Uses of Interface
pal.math.OrthogonalHints
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Packages that use OrthogonalHints Package Description pal.eval Classes for evaluating evolutionary hypothesis (chi-square and likelihood criteria) and estimating model parameters.pal.math Classes for math stuff such as optimisation, numerical derivatives, matrix exponentials, random numbers, special function etc.pal.mep Classes for the analysis of "measurably evolving populations" (mep).pal.substmodel Classes describing substitution models, i.e.pal.tree 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 OrthogonalHints Modifier and Type Method Description OrthogonalHints
ChiSquareValue. getOrthogonalHints()
OrthogonalHints
DemographicValue. getOrthogonalHints()
OrthogonalHints
ModelParameters. getOrthogonalHints()
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Uses of OrthogonalHints in pal.math
Methods in pal.math that return OrthogonalHints Modifier and Type Method Description static OrthogonalHints
OrthogonalHints.Utils. getAdjusted(OrthogonalHints toAdjust, int adjustmentFactor)
static OrthogonalHints
OrthogonalHints.Utils. getCombined(OrthogonalHints first, int numberOfFirstParameters, OrthogonalHints second, int numberOfSecondParameters)
static OrthogonalHints
OrthogonalHints.Utils. getNull()
OrthogonalHints
BoundsCheckedFunction. getOrthogonalHints()
OrthogonalHints
EvaluationCounter. getOrthogonalHints()
OrthogonalHints
MultivariateFunction. getOrthogonalHints()
Methods in pal.math with parameters of type OrthogonalHints Modifier and Type Method Description static OrthogonalHints
OrthogonalHints.Utils. getAdjusted(OrthogonalHints toAdjust, int adjustmentFactor)
static OrthogonalHints
OrthogonalHints.Utils. getCombined(OrthogonalHints first, int numberOfFirstParameters, OrthogonalHints second, int numberOfSecondParameters)
static double[]
OrthogonalHints.Utils. getInternalParameterBoundaries(OrthogonalHints base, int parameter)
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Uses of OrthogonalHints in pal.mep
Methods in pal.mep that return OrthogonalHints Modifier and Type Method Description OrthogonalHints
DeltaModel.Instance. getOrthogonalHints()
OrthogonalHints
MutationRateModel. getOrthogonalHints()
Overide if there is any orthogonal hint information available -
Uses of OrthogonalHints in pal.substmodel
Methods in pal.substmodel that return OrthogonalHints Modifier and Type Method Description OrthogonalHints
AbstractRateMatrix. getOrthogonalHints()
OrthogonalHints
CachedRateMatrix. getOrthogonalHints()
OrthogonalHints
GeneralRateDistributionSubstitutionModel. getOrthogonalHints()
OrthogonalHints
RateMatrix. getOrthogonalHints()
OrthogonalHints
SingleClassSubstitutionModel. getOrthogonalHints()
OrthogonalHints
SubstitutionModel. getOrthogonalHints()
May return nullOrthogonalHints
YangCodonModel.SimpleNeutralSelection. getOrthogonalHints()
OrthogonalHints
YangCodonModel.SimplePositiveSelection. getOrthogonalHints()
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Uses of OrthogonalHints in pal.tree
Classes in pal.tree that implement OrthogonalHints Modifier and Type Class Description class
MutationRateModelTree
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 OrthogonalHints Modifier and Type Method Description OrthogonalHints
MutationRateModelTree. getOrthogonalHints()
OrthogonalHints
ParameterizedTree. getOrthogonalHints()
OrthogonalHints
ParameterizedTree.ParameterizedTreeBase. getOrthogonalHints()
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