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.treesearch |
Modifier and Type | Method and Description |
---|---|
static double |
LikelihoodOptimiser.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 |
LikelihoodOptimiser.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 |
LikelihoodOptimiser.optimiseLogLikelihood(Parameterized parameters,
MultivariateMinimum minimiser,
int fxFracDigits,
int xFracDigits,
MinimiserMonitor monitor) |
static double |
LikelihoodOptimiser.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 |
LikelihoodOptimiser.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.
|
Modifier and Type | Method and Description |
---|---|
static MinimiserMonitor |
MinimiserMonitor.Utils.createNullMonitor()
Creates a MinimiserMonitor that looses all output
|
static MinimiserMonitor |
MinimiserMonitor.Utils.createSimpleMonitor(java.io.PrintWriter output)
Creates a MinimiserMonitor that outputs current minimum to a print stream
|
static MinimiserMonitor |
MinimiserMonitor.Utils.createSplitMonitor(MinimiserMonitor a,
MinimiserMonitor b) |
static MinimiserMonitor |
MinimiserMonitor.Utils.createStringMonitor()
Creates a MinimiserMonitor that Stores output (use toString() to access current results)
|
static MinimiserMonitor |
MinimiserMonitor.Utils.createSystemErrorMonitor()
Creates a MinimiserMonitor that outputs current minimum to a System.err
|
static MinimiserMonitor |
MinimiserMonitor.Utils.createSystemOuptutMonitor()
Creates a MinimiserMonitor that outputs current minimum to a System.out
|
Modifier and Type | Method and Description |
---|---|
static MinimiserMonitor |
MinimiserMonitor.Utils.createSplitMonitor(MinimiserMonitor a,
MinimiserMonitor b) |
double |
OrthogonalSearch.RoundOptimiser.doRound(double[] xvec,
UnivariateMinimum um,
double tolx,
double fx,
MinimiserMonitor monitor) |
double |
MultivariateMinimum.findMinimum(MultivariateFunction f,
double[] xvec,
int fxFracDigits,
int xFracDigits,
MinimiserMonitor monitor)
Find minimum close to vector x
(desired fractional digits for each parameter is specified)
|
void |
MultivariateMinimum.optimize(MultivariateFunction f,
double[] xvec,
double tolfx,
double tolx,
MinimiserMonitor monitor)
The actual optimization routine
It finds a minimum close to vector x when the
absolute tolerance for each parameter is specified.
|
void |
OrthogonalSearch.optimize(MultivariateFunction f,
double[] xvec,
double tolfx,
double tolx,
MinimiserMonitor monitor) |
void |
ConjugateDirectionSearch.optimize(MultivariateFunction f,
double[] xvector,
double tolfx,
double tolx,
MinimiserMonitor monitor) |
void |
DifferentialEvolution.optimize(MultivariateFunction func,
double[] xvec,
double tolfx,
double tolx,
MinimiserMonitor monitor) |
void |
GeneralizedDEOptimizer.optimize(MultivariateFunction f,
double[] xvec,
double tolfx,
double tolx,
MinimiserMonitor monitor)
The actual optimization routine
It finds a minimum close to vector x when the
absolute tolerance for each parameter is specified.
|
void |
ConjugateGradientSearch.optimize(MultivariateFunction f,
double[] x,
double tolfx,
double tolx,
MinimiserMonitor monitor) |
Modifier and Type | Method and Description |
---|---|
UndoableAction |
UnrootedMLSearcher.getModelOptimiseAction(MultivariateMinimum minimiser,
MinimiserMonitor monitor,
int fxFracDigits,
int xFracDigits) |
double |
GeneralLikelihoodSearcher.optimiseAllFullHeirarchy(StoppingCriteria mainStopper,
StoppingCriteria subStopper,
MultivariateMinimum rateMinimiser,
int fxFracDigits,
int xFracDigits,
AlgorithmCallback callback,
SearchMonitor monitor,
MinimiserMonitor rateMonitor) |
double |
GeneralConstraintGroupManager.optimiseAllGlobalClockConstraints(MultivariateMinimum minimiser,
GeneralConstraintGroupManager.LikelihoodScoreAccess scoreAccess,
int fxFracDigits,
int xFracDigits,
MinimiserMonitor rateMonitor)
Optimise all the global clock parameters related to this group
|
double |
GeneralLikelihoodSearcher.optimiseAllPlusSubstitutionModel(StoppingCriteria stopper,
MultivariateMinimum rateMinimiser,
MultivariateMinimum substitutionModelMinimiser,
int fxFracDigits,
int xFracDigits,
AlgorithmCallback callback,
SearchMonitor monitor,
int substitutionModelOptimiseFrequency,
MinimiserMonitor substitutionModelMonitor,
MinimiserMonitor rateMonitor) |
double |
GeneralLikelihoodSearcher.optimiseAllSimple(StoppingCriteria stopper,
MultivariateMinimum rateMinimiser,
int fxFracDigits,
int xFracDigits,
AlgorithmCallback callback,
SearchMonitor monitor,
MinimiserMonitor rateMonitor) |
double |
GeneralLikelihoodSearcher.optimiseAllSimple(StoppingCriteria stopper,
MultivariateMinimum rateMinimiser,
int fxFracDigits,
int xFracDigits,
AlgorithmCallback callback,
SearchMonitor monitor,
MinimiserMonitor rateMonitor,
int groupOptimistionType) |
double |
GeneralLikelihoodSearcher.optimiseAllSimpleHeirarchy(StoppingCriteria stopper,
MultivariateMinimum rateMinimiser,
int fxFracDigits,
int xFracDigits,
AlgorithmCallback callback,
SearchMonitor monitor,
MinimiserMonitor rateMonitor) |
double |
GeneralLikelihoodSearcher.optimiseConstraintRateModels(MultivariateMinimum minimiser,
int fxFracDigits,
int xFracDigits,
MinimiserMonitor rateMonitor) |
double |
GeneralConstraintGroupManager.optimisePrimaryGlobalClockConstraints(MultivariateMinimum minimiser,
GeneralConstraintGroupManager.LikelihoodScoreAccess scoreAccess,
int fxFracDigits,
int xFracDigits,
MinimiserMonitor rateMonitor)
Optimise the global clock parameters marked as primary related to this group
|
double |
GeneralConstraintGroupManager.optimiseSecondaryGlobalClockConstraints(MultivariateMinimum minimiser,
GeneralConstraintGroupManager.LikelihoodScoreAccess scoreAccess,
int fxFracDigits,
int xFracDigits,
MinimiserMonitor rateMonitor)
Optimise the global clock parameters marked as secondary related to this group
|
double |
GeneralLikelihoodSearcher.optimiseSubstitutionModels(MultivariateMinimum minimiser,
int fxFracDigits,
int xFracDigits,
MinimiserMonitor monitor) |