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