Package org.biojava.nbio.survival.cox
Class SurvivalInfoHelper
- java.lang.Object
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- org.biojava.nbio.survival.cox.SurvivalInfoHelper
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public class SurvivalInfoHelper extends java.lang.Object
Used to work with SurvivalInfo- Author:
- Scooter Willis
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Constructor Summary
Constructors Constructor Description SurvivalInfoHelper()
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Method Summary
All Methods Static Methods Concrete Methods 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 calculationsstatic 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
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Method Detail
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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
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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
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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:
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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
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getGroupCategories
public static java.util.ArrayList<java.lang.String> getGroupCategories(java.lang.String groupName, java.util.ArrayList<SurvivalInfo> survivalInfoList)
- Parameters:
groupName
-survivalInfoList
-- Returns:
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