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Packages that use pal.math | |
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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 | |
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UnivariateFunction
interface for a function of one variable |
Classes in pal.math used by pal.eval | |
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MinimiserMonitor
interface for a classes that wish to monitor the progress of a Minimiser |
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MultivariateFunction
interface for a function of several variables |
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MultivariateMinimum
abstract base class for minimisation of a multivariate function |
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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.math | |
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LMSSolver
Title: LMSSolver |
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Matrix
Title: Matrix |
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MersenneTwisterFast
MersenneTwisterFast: A simulation quality fast random number generator (MT19937) with the same public methods as java.util.Random. |
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MinimiserMonitor
interface for a classes that wish to monitor the progress of a Minimiser |
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MultivariateFunction
interface for a function of several variables |
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MultivariateMinimum
abstract base class for minimisation of a multivariate function |
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MultivariateMinimum.Factory
A factory interface for MultivariateMinimums (because they aren't statefree) |
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OrderEnumerator
A means for describing odering information, and Utilities for creating such Orderings |
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OrderEnumerator.OEFactory
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OrthogonalHints
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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OrthogonalSearch.RoundOptimiser
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UnivariateFunction
interface for a function of one variable |
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UnivariateMinimum
minimization of a real-valued function of one variable without using derivatives. |
Classes in pal.math used by pal.mep | |
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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 | |
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MultivariateFunction
interface for a function of several variables |
Classes in pal.math used by pal.substmodel | |
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MersenneTwisterFast
MersenneTwisterFast: A simulation quality fast random number generator (MT19937) with the same public methods as java.util.Random. |
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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 | |
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LMSSolver
Title: LMSSolver |
Classes in pal.math used by pal.tree | |
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OrderEnumerator
A means for describing odering information, and Utilities for creating such Orderings |
|
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.treesearch | |
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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 Minimiser |
|
MultivariateMinimum
abstract base class for minimisation of a multivariate function |
|
UnivariateMinimum
minimization of a real-valued function of one variable without using derivatives. |
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