Package org.biojava.nbio.survival.cox

Class CoxInfo

java.lang.Object

org.biojava.nbio.survival.cox.CoxInfo

public class CoxInfo
extends Object

Holds the results of a cox analysis where calling dump(), toString() will give an output similar to R

Author:

Scooter Willis

Field Summary

Fields

Modifier and Type	Field	Description
ExpressionFigure	ef
KaplanMeierFigure	kmf

Constructor Summary

Constructors

Constructor	Description
CoxInfo()

Method Summary

Modifier and Type	Method	Description
void	dump()
static String	fmt(Double d, int precision, int pad)
String	fmtpl(String d, int pad)	Pad left a string with spaces
String	fmtpr(String d, int pad)
double	getChiSquare()
CoxCoefficient	getCoefficient(String name)
LinkedHashMap<String,CoxCoefficient>	getCoefficientsList()
String	getCoefficientText(boolean header, String beginLine, String beginCell, String endCell, String endLine)
double	getDegreeFreedom()
double[][]	getImat()
LinkedHashMap<String,String>	getMetaDataFilter()
double[][]	getNaive_imat()
double[][]	getNaiveVariance()
int	getNumberCoefficients()
double	getOverallModelFitPvalue()
Double	getRscore()
Double	getRscoreLogrankTestpvalue()
Double	getScoreLogrankTest()
Double	getScoreLogrankTestpvalue()
ArrayList<SurvivalInfo>	getSurvivalInfoList()
double[][]	getVariableResiduals()
double[][]	getVariance()
WaldTestInfo	getWaldTestInfo()
double[]	getWeighted()
void	setCoefficient(String name, CoxCoefficient coefficient)
void	setDegreeFreedom(double degreeFreedom)
void	setMetaDataFilter(LinkedHashMap<String,String> metaDataFilter)
void	setNaiveVariance(double[][] var)
void	setRscore(Double rscore)
void	setRscoreLogrankTestpvalue(Double rscoreLogrankTestpvalue)
void	setScoreLogrankTest(Double scoreLogrankTest)
void	setScoreLogrankTestpvalue(Double scoreLogrankTestpvalue)
void	setSurvivalInfoList(ArrayList<SurvivalInfo> data)
void	setVariableResiduals(double[][] rr)
void	setVariance(double[][] var)
void	setWaldTestInfo(WaldTestInfo waldTestInfo)
String	toString()
String	toString(String beginLine, String del, String endLine)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Details

kmf

public KaplanMeierFigure kmf

ef

public ExpressionFigure ef

Constructor Details

CoxInfo

public CoxInfo()

Method Details

getSurvivalInfoList

public ArrayList<SurvivalInfo> getSurvivalInfoList()

Returns:

setVariance

public void setVariance(double[][] var)
                 throws Exception

Parameters:

var -

Throws:

Exception

getVariance

public double[][] getVariance()

Returns:

setNaiveVariance

public void setNaiveVariance(double[][] var)
                      throws Exception

Parameters:

var -

Throws:

Exception

getNaiveVariance

public double[][] getNaiveVariance()

Returns:

setSurvivalInfoList

public void setSurvivalInfoList(ArrayList<SurvivalInfo> data)

Parameters:

data -

getWeighted

public double[] getWeighted()

Returns:

getVariableResiduals

public double[][] getVariableResiduals()

Returns:

setVariableResiduals

public void setVariableResiduals(double[][] rr)

Parameters:

rr -

getNumberCoefficients

public int getNumberCoefficients()

Returns:

getCoefficient

public CoxCoefficient getCoefficient(String name)

Parameters:

name -

Returns:

setCoefficient

public void setCoefficient(String name,
 CoxCoefficient coefficient)

Parameters:

name -

coefficient -

getCoefficientText

public String getCoefficientText(boolean header,
 String beginLine,
 String beginCell,
 String endCell,
 String endLine)

Parameters:

header -

beginLine -

beginCell -

endCell -

endLine -

Returns:

fmt

public static String fmt(Double d,
 int precision,
 int pad)

Parameters:

d -

precision -

pad -

Returns:

dump

public void dump()

fmtpr

public String fmtpr(String d,
 int pad)

Parameters:

d -

pad -

Returns:

fmtpl

public String fmtpl(String d,
 int pad)

Pad left a string with spaces

Parameters:

d -

pad -

Returns:

toString

public String toString()

Overrides:

toString in class Object

toString

public String toString(String beginLine,
 String del,
 String endLine)

Parameters:

beginLine -

del -

endLine -

Returns:

getChiSquare

public double getChiSquare()

Returns:

the scoreLogrankTest

getDegreeFreedom

public double getDegreeFreedom()

Returns:

the degreeFreedom

getOverallModelFitPvalue

public double getOverallModelFitPvalue()

Returns:

the scoreLogrankTestpvalue

getRscore

public Double getRscore()

Returns:

the rscore

setRscore

public void setRscore(Double rscore)

Parameters:

rscore - the rscore to set

getRscoreLogrankTestpvalue

public Double getRscoreLogrankTestpvalue()

Returns:

the rscoreLogrankTestpvalue

setRscoreLogrankTestpvalue

public void setRscoreLogrankTestpvalue(Double rscoreLogrankTestpvalue)

Parameters:

rscoreLogrankTestpvalue - the rscoreLogrankTestpvalue to set

getScoreLogrankTest

public Double getScoreLogrankTest()

Returns:

the scoreLogrankTest

setScoreLogrankTest

public void setScoreLogrankTest(Double scoreLogrankTest)

Parameters:

scoreLogrankTest - the scoreLogrankTest to set

getScoreLogrankTestpvalue

public Double getScoreLogrankTestpvalue()

Returns:

the scoreLogrankTestpvalue

setScoreLogrankTestpvalue

public void setScoreLogrankTestpvalue(Double scoreLogrankTestpvalue)

Parameters:

scoreLogrankTestpvalue - the scoreLogrankTestpvalue to set

getMetaDataFilter

public LinkedHashMap<String,String> getMetaDataFilter()

Returns:

the metaDataFilter

setMetaDataFilter

public void setMetaDataFilter(LinkedHashMap<String,String> metaDataFilter)

Parameters:

metaDataFilter - the metaDataFilter to set

getCoefficientsList

public LinkedHashMap<String,CoxCoefficient> getCoefficientsList()

Returns:

the coefficientsList

getWaldTestInfo

public WaldTestInfo getWaldTestInfo()

Returns:

the waldTestInfo

getImat

public double[][] getImat()

Returns:

the imat

getNaive_imat

public double[][] getNaive_imat()

Returns:

the naive_imat

setDegreeFreedom

public void setDegreeFreedom(double degreeFreedom)

Parameters:

degreeFreedom - the degreeFreedom to set

setWaldTestInfo

public void setWaldTestInfo(WaldTestInfo waldTestInfo)

Parameters:

waldTestInfo - the waldTestInfo to set