Likelihood
Class ConfidenceInterval

java.lang.Object
  extended by Likelihood.ConfidenceInterval

public class ConfidenceInterval
extends java.lang.Object

Used to calculate congfidence intervals for a parameter. Due to computational constraints this is not done properly. When searching for the edges of the confidence interval we only update the parameter of interest rather than optomising every parameter at each step.

Version:
1.0

Constructor Summary
ConfidenceInterval(Calculator l, Parameters p)
          Default constructor
 
Method Summary
 Range getCI(Parameter param, double conf)
          Calculates the confidence interval for a single parameter
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

ConfidenceInterval

public ConfidenceInterval(Calculator l,
                          Parameters p)
Default constructor

Parameters:
l - The likelihod calculator to be used in constrcuting confidence intervals
p - The parameters to construct confidence intervals for
Method Detail

getCI

public Range getCI(Parameter param,
                   double conf)
            throws RateCategory.RateException,
                   Model.ModelException,
                   TreeException,
                   Parameters.ParameterException
Calculates the confidence interval for a single parameter

Parameters:
param - The parameter to construct the interval for
conf - The confidence level
Returns:
The confidence interval
Throws:
RateCategory.RateException - Thrown if there is an issue with a rate category in the model (e.g. a badly formatted rate).
Model.ModelException - Thrown if there is a problem with the model (e.g. the rate categories differ in their states)
TreeException - Thrown if there is a problem with the tree.
Parameters.ParameterException - Thrown if there is a problem with the parameters (e.g. a requied parameter is not present)