Uses of Package
pal.math
Packages that use pal.math
Package
Description
Classes for reading and generating distance matrices, including computation
of pairwise distances for sequence data (maximum-likelihood and observed
distances).
Classes for evaluating evolutionary hypothesis (chi-square and likelihood
criteria) and estimating model parameters.
Classes for math stuff such as optimisation, numerical derivatives, matrix exponentials,
random numbers, special function etc.
Classes for the analysis of "measurably evolving populations" (mep).
Classes that don't fit elsewhere ;^)
Classes describing substitution models, i.e.
Classes for providing the data structure of
trees, for constructing and modifying trees, and for parameterizing
trees (e.g., clock constraint).
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Classes in pal.math used by pal.distance
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ClassDescriptioninterface for a classes that wish to monitor the progress of a Minimiserinterface for a function of several variablesabstract base class for minimisation of a multivariate functionProvides a means for giving an Orthogonal base optimiser (IE, OrthognalMinimum) hints about the function that may alow it to optimise better.
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ClassDescriptionTitle: LMSSolverTitle: MatrixMersenneTwisterFast: A simulation quality fast random number generator (MT19937) with the same public methods as java.util.Random.interface for a classes that wish to monitor the progress of a Minimiserinterface for a function of several variablesabstract base class for minimisation of a multivariate functionA factory interface for MultivariateMinimums (because they aren't statefree)A means for describing odering information, and Utilities for creating such OrderingsProvides a means for giving an Orthogonal base optimiser (IE, OrthognalMinimum) hints about the function that may alow it to optimise better.interface for a function of one variableminimization of a real-valued function of one variable without using derivatives.
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ClassDescriptionProvides a means for giving an Orthogonal base optimiser (IE, OrthognalMinimum) hints about the function that may alow it to optimise better.
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Classes in pal.math used by pal.substmodelClassDescriptionMersenneTwisterFast: A simulation quality fast random number generator (MT19937) with the same public methods as java.util.Random.Provides a means for giving an Orthogonal base optimiser (IE, OrthognalMinimum) hints about the function that may alow it to optimise better.
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Classes in pal.math used by pal.supgma
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ClassDescriptionA means for describing odering information, and Utilities for creating such OrderingsProvides a means for giving an Orthogonal base optimiser (IE, OrthognalMinimum) hints about the function that may alow it to optimise better.
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Classes in pal.math used by pal.treesearchClassDescriptionMersenneTwisterFast: A simulation quality fast random number generator (MT19937) with the same public methods as java.util.Random.interface for a classes that wish to monitor the progress of a Minimiserabstract base class for minimisation of a multivariate functionminimization of a real-valued function of one variable without using derivatives.