net.maizegenetics.analysis.association

Class PhenotypeLM

net.maizegenetics.analysis.association.PhenotypeLM

public class PhenotypeLM

Field Detail

myDatum

protected Datum myDatum

myPhenotype

protected Phenotype myPhenotype

myBlues

protected Phenotype myBlues

reportBuilder

protected TableReportBuilder reportBuilder

myTaxaList

protected TaxaList myTaxaList

numberOfObservations

protected int numberOfObservations

myDataAttributes

protected java.util.List<net.maizegenetics.phenotype.PhenotypeAttribute> myDataAttributes

myFactorAttributes

protected java.util.List<net.maizegenetics.phenotype.PhenotypeAttribute> myFactorAttributes

myCovariateAttributes

protected java.util.List<net.maizegenetics.phenotype.PhenotypeAttribute> myCovariateAttributes

myTaxa

protected Taxon[] myTaxa

taxaInModel

protected java.util.ArrayList<net.maizegenetics.taxa.Taxon> taxaInModel

taxaInModelMap

protected java.util.Map<net.maizegenetics.taxa.Taxon,java.lang.Integer> taxaInModelMap

Constructor Detail

PhenotypeLM

public PhenotypeLM(Datum phenotypeOnly)

Method Detail

blues

public Phenotype blues()

report

public TableReport report()

datumList

public java.util.List<net.maizegenetics.plugindef.Datum> datumList()

initialize

protected void initialize()

solve

protected void solve()

testTaxaReplication

protected void testTaxaReplication()

model

protected java.util.ArrayList<net.maizegenetics.stats.linearmodels.ModelEffect> model(BitSet missingObs,
                                                                                      int numberOfNonmissingObs)