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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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