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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(Map<String, Model>, Alignment, Tree)
- Constructor for class Likelihood.
Calculator
Creates a class to calculate the likelihood for a given set of models, an alignment, and a tree.
Calculator(Map<String, Model>, Alignment, Tree, Alignment)
- Constructor for class Likelihood.
Calculator
Creates a class to calculate the likelihood for a given set of models, an alignment, a tree, and unobserved data.
Calculator(Map<String, Model>, Alignment, Tree, Map<String, Constrainer>)
- Constructor for class Likelihood.
Calculator
Creates a class to calculate the likelihood for a given set of models, an alignment, a tree and a set of constraints.
Calculator(Map<String, Model>, Alignment, Tree, Alignment, Map<String, Constrainer>)
- Constructor for class Likelihood.
Calculator
Creates a class to calculate the likelihood for a given set of models, an alignment, a tree, unobserved data and a set of constraints.
Calculator.SiteCalculator
- Class in
Likelihood
Calculates the likelihood of a single site.
Calculator.SiteCalculator(Tree, Probabilities, ArrayMap<String, Likelihood.NodeLikelihood>)
- Constructor for class Likelihood.
Calculator.SiteCalculator
Standard constructor
Calculator.SiteCalculator(Site, Tree, SiteConstraints, Probabilities)
- Constructor for class Likelihood.
Calculator.SiteCalculator
Constructor mainly for backwards compitability although also still used by some of the ancestral calculations.
call()
- Method in class Likelihood.
Calculator.SiteCalculator
check(Map<String, ?>)
- Method in class Alignments.
Alignment
Checks whether the map contains an entry for every class in the alignment
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 Likelihood.
Likelihood.NodeLikelihood
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
CompiledFunction
- Interface in
Maths
Represents a mahematical function, variable or constant
CompiledFunction.Add
- Class in
Maths
The addition function
CompiledFunction.Add(CompiledFunction, CompiledFunction)
- Constructor for class Maths.
CompiledFunction.Add
Default constructor
CompiledFunction.Constant
- Class in
Maths
Represents a constant
CompiledFunction.Constant(double)
- Constructor for class Maths.
CompiledFunction.Constant
Default constructor
CompiledFunction.Divide
- Class in
Maths
The divide function
CompiledFunction.Divide(CompiledFunction, CompiledFunction)
- Constructor for class Maths.
CompiledFunction.Divide
Default constructor
CompiledFunction.Function
- Class in
Maths
Represents an arbitary function defined in a
FunctionParser
CompiledFunction.Function(FunctionParser, String, CompiledFunction[])
- Constructor for class Maths.
CompiledFunction.Function
Default constructor
CompiledFunction.Multiply
- Class in
Maths
The multiply function
CompiledFunction.Multiply(CompiledFunction, CompiledFunction)
- Constructor for class Maths.
CompiledFunction.Multiply
Default constructor
CompiledFunction.Power
- Class in
Maths
The power function
CompiledFunction.Power(CompiledFunction, CompiledFunction)
- Constructor for class Maths.
CompiledFunction.Power
Default constructor
CompiledFunction.Subtract
- Class in
Maths
The subtract function
CompiledFunction.Subtract(CompiledFunction, CompiledFunction)
- Constructor for class Maths.
CompiledFunction.Subtract
Default constructor
CompiledFunction.Variable
- Class in
Maths
Represents a variable - simply returns the value of the variable
CompiledFunction.Variable(String)
- Constructor for class Maths.
CompiledFunction.Variable
Default constructor
compileFunction(String)
- Method in class Maths.
MathsParse
Parses an equation and returns a compiled function that can then be used to compute the value fo an equation.
compute(Map<String, Double>)
- Method in class Maths.
CompiledFunction.Add
compute(Map<String, Double>)
- Method in interface Maths.
CompiledFunction
Computes the result of the function
compute(Map<String, Double>)
- Method in class Maths.
CompiledFunction.Constant
compute(Map<String, Double>)
- Method in class Maths.
CompiledFunction.Divide
compute(Map<String, Double>)
- Method in class Maths.
CompiledFunction.Function
compute(Map<String, Double>)
- Method in class Maths.
CompiledFunction.Multiply
compute(Map<String, Double>)
- Method in class Maths.
CompiledFunction.Power
compute(Map<String, Double>)
- Method in class Maths.
CompiledFunction.Subtract
compute(Map<String, Double>)
- Method in class Maths.
CompiledFunction.Variable
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.
containsKey(K)
- Method in class Utils.
ArrayMap
Tests whether the map contains a key
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