pal.eval
Class LikelihoodOptimiser

java.lang.Object
  extended by pal.eval.LikelihoodOptimiser

public class LikelihoodOptimiser
extends java.lang.Object


Constructor Summary
LikelihoodOptimiser(Tree tree, Alignment alignment, SubstitutionModel model)
           
 
Method Summary
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.
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.
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.
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.
 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.
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.
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.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

LikelihoodOptimiser

public LikelihoodOptimiser(Tree tree,
                           Alignment alignment,
                           SubstitutionModel model)
Method Detail

optimiseLogLikelihood

public double optimiseLogLikelihood(Parameterized parameters,
                                    MultivariateMinimum minimiser,
                                    int fxFracDigits,
                                    int xFracDigits,
                                    MinimiserMonitor monitor)

optimiseLogLikelihood

public double optimiseLogLikelihood(Parameterized parameters,
                                    MultivariateMinimum minimiser,
                                    int fxFracDigits,
                                    int xFracDigits)

optimiseCombined

public static final 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. That is, model and tree are optimised concurrently.

Parameters:
tree - The tree to be optimised (will be altered by optimisation)
alignment - The alignment related to tree
model - The substitution model to be optimised (will be altered by optimisation)
fxFracDigits - The number of decimal placess to stabilise to in the log likelihood
xFracDigits - The number of decimal placess to stabilise to in the model/tree parameters
minimiser - The MultivariateMinimum object that is used for minimising
monitor - A minimiser monitor to monitor progress
Returns:
The maximal log likelihood found

optimiseCombined

public static final double optimiseCombined(ParameterizedTree tree,
                                            Alignment alignment,
                                            SubstitutionModel model,
                                            MultivariateMinimum minimiser,
                                            int fxFracDigits,
                                            int xFracDigits)
Optimise parameters to acheive maximum likelihood using a combined stategy. That is, model and tree are optimised concurrently.

Parameters:
tree - The tree to be optimised (will be altered by optimisation)
alignment - The alignment related to tree
model - The substitution model to be optimised (will be altered by optimisation)
fxFracDigits - The number of decimal placess to stabilise to in the log likelihood
xFracDigits - The number of decimal placess to stabilise to in the model/tree parameters
minimiser - The MultivariateMinimum object that is used for minimising
Returns:
The maximal log likelihood found

optimiseAlternate

public static final double optimiseAlternate(ParameterizedTree tree,
                                             Alignment alignment,
                                             SubstitutionModel model,
                                             MultivariateMinimum minimiser,
                                             int fxFracDigits,
                                             int xFracDigits)
Optimise parameters to acheive maximum likelihood using an alternating stategy. That is first the model is optimised, than the tree branch lengths, then the model, then the tree, and so on until convergence.

Parameters:
tree - The tree to be optimised (will be altered by optimisation)
alignment - The alignment related to tree
model - The substitution model to be optimised (will be altered by optimisation)
fxFracDigits - The number of decimal placess to stabilise to in the log likelihood
xFracDigits - The number of decimal placess to stabilise to in the model/tree parameters
minimiser - The MultivariateMinimum object that is used for minimising
Returns:
The maximal log likelihood found

optimiseAlternate

public static final 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. That is first the model is optimised, than the tree branch lengths, then the model, then the tree, and so on until convergence.

Parameters:
tree - The tree to be optimised (will be altered by optimisation)
alignment - The alignment related to tree
model - The substitution model to be optimised (will be altered by optimisation)
fxFracDigits - The number of decimal placess to stabilise to in the log likelihood
xFracDigits - The number of decimal placess to stabilise to in the model/tree parameters
minimiser - The MultivariateMinimum object that is used for minimising
monitor - A minimiser monitor to monitor progress
Returns:
The maximal log likelihood found

optimiseTree

public static final 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.

Parameters:
tree - The tree to be optimised (will be altered by optimisation)
alignment - The alignment related to tree
model - The substitution model to be optimised (will *not * be altered by optimisation)
fxFracDigits - The number of decimal placess to stabilise to in the log likelihood
xFracDigits - The number of decimal placess to stabilise to in the model/tree parameters
minimiser - The MultivariateMinimum object that is used for minimising
Returns:
The maximal log likelihood found

optimiseTree

public static final 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.

Parameters:
tree - The tree to be optimised (will be altered by optimisation)
alignment - The alignment related to tree
model - The substitution model to be optimised (will *not * be altered by optimisation)
fxFracDigits - The number of decimal placess to stabilise to in the log likelihood
xFracDigits - The number of decimal placess to stabilise to in the model/tree parameters
minimiser - The MultivariateMinimum object that is used for minimising
monitor - A minimiser monitor to monitor progress
Returns:
The maximal log likelihood found

optimiseModel

public static final 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.

Parameters:
tree - The tree to be optimised (will *not* be altered by optimisation)
alignment - The alignment related to tree
model - The substitution model to be optimised (will be altered by optimisation)
fxFracDigits - The number of decimal placess to stabilise to in the log likelihood
xFracDigits - The number of decimal placess to stabilise to in the model/tree parameters
minimiser - The MultivariateMinimum object that is used for minimising
monitor - A minimiser monitor to monitor progress
Returns:
The maximal log likelihood found