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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
Abstract method for actually calculating the likelihood
calculate(SiteLikelihood.NodeLikelihood) - Method in class Likelihood.FitzJohnRoot
 
calculate(SiteLikelihood.NodeLikelihood) - Method in interface Likelihood.Root
Calculate the total likelihood from the root node likelihood
calculate(SiteLikelihood.NodeLikelihood) - Method in class Likelihood.StandardRoot
 
calculate(Parameters) - Method in interface Optimizers.Optimizable
The optimisable likelihood function.
calculateSite(Site, Tree, Parameters, Probabilities, Map<String, SiteLikelihood.NodeLikelihood>) - Method in class Likelihood.Calculator
Calculate the likelihood for a single site.
calculateSite(Site, Tree, Parameters, Probabilities, Map<String, SiteLikelihood.NodeLikelihood>) - Method in class Likelihood.StandardCalculator
 
Calculator<R extends Likelihood> - Class in Likelihood
Abstract class for calculating a likelihood.
Calculator(Map<String, Model>, Map<String, Tree>, HashMap<Site, Map<String, SiteLikelihood.NodeLikelihood>>) - Constructor for class Likelihood.Calculator
Default constructor.
Calculator.CalculatorException - Exception in Likelihood
Exception thrown when there is a problem with the calculation
Calculator.CalculatorException(String) - Constructor for exception Likelihood.Calculator.CalculatorException
Constructor when there is no underlying Throwable that caused the problem.
Calculator.CalculatorException(String, Exception) - Constructor for exception Likelihood.Calculator.CalculatorException
Constructor when there is an underlying Throwable that caused the problem.
Calculator.SiteCalculator - Class in Likelihood
Calculates the likelihood of a single site.
Calculator.SiteCalculator(Site, Tree, Parameters, Probabilities, Map<String, SiteLikelihood.NodeLikelihood>) - Constructor for class Likelihood.Calculator.SiteCalculator
Standard constructor
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 Ancestors.Assignment
 
clone() - Method in class Likelihood.SiteLikelihood.NodeLikelihood
 
clone() - Method in class Parameters.Parameter
 
clone() - Method in class Parameters.Parameters
 
close() - Method in class Utils.CommentedFileReader
Close the file reader
combineSites(Map<Site, SiteLikelihood>, Parameters) - Method in class Likelihood.Calculator
Combines the likelihood from each site into a alignment likelihood
combineSites(Map<Site, SiteLikelihood>, Parameters) - Method in class Likelihood.StandardCalculator
 
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 mathematical 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 confidence intervals for a parameter.
ConfidenceInterval(StandardCalculator, Parameters) - Constructor for class Likelihood.ConfidenceInterval
Default constructor
ConjugateGradient - Class in Optimizers
Implements the Conjugate Gradient method of parameter optimisation.
ConjugateGradient() - Constructor for class Optimizers.ConjugateGradient
Constructor that uses default values for rigour (1e-7), update method (BEALE_SORENSON_HESTENES_STIEFEL) and output (none)
ConjugateGradient(double) - Constructor for class Optimizers.ConjugateGradient
Constructor that uses the given value for rigour and default values for update method (BEALE_SORENSON_HESTENES_STIEFEL) and output (none)
ConjugateGradient(ConjugateGradient.Update) - Constructor for class Optimizers.ConjugateGradient
Constructor that uses the givemn update method and default values for rigour (1e-7) and output (none)
ConjugateGradient(double, ConjugateGradient.Update) - Constructor for class Optimizers.ConjugateGradient
Constructor that uses the given tolerance and update method but the default output (none)
ConjugateGradient(ConjugateGradient.ProgressLevel) - Constructor for class Optimizers.ConjugateGradient
Constructor that uses the given output level but default values for rigour (1e-7) and update method (BEALE_SORENSON_HESTENES_STIEFEL)
ConjugateGradient(double, ConjugateGradient.ProgressLevel) - Constructor for class Optimizers.ConjugateGradient
Constructor that uses the given tolerance and output level but the default update method (BEALE_SORENSON_HESTENES_STIEFEL)
ConjugateGradient(ConjugateGradient.Update, ConjugateGradient.ProgressLevel) - Constructor for class Optimizers.ConjugateGradient
Constructor that uses the given update method (BEALE_SORENSON_HESTENES_STIEFEL) and output (none) but the default values for rigour (1e-7),
ConjugateGradient(double, ConjugateGradient.Update, ConjugateGradient.ProgressLevel) - Constructor for class Optimizers.ConjugateGradient
Constructor that uses the given values for rigour, update method and output
ConjugateGradient.ProgressLevel - Enum in Optimizers
Enumeration of the different levels of output
ConjugateGradient.Update - Enum in Optimizers
Enumeration of the different update methods
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