net.maizegenetics.stats.linearmodels

Class SolveByOrthogonalizing

java.lang.Object

net.maizegenetics.stats.linearmodels.SolveByOrthogonalizing

public class SolveByOrthogonalizing
extends Object

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	SolveByOrthogonalizing.Marker

Method Summary

Modifier and Type	Method and Description
int	baseDf()
static double	calculateFfromR2(double r2, double markerDf, double errorDf)
static double	calculateP(double F, double markerDf, double errorDf)
static double	calculateR2Fromp(double alpha, double modelDf, double errorDf)
static double[]	center(double[] values)
static double[]	centerAndScale(double[] values)
List<double[]>	copyOrthogonalizedData()
List<double[]>	copyUColumns()
static SolveByOrthogonalizing	getInstanceFromModel(List<ModelEffect> baseModel, List<double[]> dataList)
static SolveByOrthogonalizing	getInstanceFromVectors(List<double[]> basisVectors, List<double[]> dataList)
List<double[]>	getOrthogonalizedData()
List<double[]>	getUColumns()
static double	innerProduct(double[] x, double[] y)
static double[]	scale(double[] values)
SolveByOrthogonalizing.Marker	solveForR(Position pos, double[] values)
SolveByOrthogonalizing.Marker	solveForR(Position pos, double[] add, double[] dom)
SolveByOrthogonalizing.Marker	solveForR(SolveByOrthogonalizing.Marker marker)

Methods inherited from class java.lang.Object

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

Method Detail

getInstanceFromModel

public static SolveByOrthogonalizing getInstanceFromModel(List<ModelEffect> baseModel,
                                                          List<double[]> dataList)

getInstanceFromVectors

public static SolveByOrthogonalizing getInstanceFromVectors(List<double[]> basisVectors,
                                                            List<double[]> dataList)

solveForR

public SolveByOrthogonalizing.Marker solveForR(SolveByOrthogonalizing.Marker marker)

solveForR

public SolveByOrthogonalizing.Marker solveForR(Position pos,
                                               double[] values)

solveForR

public SolveByOrthogonalizing.Marker solveForR(Position pos,
                                               double[] add,
                                               double[] dom)

baseDf

public int baseDf()

Returns:

the df in the base model, including 1 df for the mean

innerProduct

public static double innerProduct(double[] x,
                                  double[] y)

center

public static double[] center(double[] values)

scale

public static double[] scale(double[] values)

centerAndScale

public static double[] centerAndScale(double[] values)

calculateFfromR2

public static double calculateFfromR2(double r2,
                                      double markerDf,
                                      double errorDf)

calculateP

public static double calculateP(double F,
                                double markerDf,
                                double errorDf)

calculateR2Fromp

public static double calculateR2Fromp(double alpha,
                                      double modelDf,
                                      double errorDf)

getOrthogonalizedData

public List<double[]> getOrthogonalizedData()

copyOrthogonalizedData

public List<double[]> copyOrthogonalizedData()

getUColumns

public List<double[]> getUColumns()

copyUColumns

public List<double[]> copyUColumns()