Uses of Interface
pal.math.MinimiserMonitor
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Packages that use MinimiserMonitor 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 -
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Uses of MinimiserMonitor in pal.eval
Methods in pal.eval with parameters of type MinimiserMonitor Modifier and Type Method 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. -
Uses of MinimiserMonitor in pal.math
Methods in pal.math that return MinimiserMonitor Modifier and Type Method Description static MinimiserMonitor
MinimiserMonitor.Utils. createNullMonitor()
Creates a MinimiserMonitor that looses all outputstatic MinimiserMonitor
MinimiserMonitor.Utils. createSimpleMonitor(java.io.PrintWriter output)
Creates a MinimiserMonitor that outputs current minimum to a print streamstatic 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.errstatic MinimiserMonitor
MinimiserMonitor.Utils. createSystemOuptutMonitor()
Creates a MinimiserMonitor that outputs current minimum to a System.outMethods in pal.math with parameters of type MinimiserMonitor Modifier and Type Method 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
ConjugateDirectionSearch. optimize(MultivariateFunction f, double[] xvector, double tolfx, double tolx, MinimiserMonitor monitor)
void
ConjugateGradientSearch. optimize(MultivariateFunction f, double[] x, 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
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)
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Uses of MinimiserMonitor in pal.treesearch
Methods in pal.treesearch with parameters of type MinimiserMonitor Modifier and Type Method 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 groupdouble
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 groupdouble
GeneralConstraintGroupManager. optimiseSecondaryGlobalClockConstraints(MultivariateMinimum minimiser, GeneralConstraintGroupManager.LikelihoodScoreAccess scoreAccess, int fxFracDigits, int xFracDigits, MinimiserMonitor rateMonitor)
Optimise the global clock parameters marked as secondary related to this groupdouble
GeneralLikelihoodSearcher. optimiseSubstitutionModels(MultivariateMinimum minimiser, int fxFracDigits, int xFracDigits, MinimiserMonitor monitor)
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