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Packages that use Parameter | |
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Likelihood | Provides classes for calculating the likelihood of a tree given a model and an alignment. |
Parameters | Provides classes for defining parameters used in the various calculations. |
Uses of Parameter in Likelihood |
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Methods in Likelihood with parameters of type Parameter | |
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Range |
ConfidenceInterval.getCI(Parameter param,
double conf)
Calculates the confidence interval for a single parameter |
Uses of Parameter in Parameters |
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Methods in Parameters that return Parameter | |
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Parameter |
Parameter.clone()
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Parameter |
Parameters.getParam(java.lang.String name)
Gets the parameter with the given name |
static Parameter |
Parameter.newEstimatedBoundedParameter(java.lang.String name,
double lbound,
double ubound)
Creates a new bounded parameter that is estimated. |
static Parameter |
Parameter.newEstimatedBoundedParameter(java.lang.String name,
double lbound,
double ubound,
boolean matrix)
Creates a new bounded paramater that is estimated and is optionally in a rate matrix |
static Parameter |
Parameter.newEstimatedParameter(java.lang.String name)
Creates a new (unbounded) paramater that is estimated. |
static Parameter |
Parameter.newEstimatedParameter(java.lang.String name,
boolean matrix)
Creates a new unbounded parameter that is estimated and is optionally in a rate matrix. |
static Parameter |
Parameter.newEstimatedPositiveParameter(java.lang.String name)
Creates a new parameter that has to be positive and is estimated. |
static Parameter |
Parameter.newEstimatedPositiveParameter(java.lang.String name,
boolean matrix)
Creates a new positive parameter that is estimated and is optionally in a rate matrix. |
static Parameter |
Parameter.newFixedParameter(java.lang.String name,
double value)
Creates a new fixed parameter (i.e. |
Methods in Parameters that return types with arguments of type Parameter | |
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java.util.Iterator<Parameter> |
Parameters.iterator()
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Methods in Parameters with parameters of type Parameter | |
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void |
Parameters.addParameter(Parameter p)
Add a parameter |
void |
Parameters.setValue(Parameter p,
double v)
Sets the value of a parameter |
Constructor parameters in Parameters with type arguments of type Parameter | |
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Parameters(java.util.ArrayList<Parameter> params)
Creates a set of parameters containing the given parameters |
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