Uses of Package
pal.math
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Packages that use pal.math Package Description pal.distance Classes for reading and generating distance matrices, including computation of pairwise distances for sequence data (maximum-likelihood and observed distances).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.mep Classes for the analysis of "measurably evolving populations" (mep).pal.misc Classes that don't fit elsewhere ;^)pal.substmodel Classes describing substitution models, i.e.pal.supgma pal.tree Classes for providing the data structure of trees, for constructing and modifying trees, and for parameterizing trees (e.g., clock constraint).pal.treesearch -
Classes in pal.math used by pal.distance Class Description UnivariateFunction interface for a function of one variable -
Classes in pal.math used by pal.eval Class Description MinimiserMonitor interface for a classes that wish to monitor the progress of a MinimiserMultivariateFunction interface for a function of several variablesMultivariateMinimum abstract base class for minimisation of a multivariate functionOrthogonalHints Provides a means for giving an Orthogonal base optimiser (IE, OrthognalMinimum) hints about the function that may alow it to optimise better. -
Classes in pal.math used by pal.math Class Description LMSSolver Title: LMSSolverMatrix Title: MatrixMersenneTwisterFast MersenneTwisterFast: A simulation quality fast random number generator (MT19937) with the same public methods as java.util.Random.MinimiserMonitor interface for a classes that wish to monitor the progress of a MinimiserMultivariateFunction interface for a function of several variablesMultivariateMinimum abstract base class for minimisation of a multivariate functionMultivariateMinimum.Factory A factory interface for MultivariateMinimums (because they aren't statefree)OrderEnumerator A means for describing odering information, and Utilities for creating such OrderingsOrderEnumerator.OEFactory OrthogonalHints Provides a means for giving an Orthogonal base optimiser (IE, OrthognalMinimum) hints about the function that may alow it to optimise better.OrthogonalSearch.RoundOptimiser UnivariateFunction interface for a function of one variableUnivariateMinimum minimization of a real-valued function of one variable without using derivatives. -
Classes in pal.math used by pal.mep Class Description OrthogonalHints Provides a means for giving an Orthogonal base optimiser (IE, OrthognalMinimum) hints about the function that may alow it to optimise better. -
Classes in pal.math used by pal.misc Class Description MultivariateFunction interface for a function of several variables -
Classes in pal.math used by pal.substmodel Class Description MersenneTwisterFast MersenneTwisterFast: A simulation quality fast random number generator (MT19937) with the same public methods as java.util.Random.OrthogonalHints Provides a means for giving an Orthogonal base optimiser (IE, OrthognalMinimum) hints about the function that may alow it to optimise better. -
Classes in pal.math used by pal.supgma Class Description LMSSolver Title: LMSSolver -
Classes in pal.math used by pal.tree Class Description OrderEnumerator A means for describing odering information, and Utilities for creating such OrderingsOrthogonalHints Provides a means for giving an Orthogonal base optimiser (IE, OrthognalMinimum) hints about the function that may alow it to optimise better. -
Classes in pal.math used by pal.treesearch Class Description MersenneTwisterFast MersenneTwisterFast: A simulation quality fast random number generator (MT19937) with the same public methods as java.util.Random.MinimiserMonitor interface for a classes that wish to monitor the progress of a MinimiserMultivariateMinimum abstract base class for minimisation of a multivariate functionUnivariateMinimum minimization of a real-valued function of one variable without using derivatives.