Survival Analysis Using Kaplan-Meier

/*

January 2007. Annie Che <chea@stat.ucla.edu>. UCLA Statistics.

reference for example data and formula:
	Modern Applied Statistics with S. Fourth Edition
	by W. N. Venables and B. D. Ripley
	Note that the first method of hazard calculation is used here (see reference for details).
*/

package edu.ucla.stat.SOCR.analyses.example;

import java.util.HashMap;
import edu.ucla.stat.SOCR.analyses.data.Data;
import edu.ucla.stat.SOCR.analyses.data.DataType;
import edu.ucla.stat.SOCR.analyses.result.SurvivalResult;


public class SurvivalKaplanMeierExample {
	public static void main(String args[]) {

		double[] time = {1,10,22,7,3,32,12,23,8,22,17,6,2,16,11,34,8,32,12,25,2,11,5,20,4,19,15,6,8,17,23,35,5,6,11,13,4,9,1,6,8,10};
		byte[] censor = {1,1,1,1,1,0,1,1,1,1,1,1,1,1,1,0,1,0,1,0,1,0,1,0,1,0,1,1,1,0,1,0,1,1,1,1,1,0,1,0,1,0};
		String[] treat = {"control","6-MP","control","6-MP","control","6-MP","control","6-MP",    "control","6-MP","control","6-MP","control","6-MP","control","6-MP","control","6-MP",   "control","6-MP","control","6-MP","control","6-MP","control","6-MP","control","6-MP",    "control","6-MP","control","6-MP","control","6-MP","control","6-MP","control","6-MP",    "control","6-MP","control","6-MP"};

		try {
			Data data = new Data();
			SurvivalResult result = (SurvivalResult)data.getSurvivalResult(time, censor, treat);
			double[][] survivalTimeArray = result.getSurvivalTime();
			double[][] survivalRateArray = result.getSurvivalRate();
			double[][] upperCIArray = result.getSurvivalUpperCI();
			double[][] lowerCIArray = result.getSurvivalLowerCI();
			int[][] atRiskArray = result.getSurvivalAtRisk();
			double[][] survivalSEArray = result.getSurvivalSE();
			String timeList = result.getSurvivalTimeList();;
			double[][] survivalTime = result.getSurvivalTime();
			double[][] survivalRate = result.getSurvivalRate();
			double[][] upperCI = result.getSurvivalUpperCI();;
			double[][] lowerCI = result.getSurvivalLowerCI();
			double[][] survivalSE = result.getSurvivalSE();
			double[][] censoredTime = result.getCensoredTimeArray();;
			double[][] censoredRate = result.getCensoredRateArray();
			double[] maxTime = result.getMaxTime();
			int[][]    atRisk = result.getSurvivalAtRisk();;
			String[]   groupNames = result.getSurvivalGroupNames();

			System.out.println("\n\nSURVIVAL TIME         = " + timeList);
			System.out.println("\n\nTIME | NUMBER_AT_RISK | RATE | STANDARD_ERROR_OF_RATE | UPPER_CI | LOWER_CI ");
			for (int i = 0; i < survivalRate.length; i++) {
				System.out.println("\n\nTREATMENT GROUP = " + groupNames[i]+"\n");
				for (int j = 0; j < survivalRate[i].length; j++) {
					if (upperCI[i][j] == 1) {
						System.out.println("\n" +  survivalTime[i][j] +"\t" + atRisk[i][j] + "\t" + survivalRate[i][j] +"\t" + survivalSE[i][j] + "\t" + upperCI[i][j]+"\t\t" + lowerCI[i][j]);
					} else {
						System.out.println("\n" +  survivalTime[i][j] +"\t" + atRisk[i][j] + "\t" + survivalRate[i][j] +"\t" + survivalSE[i][j] + "\t" + upperCI[i][j]+"\t" + lowerCI[i][j]);
					}
				}
			}

		} catch (Exception e) {
			System.out.println(e);
		}
	}
}