- calculate(Parameters) - Method in class Ancestors.AncestralJoint
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Calculates the reconstruction
- calculate(Parameters) - Method in class Ancestors.AncestralJointBB
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- calculate(Parameters) - Method in class Ancestors.AncestralJointDP
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- calculate(Parameters) - Method in class Ancestors.AncestralMarginal
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Calculates the reconstruction
- calculate(Parameters) - Method in class Likelihood.Calculator
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Calculates the likelihood for a given set of parameters
- calculate() - Method in class Likelihood.Calculator.SiteCalculator
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Calculates the likelihood
- calculated() - Method in class Parameters.Parameters
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Resets the testfor whether probability matrices need to be recalculalated.
- Calculator - Class in Likelihood
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Calculates the likelihood for different parameter values.
- Calculator(Model, Alignment, Tree) - Constructor for class Likelihood.Calculator
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Creates an object to calculate the likelihood for a given model, alignment,
tree.
- Calculator(Model, Alignment, Tree, Alignment) - Constructor for class Likelihood.Calculator
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Creates a class to calculate the likelihood for a given model, alignment,
tree, missing data and constraints
- Calculator(Model, Alignment, Tree, Constrainer) - Constructor for class Likelihood.Calculator
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Creates a class to calculate the likelihood for a given model, alignment,
tree and constraints
- Calculator(Model, Alignment, Tree, Alignment, Constrainer) - Constructor for class Likelihood.Calculator
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Creates a class to calculate the likelihood for a given model, alignment,
tree, unobserved data and constraints
- Calculator.SiteCalculator - Class in Likelihood
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Calculates the likelihood of a single site.
- Calculator.SiteCalculator(Site, Tree, SiteConstraints, Probabilities) - Constructor for class Likelihood.Calculator.SiteCalculator
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Standard constructor
- chi2inv(double, double) - Static method in class Maths.Gamma
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Returns the inverse chi-squared distribution.
- clone() - Method in class Constraints.SiteConstraints
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- clone() - Method in class Parameters.Parameter
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- clone() - Method in class Parameters.Parameters
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- close() - Method in class Utils.CommentedFileReader
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Close the file reader
- CommentedFileReader - Class in Utils
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Reads from a commented file ignoring any comments
- CommentedFileReader(File) - Constructor for class Utils.CommentedFileReader
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Constructor
- ConfidenceInterval - Class in Likelihood
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Used to calculate congfidence intervals for a parameter.
- ConfidenceInterval(Calculator, Parameters) - Constructor for class Likelihood.ConfidenceInterval
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Default constructor
- Constrainer - Interface in Constraints
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Interface for classes that constrain the values of internal nodes of a tree.
- Constraints - package Constraints
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Provides classes to constrain the state of internal nodes.