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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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