pal.eval
public class LikelihoodOptimiser extends java.lang.Object
Constructor and Description |
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LikelihoodOptimiser(Tree tree,
Alignment alignment,
SubstitutionModel model) |
Modifier and Type | Method and Description |
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static double |
optimiseAlternate(ParameterizedTree tree,
Alignment alignment,
SubstitutionModel model,
MultivariateMinimum minimiser,
int fxFracDigits,
int xFracDigits)
Optimise parameters to acheive maximum likelihood using an alternating stategy.
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static double |
optimiseAlternate(ParameterizedTree tree,
Alignment alignment,
SubstitutionModel model,
MultivariateMinimum minimiser,
int fxFracDigits,
int xFracDigits,
MinimiserMonitor monitor)
Optimise parameters to acheive maximum likelihood using an alternating stategy.
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static double |
optimiseCombined(ParameterizedTree tree,
Alignment alignment,
SubstitutionModel model,
MultivariateMinimum minimiser,
int fxFracDigits,
int xFracDigits)
Optimise parameters to acheive maximum likelihood using a combined stategy.
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static double |
optimiseCombined(ParameterizedTree tree,
Alignment alignment,
SubstitutionModel model,
MultivariateMinimum minimiser,
int fxFracDigits,
int xFracDigits,
MinimiserMonitor monitor)
Optimise parameters to acheive maximum likelihood using a combined stategy.
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double |
optimiseLogLikelihood(Parameterized parameters,
MultivariateMinimum minimiser,
int fxFracDigits,
int xFracDigits) |
double |
optimiseLogLikelihood(Parameterized parameters,
MultivariateMinimum minimiser,
int fxFracDigits,
int xFracDigits,
MinimiserMonitor monitor) |
static double |
optimiseModel(Tree tree,
Alignment alignment,
SubstitutionModel model,
MultivariateMinimum minimiser,
int fxFracDigits,
int xFracDigits,
MinimiserMonitor monitor)
Optimise model parameters only to acheive maximum likelihood using a combined stategy.
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static double |
optimiseTree(ParameterizedTree tree,
Alignment alignment,
SubstitutionModel model,
MultivariateMinimum minimiser,
int fxFracDigits,
int xFracDigits)
Optimise tree branchlengths only to acheive maximum likelihood using a combined stategy.
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static double |
optimiseTree(ParameterizedTree tree,
Alignment alignment,
SubstitutionModel model,
MultivariateMinimum minimiser,
int fxFracDigits,
int xFracDigits,
MinimiserMonitor monitor)
Optimise tree branchlengths only to acheive maximum likelihood using a combined stategy.
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public LikelihoodOptimiser(Tree tree, Alignment alignment, SubstitutionModel model)
public double optimiseLogLikelihood(Parameterized parameters, MultivariateMinimum minimiser, int fxFracDigits, int xFracDigits, MinimiserMonitor monitor)
public double optimiseLogLikelihood(Parameterized parameters, MultivariateMinimum minimiser, int fxFracDigits, int xFracDigits)
public static final double optimiseCombined(ParameterizedTree tree, Alignment alignment, SubstitutionModel model, MultivariateMinimum minimiser, int fxFracDigits, int xFracDigits, MinimiserMonitor monitor)
tree
- The tree to be optimised (will be altered by optimisation)alignment
- The alignment related to treemodel
- The substitution model to be optimised (will be altered by optimisation)fxFracDigits
- The number of decimal placess to stabilise to in the log likelihoodxFracDigits
- The number of decimal placess to stabilise to in the model/tree parametersminimiser
- The MultivariateMinimum object that is used for minimisingmonitor
- A minimiser monitor to monitor progresspublic static final double optimiseCombined(ParameterizedTree tree, Alignment alignment, SubstitutionModel model, MultivariateMinimum minimiser, int fxFracDigits, int xFracDigits)
tree
- The tree to be optimised (will be altered by optimisation)alignment
- The alignment related to treemodel
- The substitution model to be optimised (will be altered by optimisation)fxFracDigits
- The number of decimal placess to stabilise to in the log likelihoodxFracDigits
- The number of decimal placess to stabilise to in the model/tree parametersminimiser
- The MultivariateMinimum object that is used for minimisingpublic static final double optimiseAlternate(ParameterizedTree tree, Alignment alignment, SubstitutionModel model, MultivariateMinimum minimiser, int fxFracDigits, int xFracDigits)
tree
- The tree to be optimised (will be altered by optimisation)alignment
- The alignment related to treemodel
- The substitution model to be optimised (will be altered by optimisation)fxFracDigits
- The number of decimal placess to stabilise to in the log likelihoodxFracDigits
- The number of decimal placess to stabilise to in the model/tree parametersminimiser
- The MultivariateMinimum object that is used for minimisingpublic static final double optimiseAlternate(ParameterizedTree tree, Alignment alignment, SubstitutionModel model, MultivariateMinimum minimiser, int fxFracDigits, int xFracDigits, MinimiserMonitor monitor)
tree
- The tree to be optimised (will be altered by optimisation)alignment
- The alignment related to treemodel
- The substitution model to be optimised (will be altered by optimisation)fxFracDigits
- The number of decimal placess to stabilise to in the log likelihoodxFracDigits
- The number of decimal placess to stabilise to in the model/tree parametersminimiser
- The MultivariateMinimum object that is used for minimisingmonitor
- A minimiser monitor to monitor progresspublic static final double optimiseTree(ParameterizedTree tree, Alignment alignment, SubstitutionModel model, MultivariateMinimum minimiser, int fxFracDigits, int xFracDigits)
tree
- The tree to be optimised (will be altered by optimisation)alignment
- The alignment related to treemodel
- The substitution model to be optimised (will *not * be altered by optimisation)fxFracDigits
- The number of decimal placess to stabilise to in the log likelihoodxFracDigits
- The number of decimal placess to stabilise to in the model/tree parametersminimiser
- The MultivariateMinimum object that is used for minimisingpublic static final double optimiseTree(ParameterizedTree tree, Alignment alignment, SubstitutionModel model, MultivariateMinimum minimiser, int fxFracDigits, int xFracDigits, MinimiserMonitor monitor)
tree
- The tree to be optimised (will be altered by optimisation)alignment
- The alignment related to treemodel
- The substitution model to be optimised (will *not * be altered by optimisation)fxFracDigits
- The number of decimal placess to stabilise to in the log likelihoodxFracDigits
- The number of decimal placess to stabilise to in the model/tree parametersminimiser
- The MultivariateMinimum object that is used for minimisingmonitor
- A minimiser monitor to monitor progresspublic static final double optimiseModel(Tree tree, Alignment alignment, SubstitutionModel model, MultivariateMinimum minimiser, int fxFracDigits, int xFracDigits, MinimiserMonitor monitor)
tree
- The tree to be optimised (will *not* be altered by optimisation)alignment
- The alignment related to treemodel
- The substitution model to be optimised (will be altered by optimisation)fxFracDigits
- The number of decimal placess to stabilise to in the log likelihoodxFracDigits
- The number of decimal placess to stabilise to in the model/tree parametersminimiser
- The MultivariateMinimum object that is used for minimisingmonitor
- A minimiser monitor to monitor progress