num4anova 0.0.2-java → 0.0.4-java
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- checksums.yaml +4 -4
- data/CHANGELOG.md +10 -0
- data/ext/num4anova/MultiComp.java +146 -1
- data/ext/num4anova/OneWayLayout.java +137 -0
- data/lib/dunnet.rb +89 -0
- data/lib/multicomp.rb +7 -2
- data/lib/num4anova.rb +58 -14
- metadata +3 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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1
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---
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2
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SHA256:
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-
metadata.gz:
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data.tar.gz:
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metadata.gz: ca0164a7092861bfca67f257129332375e90bfae762365194ced78ef75a293a7
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4
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data.tar.gz: 16f17fb717e3d92c27c4c651e034704cd81609a3adc293555eac54f9209884be
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SHA512:
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-
metadata.gz:
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data.tar.gz:
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metadata.gz: e14efb373cde03fc5872f3dfb1d4186e5d2263b0b7597970d1629c562cfb6696ecf2cdbfc3325aa2d732e252241de093c156b7d9da21b51a8ea305f3e24e0e0f
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7
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data.tar.gz: c9b7f310d00d060d1c6fee3e8e9f5c43fce812a65d51b192315c72a378de7e2bc775e1118346373a93047c1cd8880240d03d52309ec0d8f567481923f14e31b4
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data/CHANGELOG.md
CHANGED
@@ -23,6 +23,28 @@ public class MultiComp {
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double[][] statistic = hypoth.calcTestStatistic(xi);
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return hypoth.executeTest(statistic, a * 0.5);
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}
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public boolean scheffe_test(double[][] xi, double a) {
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return false;
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}
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public boolean[][] twosideTest(double[][] xi, double a) {
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HypothesisTest hypoth = new TwoSideTest();
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double[][] statistic = hypoth.calcTestStatistic(xi);
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return hypoth.executeTest(statistic, a / 2.0);
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}
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public boolean[][] rightsideTest(double[][] xi, double a) {
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HypothesisTest hypoth = new RightSideTest();
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double[][] statistic = hypoth.calcTestStatistic(xi);
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return hypoth.executeTest(statistic, a);
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}
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public boolean[][] leftsideTest(double[][] xi, double a) {
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HypothesisTest hypoth = new LeftSideTest();
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double[][] statistic = hypoth.calcTestStatistic(xi);
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return hypoth.executeTest(statistic, a);
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}
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/*********************************/
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/* interface define */
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/*********************************/
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@@ -145,7 +167,6 @@ public class MultiComp {
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TDistribution tDist = new TDistribution(v);
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double t =
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tDist.inverseCumulativeProbability(p);
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-
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return Math.sqrt(2) * t;
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}
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}
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@@ -220,6 +241,130 @@ public class MultiComp {
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return sumSq / na;
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}
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}
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// ダネット法
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private class DunnetTest{
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private int k = 0;
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private int v = 0;
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private double[] mean = null;
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private double[] n = null;
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protected int getK() { return k;}
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protected int getV() { return v;}
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public double[][] calcTestStatistic(double[][] xi) {
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k = xi.length;
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mean = new double[k];
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n = new double[k];
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double[][] statistic = new double[k][k];
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double ve = calcVe(xi);
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for(int i = 0; i < k; i++) {
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for(int j = 0; j < k; j++) {
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statistic[i][j] = (mean[j] - mean[i])
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/ Math.sqrt(ve * (1.0 / n[j] + 1.0 / n[i]));
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}
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}
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return statistic;
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}
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private double calcVe(double[][] xi) {
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double sumSq = 0.0;
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int sumN = 0;
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for(int i = 0; i < k; i++) {
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DescriptiveStatistics stat = new DescriptiveStatistics();
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Arrays.stream(xi[i]).forEach(stat::addValue);
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mean[i] = stat.getMean();
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n[i] = stat.getN();
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sumSq += (n[i] - 1) * stat.getVariance();
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sumN += n[i];
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stat.clear();
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}
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v = sumN - k;
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return sumSq / v;
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}
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}
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private class TwoSideTest extends DunnetTest
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implements HypothesisTest {
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public boolean[][] executeTest(double[][] statistic, double a) {
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int v = super.getV();
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int k = super.getK();
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double den = k - 1;
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+
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TDistribution tDist = new TDistribution(v);
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double l_val = tDist.inverseCumulativeProbability(a / den);
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double r_val = tDist.inverseCumulativeProbability(1.0 - a / den);
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boolean[][] ret = new boolean[k][k];
