Likelihood

Class ConfidenceInterval

java.lang.Object

Likelihood.ConfidenceInterval

public class ConfidenceInterval
extends java.lang.Object

Used to calculate confidence 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 optimising every parameter at each step.

Version:

2.0

Constructor Summary

Constructors

Constructor and Description
ConfidenceInterval(StandardCalculator l, Parameters p) Default constructor

Method Summary

Methods

Modifier and Type	Method and Description
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(StandardCalculator l,
                  Parameters p)

Default constructor

Parameters:

l - The likelihood calculator to be used in constructing 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,
                   Calculator.CalculatorException

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)

Calculator.CalculatorException - If an unexpected (i.e. positive or NaN) log likelihood is calculated