org.biojava.nbio.survival.cox

Class SurvivalInfoHelper

java.lang.Object

org.biojava.nbio.survival.cox.SurvivalInfoHelper

public class SurvivalInfoHelper
extends Object

Used to work with SurvivalInfo

Author:

Scooter Willis

Constructor Summary

Constructors

Constructor and Description
SurvivalInfoHelper()

Method Summary

Modifier and Type	Method and Description
static ArrayList<String>	addInteraction(String variable1, String variable2, ArrayList<SurvivalInfo> survivalInfoList) To test for interactions use two variables and create a third variable where the two are multiplied together.
static void	categorizeData(ArrayList<SurvivalInfo> DataT) Take a collection of categorical data and convert it to numeric to be used in cox calculations
static void	dump(ArrayList<SurvivalInfo> DataT, PrintStream ps, String delimiter) For each analysis this allows outputing of the data used in the calculations to a printstream/file.
static ArrayList<String>	getGroupCategories(String groupName, ArrayList<SurvivalInfo> survivalInfoList)
static void	groupByRange(double[] range, String variable, String groupName, 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(ArrayList<SurvivalInfo> DataT,
                        PrintStream ps,
                        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(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 ArrayList<String> addInteraction(String variable1,
                                               String variable2,
                                               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,
                                String variable,
                                String groupName,
                                ArrayList<SurvivalInfo> survivalInfoList)
                         throws Exception

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

Parameters:

range -

variable -

groupName -

survivalInfoList -

Throws:

Exception

getGroupCategories

public static ArrayList<String> getGroupCategories(String groupName,
                                                   ArrayList<SurvivalInfo> survivalInfoList)

Parameters:

groupName -

survivalInfoList -

Returns: