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).
|
Modifier and Type | Method | Description |
---|---|---|
OrthogonalHints |
ChiSquareValue.getOrthogonalHints() |
|
OrthogonalHints |
DemographicValue.getOrthogonalHints() |
|
OrthogonalHints |
ModelParameters.getOrthogonalHints() |
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() |
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) |
Modifier and Type | Method | Description |
---|---|---|
OrthogonalHints |
DeltaModel.Instance.getOrthogonalHints() |
|
OrthogonalHints |
MutationRateModel.getOrthogonalHints() |
Overide if there is any orthogonal hint information available
|
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 null
|
OrthogonalHints |
YangCodonModel.SimpleNeutralSelection.getOrthogonalHints() |
|
OrthogonalHints |
YangCodonModel.SimplePositiveSelection.getOrthogonalHints() |
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).
|
Modifier and Type | Method | Description |
---|---|---|
OrthogonalHints |
MutationRateModelTree.getOrthogonalHints() |
|
OrthogonalHints |
ParameterizedTree.getOrthogonalHints() |
|
OrthogonalHints |
ParameterizedTree.ParameterizedTreeBase.getOrthogonalHints() |