditionalProbabilityStore |
LHCalculator.Internal.calculateFlat(PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilities,
ConditionalProbabilityStore rightConditionalProbabilities)
calculate flat probability information (not extended over a branch).
|
ConditionalProbabilityStore |
SimpleUnconstrainedLikelihoodModel.InternalImpl.calculateFlat(PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilities,
ConditionalProbabilityStore rightConditionalProbabilities) |
void |
UnconstrainedLikelihoodModel.External.calculateFlat(PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilities,
ConditionalProbabilityStore rightConditionalProbabilities,
ConditionalProbabilityStore resultStore) |
void |
LHCalculator.External.calculateFlat(PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilities,
ConditionalProbabilityStore rightConditionalProbabilities,
ConditionalProbabilityStore resultStore) |
void |
MolecularClockLikelihoodModel.External.calculateFlatConditionals(double rootHeight,
PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilitiesStore,
ConditionalProbabilityStore rightConditionalProbabilitiesStore,
ConditionalProbabilityStore resultConditionalProbabilitiesStore) |
ConditionalProbabilityStore |
MolecularClockLikelihoodModel.Internal.calculateFlatConditionals(PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilityProbabilties,
ConditionalProbabilityStore rightConditionalProbabilityProbabilties) |
double |
MolecularClockLikelihoodModel.External.calculateLogLikelihood(double rootHeight,
PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilitiesStore,
ConditionalProbabilityStore rightConditionalProbabilitiesStore)
Calculate the likelihood given two sub trees (left, right) and their extended likeihood probabilities
|
double |
UnconstrainedLikelihoodModel.External.calculateLogLikelihood(double distance,
PatternInfo centerPattern,
ConditionalProbabilityStore leftFlatConditionalProbabilities,
ConditionalProbabilityStore rightFlatConditionalProbabilities,
ConditionalProbabilityStore tempStore)
Calculate the likelihood given two sub trees (left, right) and their flat (unextend) likeihood probabilities
|
double |
LHCalculator.External.calculateLogLikelihood(double distance,
SubstitutionModel model,
PatternInfo centerPattern,
ConditionalProbabilityStore leftFlatConditionalProbabilities,
ConditionalProbabilityStore rightFlatConditionalProbabilities,
ConditionalProbabilityStore tempStore)
Calculate the likelihood given two sub trees (left, right) and their flat (unextend) likeihood probabilities
|
double |
UnconstrainedLikelihoodModel.External.calculateLogLikelihood(PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilities,
ConditionalProbabilityStore rightConditionalProbabilities)
Calculate the likelihood given two sub trees (left, right) and their extended likeihood probabilities
|
double |
LHCalculator.External.calculateLogLikelihood(SubstitutionModel model,
PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilities,
ConditionalProbabilityStore rightConditionalProbabilities)
Calculate the likelihood given two sub trees (left, right) and their extended likeihood probabilities
|
double |
MolecularClockLikelihoodModel.External.calculateLogLikelihoodNonRoot(double nodeHeight,
PatternInfo centerPattern,
ConditionalProbabilityStore ascendentConditionalProbabilitiesStore,
ConditionalProbabilityStore descendentConditionalProbabilitiesStore)
Calculate the likelihood given a non root node
|
double |
MolecularClockLikelihoodModel.External.calculateLogLikelihoodSingle(double rootHeight,
PatternInfo centerPattern,
ConditionalProbabilityStore conditionalProbabilitiesStore) |
double |
UnconstrainedLikelihoodModel.External.calculateLogLikelihoodSingle(int[] patternWeights,
int numberOfPatterns,
ConditionalProbabilityStore conditionalProbabilityStore)
Calculate the likelihood given the conditional probabilites at the root
|
double |
LHCalculator.External.calculateLogLikelihoodSingle(SubstitutionModel model,
int[] patternWeights,
int numberOfPatterns,
ConditionalProbabilityStore conditionalProbabilityStore)
Calculate the likelihood given the conditional probabilites at the root
|
ConditionalProbabilityStore |
LHCalculator.Internal.calculatePostExtendedFlat(double distance,
SubstitutionModel model,
PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilities,
ConditionalProbabilityStore rightConditionalProbabilities,
boolean modelChangedSinceLastCall) |
ConditionalProbabilityStore |
MolecularClockLikelihoodModel.Internal.calculatePostExtendedFlatConditionals(double topBaseHeight,
double bottomBaseHeight,
PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilityProbabilties,
ConditionalProbabilityStore rightConditionalProbabilityProbabilties)
Extends left and right conditionals by type and then calculates flat conditionals
|
void |
MolecularClockLikelihoodModel.External.calculateSingleAscendentExtendedConditionalsDirect(double topBaseHeight,
double bottomBaseHeight,
PatternInfo centerPattern,
ConditionalProbabilityStore ascendentConditionalProbabilityProbabilties) |
void |
MolecularClockLikelihoodModel.External.calculateSingleAscendentExtendedConditionalsIndirect(double topBaseHeight,
double bottomBaseHeight,
PatternInfo centerPattern,
ConditionalProbabilityStore baseAscendentConditionalProbabilityProbabilties,
ConditionalProbabilityStore resultConditionalProbabilityProbabilties) |
void |
MolecularClockLikelihoodModel.External.calculateSingleDescendentExtendedConditionals(double topBaseHeight,
double bottomBaseHeight,
PatternInfo centerPattern,
ConditionalProbabilityStore descendentConditionalProbabilities) |
void |
UnconstrainedLikelihoodModel.External.calculateSingleExtendedDirect(double distance,
int numberOfPatterns,
ConditionalProbabilityStore conditionalProbabilities)
Extend the conditionals back in time by some distance
|
void |
LHCalculator.External.calculateSingleExtendedDirect(double distance,
SubstitutionModel model,
int numberOfPatterns,
ConditionalProbabilityStore conditionalProbabilities)
Extend the conditionals back in time by some distance, with some model
|
void |
UnconstrainedLikelihoodModel.External.calculateSingleExtendedIndirect(double distance,
int numberOfPatterns,
ConditionalProbabilityStore baseConditionalProbabilities,
ConditionalProbabilityStore resultConditionalProbabilities)
Extend the conditionals back in time by some distance
|
void |
LHCalculator.External.calculateSingleExtendedIndirect(double distance,
SubstitutionModel model,
int numberOfPatterns,
ConditionalProbabilityStore baseConditionalProbabilities,
ConditionalProbabilityStore resultConditionalProbabilities)
Extend the conditionals back in time by some distance, with some model
|
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) |
void |
ConditionalProbabilityStore.ExtraProcessor.setParent(ConditionalProbabilityStore parent) |