Uses of Package
pal.math

Packages that use pal.math

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

UnivariateFunction
interface for a function of one variable

Classes in pal.math used by pal.eval

MinimiserMonitor
interface for a classes that wish to monitor the progress of a Minimiser

MultivariateFunction
interface for a function of several variables

MultivariateMinimum
abstract base class for minimisation of a multivariate function

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

LMSSolver
Title: LMSSolver

Matrix
Title: Matrix

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

MultivariateFunction
interface for a function of several variables

MultivariateMinimum
abstract base class for minimisation of a multivariate function

MultivariateMinimum.Factory
A factory interface for MultivariateMinimums (because they aren't statefree)

OrderEnumerator
A means for describing odering information, and Utilities for creating such Orderings

OrderEnumerator.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 variable

UnivariateMinimum
minimization of a real-valued function of one variable without using derivatives.

Classes in pal.math used by pal.mep

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

MultivariateFunction
interface for a function of several variables

Classes in pal.math used by pal.substmodel

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

LMSSolver
Title: LMSSolver

Classes in pal.math used by pal.tree

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

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.