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Packages that use RateCategory.RateException | |
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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. |
Models | Provides classes for defing a phylogenetic model. |
Optimizers | Provides classes for optimising a likelihood. |
Simulations | Provides a class to create simulate data. |
Uses of RateCategory.RateException in Ancestors |
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Methods in Ancestors that throw RateCategory.RateException | |
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abstract Alignment |
AncestralJoint.calculate(Parameters params)
Calculates the reconstruction |
Alignment |
AncestralJointBB.calculate(Parameters p)
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Alignment |
AncestralJointDP.calculate(Parameters params)
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AncestralMarginal.Result |
AncestralMarginal.calculate(Parameters params)
Calculates the reconstruction |
Uses of RateCategory.RateException in Likelihood |
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Methods in Likelihood that throw RateCategory.RateException | |
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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 RateCategory.RateException | |
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Probabilities(Model m,
Tree t,
Parameters p)
Constructor |
Uses of RateCategory.RateException in Models |
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Methods in Models that throw RateCategory.RateException | |
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static Model |
Model.fromFile(java.io.File f)
Creates a new model from a file. |
static RateCategory |
RateCategory.fromFile(java.io.File mfile)
Creates an instance from the information in a file. |
SquareMatrix |
RateCategory.getP(double length)
Gets the P-matrix for a given length |
void |
Model.setParameters(Parameters p)
Sets the parameters of a model to the values contained in the Parameters data structure. |
void |
RateCategory.setParameters(Parameters p)
Updates the parameters in the RateCategory. |
Constructors in Models that throw RateCategory.RateException | |
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RateCategory(java.lang.String[][] rates,
RateCategory.FrequencyType freqType,
java.util.HashMap<java.lang.String,java.lang.Integer> map)
Constrcutor for when the root distribution is defined as the stationary or quasi-staionary distribution. |
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RateCategory(java.lang.String[][] rates,
java.lang.String[] freq,
java.util.HashMap<java.lang.String,java.lang.Integer> map)
Constructor for when the root distribution is defined. |
Uses of RateCategory.RateException in Optimizers |
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Methods in Optimizers that throw RateCategory.RateException | |
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Likelihood |
GoldenSection.maximise(Calculator l,
Parameters params)
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Likelihood |
NelderMead.maximise(Calculator l,
Parameters params)
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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 |
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 |
GoldenSection.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 |
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 |
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 RateCategory.RateException in Simulations |
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Constructors in Simulations that throw RateCategory.RateException | |
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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. |
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