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.