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N

NelderMead - Class in Optimizers
Implements Nelder-Mead parameter optimization.
NelderMead() - Constructor for class Optimizers.NelderMead
Constrcutor that defaults to no debug output
NelderMead(NelderMead.DebugLevel) - Constructor for class Optimizers.NelderMead
Constructor that allows user defined debug level
NelderMead.DebugLevel - Enum in Optimizers
Enumeration of the debug level
newEstimatedBoundedParameter(String, double, double) - Static method in class Parameters.Parameter
Creates a new bounded parameter that is estimated.
newEstimatedBoundedParameter(String, double, double, boolean) - Static method in class Parameters.Parameter
Creates a new bounded paramater that is estimated and is optionally in a rate matrix
newEstimatedParameter(String) - Static method in class Parameters.Parameter
Creates a new (unbounded) paramater that is estimated.
newEstimatedParameter(String, boolean) - Static method in class Parameters.Parameter
Creates a new unbounded parameter that is estimated and is optionally in a rate matrix.
newEstimatedPositiveParameter(String) - Static method in class Parameters.Parameter
Creates a new parameter that has to be positive and is estimated.
newEstimatedPositiveParameter(String, boolean) - Static method in class Parameters.Parameter
Creates a new positive parameter that is estimated and is optionally in a rate matrix.
newFixedParameter(String, double) - Static method in class Parameters.Parameter
Creates a new fixed parameter (i.e.
newInstance(Model, Alignment, Tree) - Static method in class Ancestors.AncestralJoint
Returns an object of this class that can be used for joint reconstruction.
NoConstraints - Class in Constraints
Simple implementation of Constrainer that imposes no constraints
NoConstraints(Set<String>) - Constructor for class Constraints.NoConstraints
Constructor
nodeIsConstrained(String) - Method in class Constraints.SiteConstraints
Tests whether a node has a constraint
norm() - Method in class Maths.SquareMatrix
Calculates the maximum absolute column sum norm
NoSuchFunction - Exception in Maths
Exception that is thrown when a function has not been defined
NoSuchFunction(String) - Constructor for exception Maths.NoSuchFunction
Default constructor
numberEstimate() - Method in class Parameters.Parameters
Gets the number of parameters to be estimated
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