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Packages that use Parameters.ParameterException | |
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Ancestors | Provides classed to calculate ancestral reconstruction. |
Likelihood | Provides classes for calculating the likelihood of a tree given a model and an alignment. |
Optimizers | Provides classes for optimising a likelihood. |
Parameters | Provides classes for defining parameters used in the various calculations. |
Simulations | Provides a class to create simulate data. |
Trees | Provides classes to define a tree and any constraints on that tree. |
Uses of Parameters.ParameterException in Ancestors |
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Methods in Ancestors that throw Parameters.ParameterException | |
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abstract Alignment |
AncestralJoint.calculate(Parameters params)
Calculates the reconstruction |
Alignment |
AncestralJointBB.calculate(Parameters p)
|
Alignment |
AncestralJointDP.calculate(Parameters params)
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AncestralMarginal.Result |
AncestralMarginal.calculate(Parameters params)
Calculates the reconstruction |
Uses of Parameters.ParameterException in Likelihood |
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Methods in Likelihood that throw Parameters.ParameterException | |
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Likelihood |
Calculator.calculate(Parameters p)
Calculates the likelihood for a given set of parameters |
Range |
ConfidenceInterval.getCI(Parameter param,
double conf)
Calculates the confidence interval for a single parameter |
Constructors in Likelihood that throw Parameters.ParameterException | |
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Probabilities(Model m,
Tree t,
Parameters p)
Constructor |
Uses of Parameters.ParameterException in Optimizers |
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Methods in Optimizers that throw Parameters.ParameterException | |
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Likelihood |
GoldenSection.maximise(Calculator l,
Parameters params)
|
Likelihood |
GoldenSection.maximise(Calculator l,
Parameters params)
|
Likelihood |
NelderMead.maximise(Calculator l,
Parameters params)
|
Likelihood |
NelderMead.maximise(Calculator l,
Parameters params)
|
Likelihood |
Optimizer.maximise(Calculator l,
Parameters p)
Maximises the likelihood, logging to screen. |
Likelihood |
GoldenSection.maximise(Calculator l,
Parameters params,
java.io.File log)
|
Likelihood |
GoldenSection.maximise(Calculator l,
Parameters params,
java.io.File log)
|
Likelihood |
NelderMead.maximise(Calculator l,
Parameters params,
java.io.File log)
|
Likelihood |
NelderMead.maximise(Calculator l,
Parameters params,
java.io.File log)
|
Likelihood |
Optimizer.maximise(Calculator l,
Parameters params,
java.io.File log)
Maximises the likelihood, logging to a file. |
Likelihood |
Optimizer.maximise(Calculator l,
Parameters params,
java.io.File log)
Maximises the likelihood, logging to a file. |
Likelihood |
GoldenSection.restart(Calculator l,
java.io.File checkPoint)
|
Likelihood |
GoldenSection.restart(Calculator l,
java.io.File checkPoint)
|
Likelihood |
NelderMead.restart(Calculator l,
java.io.File checkPoint)
|
Likelihood |
NelderMead.restart(Calculator l,
java.io.File checkPoint)
|
Likelihood |
Optimizer.restart(Calculator l,
java.io.File checkPoint)
Maximises the likelihood starting from a checkpoint file (see Optimizer.setCheckPointFile(java.io.File) ,
logging to the screen. |
Likelihood |
Optimizer.restart(Calculator l,
java.io.File checkPoint)
Maximises the likelihood starting from a checkpoint file (see Optimizer.setCheckPointFile(java.io.File) ,
logging to the screen. |
Likelihood |
GoldenSection.restart(Calculator l,
java.io.File checkPoint,
java.io.File log)
|
Likelihood |
GoldenSection.restart(Calculator l,
java.io.File checkPoint,
java.io.File log)
|
Likelihood |
NelderMead.restart(Calculator l,
java.io.File checkPoint,
java.io.File log)
|
Likelihood |
NelderMead.restart(Calculator l,
java.io.File checkPoint,
java.io.File log)
|
Likelihood |
Optimizer.restart(Calculator l,
java.io.File checkPoint,
java.io.File log)
Maximises the likelihood starting from a checkpoint file (see Optimizer.setCheckPointFile(java.io.File) ,
logging to a file. |
Likelihood |
Optimizer.restart(Calculator l,
java.io.File checkPoint,
java.io.File log)
Maximises the likelihood starting from a checkpoint file (see Optimizer.setCheckPointFile(java.io.File) ,
logging to a file. |
Uses of Parameters.ParameterException in Parameters |
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Methods in Parameters that throw Parameters.ParameterException | |
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Parameter |
Parameters.getParam(java.lang.String name)
Gets the parameter with the given name |
double |
Parameters.getValue(java.lang.String name)
Gets the value of a parameter |
Uses of Parameters.ParameterException in Simulations |
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Methods in Simulations that throw Parameters.ParameterException | |
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double |
HypothesisTest.test(Tree t,
Alignment a,
Alignment unobserved,
Parameters nullParams,
Parameters altParams)
Does a hpyothesis test on the given data and gives a p-value |
double |
HypothesisTest.test(Tree t,
Alignment a,
Alignment unobserved,
Parameters nullParams,
Parameters altParams,
java.util.Map<java.lang.String,java.lang.String> recode)
Does a hpyothesis test on the given data and gives a p-value |
Constructors in Simulations that throw Parameters.ParameterException | |
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Simulate(java.util.Map<java.lang.String,Model> m,
Tree t,
Parameters p)
Creates an object to simulate data for a given set of models, a tree and parameters. |
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Simulate(java.util.Map<java.lang.String,Model> m,
Tree t,
Parameters p,
Alignment unobserved)
Creates an object to simulate data for a given set of models, a tree, parameters and unobserved sattes. |
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Simulate(java.util.Map<java.lang.String,Model> m,
Tree t,
Parameters p,
Alignment unobserved,
java.util.Map<java.lang.String,Constrainer> con)
Creates an object to simulate data for a given set of models, a tree, parameters, unobserved states and constrainers. |
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Simulate(Model m,
Tree t,
Parameters p)
Creates an object to simulate data for a given model, tree and parameters. |
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Simulate(Model m,
Tree t,
Parameters p,
Alignment unobserved)
Creates an object to simulate data for a given model, tree, parameters and unobserved states. |
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Simulate(Model m,
Tree t,
Parameters p,
Alignment unobserved,
Constrainer con)
Creates an object to simulate data for a given model, tree, parameters, unobserved states and constraints. |
Uses of Parameters.ParameterException in Trees |
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Constructors in Trees that throw Parameters.ParameterException | |
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Tree(Tree old,
Parameters p)
Duplicates a tree topology while replacing branch lengths using the appropiate parameter |
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