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Packages that use OrthogonalHints | |
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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). |
Uses of OrthogonalHints in pal.eval |
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Methods in pal.eval that return OrthogonalHints | |
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OrthogonalHints |
ChiSquareValue.getOrthogonalHints()
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OrthogonalHints |
ModelParameters.getOrthogonalHints()
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OrthogonalHints |
DemographicValue.getOrthogonalHints()
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Uses of OrthogonalHints in pal.math |
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Methods in pal.math that return OrthogonalHints | |
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static OrthogonalHints |
OrthogonalHints.Utils.getAdjusted(OrthogonalHints toAdjust,
int adjustmentFactor)
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static OrthogonalHints |
OrthogonalHints.Utils.getCombined(OrthogonalHints first,
int numberOfFirstParameters,
OrthogonalHints second,
int numberOfSecondParameters)
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static OrthogonalHints |
OrthogonalHints.Utils.getNull()
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OrthogonalHints |
BoundsCheckedFunction.getOrthogonalHints()
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OrthogonalHints |
EvaluationCounter.getOrthogonalHints()
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OrthogonalHints |
MultivariateFunction.getOrthogonalHints()
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Methods in pal.math with parameters of type OrthogonalHints | |
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static OrthogonalHints |
OrthogonalHints.Utils.getAdjusted(OrthogonalHints toAdjust,
int adjustmentFactor)
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static OrthogonalHints |
OrthogonalHints.Utils.getCombined(OrthogonalHints first,
int numberOfFirstParameters,
OrthogonalHints second,
int numberOfSecondParameters)
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static double[] |
OrthogonalHints.Utils.getInternalParameterBoundaries(OrthogonalHints base,
int parameter)
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Uses of OrthogonalHints in pal.mep |
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Methods in pal.mep that return OrthogonalHints | |
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OrthogonalHints |
DeltaModel.Instance.getOrthogonalHints()
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OrthogonalHints |
MutationRateModel.getOrthogonalHints()
Overide if there is any orthogonal hint information available |
Uses of OrthogonalHints in pal.substmodel |
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Methods in pal.substmodel that return OrthogonalHints | |
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OrthogonalHints |
CachedRateMatrix.getOrthogonalHints()
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OrthogonalHints |
SingleClassSubstitutionModel.getOrthogonalHints()
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OrthogonalHints |
SubstitutionModel.getOrthogonalHints()
May return null |
OrthogonalHints |
RateMatrix.getOrthogonalHints()
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OrthogonalHints |
YangCodonModel.SimplePositiveSelection.getOrthogonalHints()
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OrthogonalHints |
YangCodonModel.SimpleNeutralSelection.getOrthogonalHints()
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OrthogonalHints |
GeneralRateDistributionSubstitutionModel.getOrthogonalHints()
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OrthogonalHints |
AbstractRateMatrix.getOrthogonalHints()
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Uses of OrthogonalHints in pal.tree |
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Classes in pal.tree that implement OrthogonalHints | |
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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 | |
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OrthogonalHints |
ParameterizedTree.getOrthogonalHints()
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OrthogonalHints |
ParameterizedTree.ParameterizedTreeBase.getOrthogonalHints()
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OrthogonalHints |
MutationRateModelTree.getOrthogonalHints()
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