Package org.biojava.nbio.survival.cox

Class SurvivalInfoHelper

java.lang.Object

org.biojava.nbio.survival.cox.SurvivalInfoHelper

public class SurvivalInfoHelper
extends java.lang.Object

Used to work with SurvivalInfo

Author:

Scooter Willis

Constructor Summary

Constructors

Constructor	Description
SurvivalInfoHelper()

Method Summary

Modifier and Type	Method	Description
static java.util.ArrayList<java.lang.String>	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	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	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>	getGroupCategories(java.lang.String groupName, java.util.ArrayList<SurvivalInfo> survivalInfoList)
static void	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

Methods inherited from class java.lang.Object

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

Constructor Detail

SurvivalInfoHelper

public SurvivalInfoHelper()

Method Detail

dump

public static void 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. This then allows the file to be loaded into R and calculations can be verified.

Parameters:

DataT -

ps -

delimiter -

categorizeData

public static void categorizeData(java.util.ArrayList<SurvivalInfo> DataT)

Take a collection of categorical data and convert it to numeric to be used in cox calculations

Parameters:

DataT -

addInteraction

public static java.util.ArrayList<java.lang.String> 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.

Parameters:

variable1 -

variable2 -

survivalInfoList -

Returns:

groupByRange

public static void groupByRange(double[] range,
                                java.lang.String variable,
                                java.lang.String groupName,
                                java.util.ArrayList<SurvivalInfo> survivalInfoList)
                         throws java.lang.Exception

Need to allow a range of values similar to cut in R and a continuous c

Parameters:

range -

variable -

groupName -

survivalInfoList -

Throws:

java.lang.Exception

getGroupCategories

public static java.util.ArrayList<java.lang.String> getGroupCategories(java.lang.String groupName,
                                                                       java.util.ArrayList<SurvivalInfo> survivalInfoList)

Parameters:

groupName -

survivalInfoList -

Returns: