Uses of Interface pal.math.MinimiserMonitor

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

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 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

Methods 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)`

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 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)`