net.maizegenetics.analysis.modelfitter

Class AbstractForwardRegression

net.maizegenetics.analysis.modelfitter.AbstractForwardRegression

All Implemented Interfaces:

ForwardRegression

Direct Known Subclasses:

AdditiveModelForwardRegression, AdditiveResidualForwardRegression

public class AbstractForwardRegression
implements ForwardRegression

Field Detail

y

protected kotlin.Array[] y

myGenotypePhenotype

protected GenotypePhenotype myGenotypePhenotype

myGenotype

protected GenotypeTable myGenotype

myPhenotype

protected Phenotype myPhenotype

enterLimit

protected double enterLimit

maxVariants

protected int maxVariants

numberOfSites

protected int numberOfSites

numberOfObservations

protected int numberOfObservations

siteList

protected java.util.List<net.maizegenetics.analysis.modelfitter.AdditiveSite> siteList

myBaseModel

protected java.util.List<net.maizegenetics.stats.linearmodels.ModelEffect> myBaseModel

myModel

protected java.util.List<net.maizegenetics.stats.linearmodels.ModelEffect> myModel

myFittedVariants

protected java.util.List<kotlin.Array[]> myFittedVariants

traitname

protected java.lang.String traitname

taxaIndex

protected kotlin.Array[] taxaIndex

Constructor Detail

AbstractForwardRegression

public AbstractForwardRegression(GenotypePhenotype data)

Parameters:

data - a GenotypePhenotype object

AbstractForwardRegression

public AbstractForwardRegression(java.lang.String serialFilename,
                                 Phenotype pheno)

Parameters:

serialFilename - the base name of the serialization files that end in _taxa.bin and _sites.bin

pheno - the Phenotype object to be used in the analysis

Method Detail

resetModel

public void resetModel(int phenotypeIndex,
                       double enterLimit,
                       int maxVariants)

getBaseModel

protected java.util.List<net.maizegenetics.stats.linearmodels.ModelEffect> getBaseModel()

fittedModel

public java.util.List<kotlin.Array[]> fittedModel()

phenotype

public Phenotype phenotype()

addVariant

protected void addVariant(AdditiveSite site,
                          double p,
                          int iteration,
                          int step)