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C

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