net.maizegenetics.stats.linearmodels

Class NestedCovariateModelEffect

java.lang.Object

net.maizegenetics.stats.linearmodels.NestedCovariateModelEffect

All Implemented Interfaces:

ModelEffect

public class NestedCovariateModelEffect
extends Object
implements ModelEffect

Constructor Summary

Constructors

Constructor and Description
NestedCovariateModelEffect(CovariateModelEffect cme, FactorModelEffect fme)
NestedCovariateModelEffect(double[] covariate, FactorModelEffect fme)
NestedCovariateModelEffect(float[] covariate, FactorModelEffect fme)

Method Summary

Modifier and Type	Method and Description
ModelEffect	getCopy()
int	getEffectSize()
FactorModelEffect	getFactorModelEffect()
Object	getID()
static NestedCovariateModelEffect	getInstance(CovariateModelEffect cme, ModelEffect me)
static NestedCovariateModelEffect	getInstance(double[] covariate, ModelEffect me)
int[]	getLevelCounts()
int	getNumberOfLevels()
int	getSize()
ModelEffect	getSubSample(int[] sample)
DoubleMatrix	getX()
DoubleMatrix	getXtX()
DoubleMatrix	getXtX2(NestedCovariateModelEffect ncme)
DoubleMatrix	getXty(double[] y)
DoubleMatrix	getyhat(double[] beta)
DoubleMatrix	getyhat(DoubleMatrix beta)
void	setID(Object id)

Methods inherited from class java.lang.Object

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

Constructor Detail

NestedCovariateModelEffect

public NestedCovariateModelEffect(CovariateModelEffect cme,
                                  FactorModelEffect fme)

NestedCovariateModelEffect

public NestedCovariateModelEffect(double[] covariate,
                                  FactorModelEffect fme)

NestedCovariateModelEffect

public NestedCovariateModelEffect(float[] covariate,
                                  FactorModelEffect fme)

Method Detail

getInstance

public static NestedCovariateModelEffect getInstance(CovariateModelEffect cme,
                                                     ModelEffect me)

getInstance

public static NestedCovariateModelEffect getInstance(double[] covariate,
                                                     ModelEffect me)

getID

public Object getID()

Specified by:

getID in interface ModelEffect

Returns:

an identifier for this factor

getLevelCounts

public int[] getLevelCounts()

Specified by:

getLevelCounts in interface ModelEffect

Returns:

the number of observations for each level of this factor

getNumberOfLevels

public int getNumberOfLevels()

Specified by:

getNumberOfLevels in interface ModelEffect

Returns:

the number of levels in this factor

getSize

public int getSize()

Specified by:

getSize in interface ModelEffect

Returns:

the number of observations in the data set

getX

public DoubleMatrix getX()

Specified by:

getX in interface ModelEffect

Returns:

the design matrix for this factor

getXtX

public DoubleMatrix getXtX()

Specified by:

getXtX in interface ModelEffect

Returns:

the crossproduct of the design matrix for this factor and itself

getXty

public DoubleMatrix getXty(double[] y)

Specified by:

getXty in interface ModelEffect

Parameters:

y - the dependent variable

Returns:

the product of the transpose of the design matrix for this factor and the data, y

getyhat

public DoubleMatrix getyhat(DoubleMatrix beta)

Specified by:

getyhat in interface ModelEffect

Parameters:

beta - the effect estimate for each level of this factor

Returns:

the predicted value of this factor for each observation

getyhat

public DoubleMatrix getyhat(double[] beta)

Specified by:

getyhat in interface ModelEffect

Parameters:

beta - the effect estimate for each level of this factor

Returns:

the predicted value of this factor for each observation

setID

public void setID(Object id)

Specified by:

setID in interface ModelEffect

Parameters:

id - an identifier for this factor

getXtX2

public DoubleMatrix getXtX2(NestedCovariateModelEffect ncme)

getFactorModelEffect

public FactorModelEffect getFactorModelEffect()

getCopy

public ModelEffect getCopy()

Specified by:

getCopy in interface ModelEffect

Returns:

a copy of this model effect

getSubSample

public ModelEffect getSubSample(int[] sample)

Specified by:

getSubSample in interface ModelEffect

Parameters:

sample - the index of samples to be returned

Returns:

a new ModelEffect containing the samples in the index. Individual observations may be repeated in the subsample.

getEffectSize

public int getEffectSize()

Specified by:

getEffectSize in interface ModelEffect

Returns:

the number of columns in the design matrix. This will be the number of levels in this factor, if unrestricted. 1 - the number of levels, if restricted.