Uses of Interface
pal.math.OrthogonalHints
Packages that use OrthogonalHints
Package
Description
Classes for evaluating evolutionary hypothesis (chi-square and likelihood
criteria) and estimating model parameters.
Classes for math stuff such as optimisation, numerical derivatives, matrix exponentials,
random numbers, special function etc.
Classes for the analysis of "measurably evolving populations" (mep).
Classes describing substitution models, i.e.
Classes for providing the data structure of
trees, for constructing and modifying trees, and for parameterizing
trees (e.g., clock constraint).
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Uses of OrthogonalHints in pal.eval
Methods in pal.eval that return OrthogonalHintsModifier and TypeMethodDescriptionChiSquareValue.getOrthogonalHints()
DemographicValue.getOrthogonalHints()
ModelParameters.getOrthogonalHints()
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Uses of OrthogonalHints in pal.math
Methods in pal.math that return OrthogonalHintsModifier and TypeMethodDescriptionstatic final OrthogonalHints
OrthogonalHints.Utils.getAdjusted
(OrthogonalHints toAdjust, int adjustmentFactor) static final OrthogonalHints
OrthogonalHints.Utils.getCombined
(OrthogonalHints first, int numberOfFirstParameters, OrthogonalHints second, int numberOfSecondParameters) static final OrthogonalHints
OrthogonalHints.Utils.getNull()
BoundsCheckedFunction.getOrthogonalHints()
final OrthogonalHints
EvaluationCounter.getOrthogonalHints()
MultivariateFunction.getOrthogonalHints()
Methods in pal.math with parameters of type OrthogonalHintsModifier and TypeMethodDescriptionstatic final OrthogonalHints
OrthogonalHints.Utils.getAdjusted
(OrthogonalHints toAdjust, int adjustmentFactor) static final OrthogonalHints
OrthogonalHints.Utils.getCombined
(OrthogonalHints first, int numberOfFirstParameters, OrthogonalHints second, int numberOfSecondParameters) static final double[]
OrthogonalHints.Utils.getInternalParameterBoundaries
(OrthogonalHints base, int parameter) -
Uses of OrthogonalHints in pal.mep
Methods in pal.mep that return OrthogonalHintsModifier and TypeMethodDescriptionDeltaModel.Instance.getOrthogonalHints()
MutationRateModel.getOrthogonalHints()
Overide if there is any orthogonal hint information available -
Uses of OrthogonalHints in pal.substmodel
Methods in pal.substmodel that return OrthogonalHintsModifier and TypeMethodDescriptionAbstractRateMatrix.getOrthogonalHints()
CachedRateMatrix.getOrthogonalHints()
GeneralRateDistributionSubstitutionModel.getOrthogonalHints()
RateMatrix.getOrthogonalHints()
SingleClassSubstitutionModel.getOrthogonalHints()
SubstitutionModel.getOrthogonalHints()
May return nullYangCodonModel.SimpleNeutralSelection.getOrthogonalHints()
YangCodonModel.SimplePositiveSelection.getOrthogonalHints()
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Uses of OrthogonalHints in pal.tree
Classes in pal.tree that implement OrthogonalHintsModifier and TypeClassDescriptionclass
Provides parameter interface to any clock-like tree with serially sampled tips (parameters are the minimal node height differences at each internal node).Methods in pal.tree that return OrthogonalHintsModifier and TypeMethodDescriptionMutationRateModelTree.getOrthogonalHints()
ParameterizedTree.getOrthogonalHints()
ParameterizedTree.ParameterizedTreeBase.getOrthogonalHints()