Uses of Class
org.biojava.nbio.survival.cox.SurvivalInfo

Packages that use SurvivalInfo

Package	Description
org.biojava.nbio.survival.cox
org.biojava.nbio.survival.cox.comparators
org.biojava.nbio.survival.cox.stats
org.biojava.nbio.survival.kaplanmeier.figure

Uses of SurvivalInfo in org.biojava.nbio.survival.cox

Methods in org.biojava.nbio.survival.cox that return types with arguments of type SurvivalInfo

Modifier and Type	Method and Description
java.util.ArrayList<SurvivalInfo>	CoxInfo.getSurvivalInfoList()

Methods in org.biojava.nbio.survival.cox with parameters of type SurvivalInfo

Modifier and Type	Method and Description
int	SurvivalInfo.compareTo(SurvivalInfo o)

Method parameters in org.biojava.nbio.survival.cox with type arguments of type SurvivalInfo

Modifier and Type	Method and Description
static java.util.ArrayList<java.lang.String>	SurvivalInfoHelper.addInteraction(java.lang.String variable1, java.lang.String variable2, java.util.ArrayList<SurvivalInfo> survivalInfoList) To test for interactions use two variables and create a third variable where the two are multiplied together.
static void	SurvivalInfoHelper.categorizeData(java.util.ArrayList<SurvivalInfo> DataT) Take a collection of categorical data and convert it to numeric to be used in cox calculations
static void	SurvivalInfoHelper.dump(java.util.ArrayList<SurvivalInfo> DataT, java.io.PrintStream ps, java.lang.String delimiter) For each analysis this allows outputing of the data used in the calculations to a printstream/file.
static java.util.ArrayList<java.lang.String>	SurvivalInfoHelper.getGroupCategories(java.lang.String groupName, java.util.ArrayList<SurvivalInfo> survivalInfoList)
static void	SurvivalInfoHelper.groupByRange(double[] range, java.lang.String variable, java.lang.String groupName, java.util.ArrayList<SurvivalInfo> survivalInfoList) Need to allow a range of values similar to cut in R and a continuous c
CoxInfo	CoxR.process(java.util.ArrayList<java.lang.String> variables, java.util.ArrayList<SurvivalInfo> DataT, boolean useStrata, boolean useWeighted, boolean robust, boolean cluster)
CoxInfo	CoxR.process(java.util.ArrayList<java.lang.String> variables, java.util.ArrayList<SurvivalInfo> data, int maxiter, CoxMethod method, double eps, double toler, double[] beta, int doscale, boolean useStrata, boolean useWeighted, boolean robust, boolean cluster)
static double[]	CoxMart.process(CoxMethod method, java.util.ArrayList<SurvivalInfo> survivalInfoList, boolean useStrata)
static double[][]	CoxScore.process(CoxMethod method, java.util.ArrayList<SurvivalInfo> survivalInfoList, CoxInfo coxInfo, boolean useStrata)
void	CoxInfo.setSurvivalInfoList(java.util.ArrayList<SurvivalInfo> data)

Uses of SurvivalInfo in org.biojava.nbio.survival.cox.comparators

Methods in org.biojava.nbio.survival.cox.comparators with parameters of type SurvivalInfo

Modifier and Type	Method and Description
int	SurvivalInfoValueComparator.compare(SurvivalInfo t, SurvivalInfo t1)
int	SurvivalInfoComparator.compare(SurvivalInfo t, SurvivalInfo t1)

Uses of SurvivalInfo in org.biojava.nbio.survival.cox.stats

Method parameters in org.biojava.nbio.survival.cox.stats with type arguments of type SurvivalInfo

Modifier and Type	Method and Description
static double[][]	AgScore.process(CoxMethod method, java.util.ArrayList<SurvivalInfo> survivalInfoList, CoxInfo coxInfo, boolean useStrata)

Uses of SurvivalInfo in org.biojava.nbio.survival.kaplanmeier.figure

Methods in org.biojava.nbio.survival.kaplanmeier.figure that return types with arguments of type SurvivalInfo

Modifier and Type	Method and Description
java.util.ArrayList<SurvivalInfo>	ExpressionFigure.getSurvivalInfoList() The data used to draw the graph

Method parameters in org.biojava.nbio.survival.kaplanmeier.figure with type arguments of type SurvivalInfo

Modifier and Type	Method and Description
SurvFitInfo	SurvFitKM.process(java.lang.String variable, java.util.ArrayList<SurvivalInfo> dataT, boolean useWeighted)
SurvFitInfo	SurvFitKM.process(java.lang.String variable, java.util.ArrayList<SurvivalInfo> dataT, SurvFitKM.Method method, SurvFitKM.Error error, boolean seFit, double confInt, SurvFitKM.ConfType confType, SurvFitKM.ConfLower confLower, java.lang.Double startTime, java.lang.Double newTime, boolean useWeighted)
java.util.LinkedHashMap<java.lang.String,StrataInfo>	SurvFitKM.processStrataInfo(java.lang.String variable, java.util.ArrayList<SurvivalInfo> dataT, SurvFitKM.Method method, SurvFitKM.Error error, boolean seFit, double confInt, SurvFitKM.ConfType confType, SurvFitKM.ConfLower confLower, java.lang.Double startTime, java.lang.Double newTime, boolean useWeighted)
void	ExpressionFigure.setSurvivalInfo(java.util.ArrayList<java.lang.String> title, java.util.ArrayList<SurvivalInfo> _siList, java.lang.String variable)