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 OrthogonalHintsChiSquareValue. getOrthogonalHints()OrthogonalHintsDemographicValue. getOrthogonalHints()OrthogonalHintsModelParameters. getOrthogonalHints() -
Uses of OrthogonalHints in pal.math
Methods in pal.math that return OrthogonalHints Modifier and Type Method Description static OrthogonalHintsOrthogonalHints.Utils. getAdjusted(OrthogonalHints toAdjust, int adjustmentFactor)static OrthogonalHintsOrthogonalHints.Utils. getCombined(OrthogonalHints first, int numberOfFirstParameters, OrthogonalHints second, int numberOfSecondParameters)static OrthogonalHintsOrthogonalHints.Utils. getNull()OrthogonalHintsBoundsCheckedFunction. getOrthogonalHints()OrthogonalHintsEvaluationCounter. getOrthogonalHints()OrthogonalHintsMultivariateFunction. getOrthogonalHints()Methods in pal.math with parameters of type OrthogonalHints Modifier and Type Method Description static OrthogonalHintsOrthogonalHints.Utils. getAdjusted(OrthogonalHints toAdjust, int adjustmentFactor)static OrthogonalHintsOrthogonalHints.Utils. getCombined(OrthogonalHints first, int numberOfFirstParameters, OrthogonalHints second, int numberOfSecondParameters)static double[]OrthogonalHints.Utils. getInternalParameterBoundaries(OrthogonalHints base, int parameter) -
Uses of OrthogonalHints in pal.mep
Methods in pal.mep that return OrthogonalHints Modifier and Type Method Description OrthogonalHintsDeltaModel.Instance. getOrthogonalHints()OrthogonalHintsMutationRateModel. 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 OrthogonalHintsAbstractRateMatrix. getOrthogonalHints()OrthogonalHintsCachedRateMatrix. getOrthogonalHints()OrthogonalHintsGeneralRateDistributionSubstitutionModel. getOrthogonalHints()OrthogonalHintsRateMatrix. getOrthogonalHints()OrthogonalHintsSingleClassSubstitutionModel. getOrthogonalHints()OrthogonalHintsSubstitutionModel. getOrthogonalHints()May return nullOrthogonalHintsYangCodonModel.SimpleNeutralSelection. getOrthogonalHints()OrthogonalHintsYangCodonModel.SimplePositiveSelection. getOrthogonalHints() -
Uses of OrthogonalHints in pal.tree
Classes in pal.tree that implement OrthogonalHints Modifier and Type Class Description classMutationRateModelTreeProvides 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 OrthogonalHintsMutationRateModelTree. getOrthogonalHints()OrthogonalHintsParameterizedTree. getOrthogonalHints()OrthogonalHintsParameterizedTree.ParameterizedTreeBase. getOrthogonalHints()
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