Example usage for weka.core Statistics chiSquaredProbability

Introduction

In this page you can find the example usage for weka.core Statistics chiSquaredProbability.

Prototype

public static double chiSquaredProbability(double x, double v) 

Source Link

Document

Returns chi-squared probability for given value and degrees of freedom.

Usage

From source file:gov.nih.nci.caintegrator.plots.kaplanmeier.DefaultKMAlgorithmImpl.java

License:BSD License

public Double getLogRankPValue(Collection<KMSampleDTO> group1, Collection<KMSampleDTO> group2) {
    //need to//from  ww w .  j  ava 2  s  .  c  o  m
    ArrayList<KMSampleDTO> samples = new ArrayList<KMSampleDTO>();
    samples.addAll(group1);
    samples.addAll(group2);
    Collections.sort(samples, new KaplanMeierSampleComparator());
    float u = 0;
    float v = 0;
    float a = 0;
    float b = 0;
    float c = (float) group1.size();
    float d = (float) group2.size();
    float t = 0;
    for (int i = 0; i < samples.size(); i++) {
        KMSampleDTO event = samples.get(i);
        if (event.getSurvivalLength() > t) {
            if (a + b > 0) {
                u += a - (a + b) * (a + c) / (a + b + c + d);
                v += (a + b) * (c + d) * (a + c) * (b + d)
                        / ((a + b + c + d - 1) * (Math.pow((a + b + c + d), 2)));
            }
            a = 0;
            b = 0;
            t = event.getSurvivalLength();
        }
        if (group1.contains(event)) {
            if (event.getCensor()) {
                a += 1;
            }
            c -= 1;
        } else {
            if (event.getCensor()) {
                b += 1;
            }
            d -= 1;
        }
    }

    if ((a > 0 | b > 0) & (a + b + c + d - 1 > 0)) {
        u += a - (a + b) * (a + c) / (a + b + c + d);
        v += (a + b) * (c + d) * (a + c) * (b + d) / ((a + b + c + d - 1) * (Math.pow((a + b + c + d), 2)));
    }

    if (v > 0) {
        return new Double(Statistics.chiSquaredProbability(Math.pow(u, 2.0) / v, 1.0));
    } else {
        return new Double(UNKNOWN_PVALUE);
    }
}

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From source file:gov.nih.nci.caintegrator.ui.graphing.data.kaplanmeier.KaplanMeierAlgorithms.java

License:BSD License

public double getLogRankPValue(Collection<KaplanMeierSampleInfo> group1,
        Collection<KaplanMeierSampleInfo> group2) {
    //need to/*w  w w  .  jav a 2 s .  c  o m*/
    ArrayList<KaplanMeierSampleInfo> samples = new ArrayList<KaplanMeierSampleInfo>();
    samples.addAll(group1);
    samples.addAll(group2);
    Collections.sort(samples, new KaplanMeierSampleComparator());
    float u = 0;
    float v = 0;
    float a = 0;
    float b = 0;
    float c = (float) group1.size();
    float d = (float) group2.size();
    float t = 0;
    for (int i = 0; i < samples.size(); i++) {
        KaplanMeierSampleInfo event = (KaplanMeierSampleInfo) samples.get(i);
        if (event.getTime() > t) {
            if (a + b > 0) {
                u += a - (a + b) * (a + c) / (a + b + c + d);
                v += (a + b) * (c + d) * (a + c) * (b + d)
                        / ((a + b + c + d - 1) * (Math.pow((a + b + c + d), 2)));
            }
            a = 0;
            b = 0;
            t = event.getTime();
        }
        if (group1.contains(event)) {
            if (event.getCensor() == 1) {
                a += 1;
            }
            c -= 1;
        } else {
            if (event.getCensor() == 1) {
                b += 1;
            }
            d -= 1;
        }
    }

    if ((a > 0 | b > 0) & (a + b + c + d - 1 > 0)) {
        u += a - (a + b) * (a + c) / (a + b + c + d);
        v += (a + b) * (c + d) * (a + c) * (b + d) / ((a + b + c + d - 1) * (Math.pow((a + b + c + d), 2)));
    }

    if (v > 0) {
        return Statistics.chiSquaredProbability(Math.pow(u, 2.0) / v, 1.0);
    } else {
        return -100.0;
    }
}

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