Uses of Package
Maths

Packages that use Maths

Package	Description
Ancestors	Provides classed to calculate ancestral reconstruction.
Likelihood	Provides classes for calculating the likelihood of a tree given a model and an alignment.
Maths	Provides maths classes.
Models	Provides classes for defining a phylogenetic model.

Classes in Maths used by Ancestors

Class and Description
Real Represents a Real number.
RealFactory.RealType An enumeration of the different Real types

Classes in Maths used by Likelihood

Class and Description
Real Represents a Real number.
RealFactory.RealType An enumeration of the different Real types
SquareMatrix Represents a square matrix.

Classes in Maths used by Maths

Class and Description
CompiledFunction Represents a mathematical function, variable or constant
EigenvalueDecomposition.ConvergenceException Exception for when the Eigendecomposition does not converge
FunctionParser Interface for a function parser.
NoSuchFunction Exception that is thrown when a function has not been defined
NoSuchVariable Exception that is thrown when a function has not been defined
Real Represents a Real number.
RealFactory.RealType An enumeration of the different Real types
SmallDouble Represents a real number.
SquareMatrix Represents a square matrix.
SquareMatrix.Calculation Enumeration of the possible ways of calculating the matrix exponential
SquareMatrix.SquareMatrixException Exception thrown when there is a problem with a SquareMatrix operation
StandardDouble Represents a real.
WrongNumberOfVariables Exception that is thrown if a function is passed the wrong number of variables

Classes in Maths used by Models

Class and Description
SquareMatrix Represents a square matrix.