Package org.biojava.nbio.survival.kaplanmeier.figure

Class SurvFitKM

java.lang.Object

org.biojava.nbio.survival.kaplanmeier.figure.SurvFitKM

public class SurvFitKM
extends Object

Ported from survfitKM.S When combining multiple entries with same time not sure how the weighting adds up

Author:

Scooter Willis

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	SurvFitKM.ConfLower
static class	SurvFitKM.ConfType
static class	SurvFitKM.Error
static class	SurvFitKM.Method

Constructor Summary

Constructors

Constructor	Description
SurvFitKM()

Method Summary

Modifier and Type	Method	Description
static void	main(String[] args)
SurvFitInfo	process(String datafile, String timeColumn, String statusColumn, String weightColumn, String variableColumn, boolean useWeights)
SurvFitInfo	process(String variable, ArrayList<SurvivalInfo> dataT, boolean useWeighted)
SurvFitInfo	process(String variable, ArrayList<SurvivalInfo> dataT, SurvFitKM.Method method, SurvFitKM.Error error, boolean seFit, double confInt, SurvFitKM.ConfType confType, SurvFitKM.ConfLower confLower, Double startTime, Double newTime, boolean useWeighted)
SurvFitInfo	process(LinkedHashMap<String,ArrayList<CensorStatus>> survivalData, boolean useWeights)
LinkedHashMap<String,StrataInfo>	processStrataInfo(String variable, ArrayList<SurvivalInfo> dataT, SurvFitKM.Method method, SurvFitKM.Error error, boolean seFit, double confInt, SurvFitKM.ConfType confType, SurvFitKM.ConfLower confLower, Double startTime, Double newTime, boolean useWeighted)

Methods inherited from class java.lang.Object

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

Constructor Detail

SurvFitKM

public SurvFitKM()

Method Detail

process

public SurvFitInfo process(LinkedHashMap<String,ArrayList<CensorStatus>> survivalData,
                           boolean useWeights)
                    throws Exception

Parameters:

survivalData -

useWeights -

Returns:

Throws:

Exception

process

public SurvFitInfo process(String datafile,
                           String timeColumn,
                           String statusColumn,
                           String weightColumn,
                           String variableColumn,
                           boolean useWeights)
                    throws Exception

Parameters:

datafile -

timeColumn -

statusColumn -

weightColumn -

variableColumn -

useWeights -

Returns:

Throws:

Exception

process

public SurvFitInfo process(String variable,
                           ArrayList<SurvivalInfo> dataT,
                           boolean useWeighted)
                    throws Exception

Parameters:

variable -

dataT -

useWeighted -

Returns:

Throws:

Exception

processStrataInfo

public LinkedHashMap<String,StrataInfo> processStrataInfo(String variable,
                                                                ArrayList<SurvivalInfo> dataT,
                                                                SurvFitKM.Method method,
                                                                SurvFitKM.Error error,
                                                                boolean seFit,
                                                                double confInt,
                                                                SurvFitKM.ConfType confType,
                                                                SurvFitKM.ConfLower confLower,
                                                                Double startTime,
                                                                Double newTime,
                                                                boolean useWeighted)
                                                         throws Exception

Throws:

Exception

process

public SurvFitInfo process(String variable,
                           ArrayList<SurvivalInfo> dataT,
                           SurvFitKM.Method method,
                           SurvFitKM.Error error,
                           boolean seFit,
                           double confInt,
                           SurvFitKM.ConfType confType,
                           SurvFitKM.ConfLower confLower,
                           Double startTime,
                           Double newTime,
                           boolean useWeighted)
                    throws Exception

Parameters:

variable -

dataT -

method -

error -

seFit -

confInt -

confType -

confLower -

startTime -

newTime -

useWeighted -

Returns:

Throws:

Exception

main

public static void main(String[] args)

Parameters:

args - the command line arguments