package com.imsl.test.example.stat;

import java.text.*;
import com.imsl.stat.*;

/**
 * <p>
 * Computes the Kaplan-Meier probability estimates for censored data.
 * </p>
 * 
 * The following example is taken from Kalbfleisch and Prentice (1980, page 1).
 * The first column in <code>x</code> contains the death/censoring times for
 * rats suffering from vaginal cancer. The second column contains information as
 * to which of two forms of treatment were provided, while the third column
 * contains the censoring code. Finally, the fourth column contains the
 * frequency of each observation. The product-limit estimates of the survival
 * probabilities are computed for both groups along with their standard error
 * estimates. Tables containing these values along with other statistics are
 * printed.
 *
 *
 * @see <a href="KaplanMeierEstimatesEx1.java">Code</a>
 * @see <a href="doc-files/KaplanMeierEstimatesEx1.out">Output</a>
 */

public class KaplanMeierEstimatesEx1 {

    public static void main(String args[]) {
        double[][] x = {
            {143, 5, 0, 1}, {164, 5, 0, 1}, {188, 5, 0, 2}, {190, 5, 0, 1},
            {192, 5, 0, 1}, {206, 5, 0, 1}, {209, 5, 0, 1}, {213, 5, 0, 1},
            {216, 5, 0, 1}, {220, 5, 0, 1}, {227, 5, 0, 1}, {230, 5, 0, 1},
            {234, 5, 0, 1}, {246, 5, 0, 1}, {265, 5, 0, 1}, {304, 5, 0, 1},
            {216, 5, 1, 1}, {244, 5, 1, 1}, {142, 7, 0, 1}, {156, 7, 0, 1},
            {163, 7, 0, 1}, {198, 7, 0, 1}, {205, 7, 0, 1}, {232, 7, 0, 2},
            {233, 7, 0, 4}, {239, 7, 0, 1}, {240, 7, 0, 1}, {261, 7, 0, 1},
            {280, 7, 0, 2}, {296, 7, 0, 2}, {323, 7, 0, 1}, {204, 7, 1, 1},
            {344, 7, 1, 1}
        };
        int nobs = x.length, censorIndex = 2, frequencyIndex = 3;
        int stratumIndex = 1, responseIndex = 0;
        int i, groupValue;

        // Get Kaplan-Meir Estimates
        KaplanMeierEstimates km = new KaplanMeierEstimates(x);
        km.setCensorColumn(censorIndex);
        km.setFrequencyColumn(frequencyIndex);
        km.setStratumColumn(stratumIndex);
        int[] atRisk = km.getNumberAtRisk();
        int[] nFailing = km.getNumberOfFailures();
        double[] prob = km.getSurvivalProbabilities();
        double[] se = km.getStandardErrors();

        // Print Results
        NumberFormat nf = NumberFormat.getInstance();
        nf.setMaximumFractionDigits(4);
        nf.setMinimumFractionDigits(4);
        i = 0;
        while (i < nobs) {
            groupValue = (int) x[i][stratumIndex];
            System.out.println("\n       Kaplan-Meier Survival Probabilities");
            System.out.println("               For Group Value = "
                    + groupValue);
            System.out.println("\nNumber     Number"
                    + "                Survival     Estimated");
            System.out.println("at risk    Failing     Time"
                    + "     Probability   Std. Error");
            while (i < nobs && ((int) x[i][stratumIndex] == groupValue)) {
                if ((int) x[i][censorIndex] != 1) {
                    System.out.println("  " + atRisk[i] + "          "
                            + nFailing[i] + "" + "         "
                            + ((int) x[i][responseIndex]) + "       "
                            + nf.format(prob[i]) + "        "
                            + nf.format(se[i]));
                }
                i++;
            }
            System.out.println("\nTotal number in group = "
                    + km.getGroupTotal(groupValue));
            System.out.println("Total number failing = "
                    + km.getTotalNumberOfFailures(groupValue));
            System.out.println("Product Limit likelihood = "
                    + nf.format(km.getLogLikelihood(groupValue)));
        }
        System.out.println("\nThe number of rows of x with missing values is "
                + km.getNumberOfRowsMissing());
    }
}