ModelTest

Class HypothesisTest

java.lang.Object

ModelTest.HypothesisTest

public class HypothesisTest
extends java.lang.Object

Class to do hypothesis testing using simulation to generate the null distribution.

Version:

2.0

Constructor Summary

Constructors

Constructor and Description
HypothesisTest(java.util.Map<java.lang.String,Model> nullModel, java.util.Map<java.lang.String,Model> altModel, Optimizer o, int reps) Constructor
HypothesisTest(Model nullModel, Model altModel, Optimizer o, int reps) Constructor

Method Summary

Methods

Modifier and Type	Method and Description
double	test(java.util.Map<java.lang.String,Tree> t, Alignment a, Alignment unobserved, Parameters nullParams, Parameters altParams) Does a hypothesis test on the given data and gives a p-value
double	test(java.util.Map<java.lang.String,Tree> t, Alignment a, Alignment unobserved, Parameters nullParams, Parameters altParams, java.util.Map<java.lang.String,java.lang.String> recode) Does a hypothesis test on the given data and gives a p-value
double	test(Tree t, Alignment a, Alignment unobserved, Parameters nullParams, Parameters altParams) Does a hypothesis test on the given data and gives a p-value
double	test(Tree t, Alignment a, Alignment unobserved, Parameters nullParams, Parameters altParams, java.util.Map<java.lang.String,java.lang.String> recode) Does a hypothesis test on the given data and gives a p-value

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

HypothesisTest

public HypothesisTest(Model nullModel,
              Model altModel,
              Optimizer o,
              int reps)

Constructor

Parameters:

nullModel - The null model

altModel - The alternative model

o - The optimiser to be used

reps - The number of samples of the null distribution to generate

HypothesisTest

public HypothesisTest(java.util.Map<java.lang.String,Model> nullModel,
              java.util.Map<java.lang.String,Model> altModel,
              Optimizer o,
              int reps)

Constructor

Parameters:

nullModel - Map from site class to null model for that site class

altModel - Map from site class to the alternate model for that site class

o - The optimiser to be used

reps - The number of samples of the null distribution to generate

Method Detail

test

public double test(Tree t,
          Alignment a,
          Alignment unobserved,
          Parameters nullParams,
          Parameters altParams)
            throws GeneralException

Does a hypothesis test on the given data and gives a p-value

Parameters:

t - The tree

a - The alignment

unobserved - Any unobserved states

nullParams - The parameters of the null model

altParams - The parameters of the alternative model

Returns:

A p-value

Throws:

GeneralException - When there is a problem performing the hypothesis test

test

public double test(Tree t,
          Alignment a,
          Alignment unobserved,
          Parameters nullParams,
          Parameters altParams,
          java.util.Map<java.lang.String,java.lang.String> recode)
            throws GeneralException

Does a hypothesis test on the given data and gives a p-value

Parameters:

t - The tree

a - The alignment

unobserved - Any unobserved states

nullParams - The parameters of the null model

altParams - The parameters of the alternative model

recode - The recoding to be passed to the simulator. See Simulate.getAlignment(int, java.util.Map) for while this is necessary.

Returns:

A p-value

Throws:

GeneralException - When there is a problem performing the hypothesis test

test

public double test(java.util.Map<java.lang.String,Tree> t,
          Alignment a,
          Alignment unobserved,
          Parameters nullParams,
          Parameters altParams)
            throws GeneralException

Does a hypothesis test on the given data and gives a p-value

Parameters:

t - Map from site class to tree

a - The alignment

unobserved - Any unobserved states

nullParams - The parameters of the null model

altParams - The parameters of the alternative model

Returns:

A p-value

Throws:

GeneralException - When there is a problem performing the hypothesis test

test

public double test(java.util.Map<java.lang.String,Tree> t,
          Alignment a,
          Alignment unobserved,
          Parameters nullParams,
          Parameters altParams,
          java.util.Map<java.lang.String,java.lang.String> recode)
            throws GeneralException

Does a hypothesis test on the given data and gives a p-value

Parameters:

t - Map from site class to tree

a - The alignment

unobserved - Any unobserved states

nullParams - The parameters of the null model

altParams - The parameters of the alternative model

recode - The recoding to be passed to the simulator. See Simulate.getAlignment(int, java.util.Map) for while this is necessary.

Returns:

A p-value

Throws:

GeneralException - When there is a problem performing the hypothesis test