- neededParams() - Method in class Maths.CompiledFunction.Add
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- neededParams() - Method in class Maths.CompiledFunction.Constant
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- neededParams() - Method in class Maths.CompiledFunction.Divide
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- neededParams() - Method in class Maths.CompiledFunction.Function
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- neededParams() - Method in class Maths.CompiledFunction.Multiply
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- neededParams() - Method in interface Maths.CompiledFunction
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Returns a list of variable that the function expects to be passed to it
- neededParams() - Method in class Maths.CompiledFunction.Power
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- neededParams() - Method in class Maths.CompiledFunction.Subtract
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- neededParams() - Method in class Maths.CompiledFunction.Variable
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- negate() - Method in interface Maths.Real
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Negates this real.
- negate() - Method in class Maths.SmallDouble
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- negate() - Method in class Maths.StandardDouble
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- 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, double) - Static method in class Parameters.Parameter
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Creates a new bounded parameter that is estimated.
- newEstimatedParameter(String) - Static method in class Parameters.Parameter
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Creates a new (unbounded) parameter that is estimated.
- newEstimatedParameter(String, double) - Static method in class Parameters.Parameter
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Creates a new (unbounded) parameter that is estimated.
- 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, double) - Static method in class Parameters.Parameter
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Creates a new parameter that has to be positive and is estimated.
- 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.
- newInstance(Map<String, 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.
- newInstance(Model, Alignment, Map<String, Tree>) - Static method in class Ancestors.AncestralJoint
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Returns an object of this class that can be used for joint reconstruction.
- newInstance(Map<String, Model>, Alignment, Map<String, Tree>) - Static method in class Ancestors.AncestralJoint
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Returns an object of this class that can be used for joint reconstruction.
- newInstance(Model, Alignment, Tree) - Static method in class Ancestors.AncestralMarginal
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Returns an object of this class that can be used for marginal
reconstruction.
- newInstance(Map<String, Model>, Alignment, Tree) - Static method in class Ancestors.AncestralMarginal
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Returns an object of this class that can be used for marginal
reconstruction.
- newThread(Runnable) - Method in class Utils.DaemonThreadFactory
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- nodeIsAssigned(String) - Method in class Ancestors.Assignment
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Tests whether a node has an assignment
- 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
- NoSuchVariable - Exception in Maths
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Exception that is thrown when a function has not been defined
- NoSuchVariable(String) - Constructor for exception Maths.NoSuchVariable
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Default constructor
- numberEstimate() - Method in class Parameters.Parameters
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Gets the number of parameters to be estimated
- numberInputs(String) - Method in interface Maths.FunctionParser
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Returns the number of inputs a function expects to be passed
- numberParameters() - Method in interface ModelTest.Adapter
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Return the number of parameters associated with the adapter
- numberParameters() - Method in class ModelTest.EmpiricalAdapter
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- numberParameters() - Method in class ModelTest.EqualAdapter
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- numberParameters() - Method in class ModelTest.IdentityAdapter
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