net.maizegenetics.analysis.modelfitter

Class StepwiseAddDomModelFitter

StepwiseAdditiveModelFitter

net.maizegenetics.analysis.modelfitter.StepwiseAddDomModelFitter

public class StepwiseAddDomModelFitter
extends StepwiseAdditiveModelFitter

Fits an additive plus dominance model in a stepwise fashion. See StepwiseAdditiveModelFitter for a desription of outputs available.

Constructor Detail

StepwiseAddDomModelFitter

public StepwiseAddDomModelFitter(GenotypePhenotype genopheno,
                                 java.lang.String datasetName)

Parameters:

genopheno - a GenotypePhenotype object

datasetName - a name for the genopheno

Throws:

IllegalArgumentException - if any phenotype data is missing

Method Detail

runAnalysis

public void runAnalysis()

forwardStep

protected double forwardStep(double prevCriterionValue)

scanToFindCI

protected java.util.List<kotlin.Array[]> scanToFindCI()

testAddedTerm

protected double testAddedTerm(int testedTerm,
                               AdditiveSite addedTerm,
                               java.util.List<net.maizegenetics.stats.linearmodels.ModelEffect> theModel)

bestTerm

protected AdditiveSite bestTerm(java.util.List<net.maizegenetics.stats.linearmodels.ModelEffect> baseModel,
                                kotlin.Array[] interval)

runPermutationTest

public void runPermutationTest()

addToMarkerEffectReport

protected void addToMarkerEffectReport(boolean CI)