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for(int i = 0; i < k; i++) {
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for(int j = 0; j < k; j++) {
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ret[i][j] = evaluation(statistic[i][j], l_val, r_val );
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}
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}
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return ret;
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}
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private boolean evaluation(double statistic, double l_val, double r_val) {
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boolean ret = true;
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if ((l_val < statistic) && (statistic < r_val)) {
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ret = false;
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}
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return ret;
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}
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}
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private class RightSideTest extends DunnetTest
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implements HypothesisTest {
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public boolean[][] executeTest(double[][] statistic, double a) {
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int v = super.getV();
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int k = super.getK();
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double den = k - 1;
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double p = 1.0 - a / den;
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TDistribution tDist = new TDistribution(v);
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double r_val = tDist.inverseCumulativeProbability(1.0 - a);
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boolean[][] ret = new boolean[k][k];
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for(int i = 0; i < k; i++) {
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for(int j = 0; j < k; j++) {
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ret[i][j] = evaluation(statistic[i][j], r_val );
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}
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}
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return ret;
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}
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private boolean evaluation(double statistic, double r_val) {
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boolean ret = true;
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if (statistic < r_val) {
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ret = false;
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}
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return ret;
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}
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}
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private class LeftSideTest extends DunnetTest
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implements HypothesisTest {
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public boolean[][] executeTest(double[][] statistic, double a) {
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int v = super.getV();
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int k = super.getK();
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double den = k - 1;
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double p = a / den;
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TDistribution tDist = new TDistribution(v);
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double l_val = tDist.inverseCumulativeProbability(a);
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boolean[][] ret = new boolean[k][k];
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for(int i = 0; i < k; i++) {
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for(int j = 0; j < k; j++) {
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ret[i][j] = evaluation(statistic[i][j], l_val );
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}
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}
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return ret;
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}
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private boolean evaluation(double statistic, double l_val) {
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boolean ret = true;
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if (l_val < statistic) {
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ret = false;
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}
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return ret;
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}
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}
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}
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}
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@@ -28,6 +28,7 @@ import java.util.ArrayList;
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import org.apache.commons.math3.stat.inference.OneWayAnova;
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import org.apache.commons.math3.stat.descriptive.DescriptiveStatistics;
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import org.apache.commons.math3.distribution.ChiSquaredDistribution;
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import org.apache.commons.math3.distribution.FDistribution;
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import java.util.Map;
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public class OneWayLayout {
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private static OneWayLayout oneWay = new OneWayLayout();
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@@ -59,6 +60,18 @@ public class OneWayLayout {
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59
60
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double statistic = oneway.calcTestStatistic(xi);
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61
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return oneway.test(statistic, a);
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62
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}
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63
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+
public void replicatePlot(String dname, Map<String, double[]> vals) {
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ChartPlot plot = new ReplicateChartPlot();
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JFreeChart chart = plot.createChart("反復測定", dname, vals);
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plot.writeJPEG("replicate.jpeg", chart, 800, 500);
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}
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public boolean replicateTest(double[][] xi, double a) {
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OneWayAnovaTest oneway = new ReplicateTest();
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double statistic = oneway.calcTestStatistic(xi);
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return oneway.test(statistic, a);
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}
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/*********************************/
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/* interface define */
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/*********************************/
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@@ -196,6 +209,7 @@ public class OneWayLayout {
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}
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}
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}
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// バートレット検定
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private class BartletTest implements OneWayAnovaTest {
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private int n = 0;
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public double calcTestStatistic(double[][] xi) {
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@@ -226,6 +240,7 @@ public class OneWayLayout {
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double invSumN = 0.0;
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int sumN = 0;
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DescriptiveStatistics stat = new DescriptiveStatistics();
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+
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for(int i = 0; i < n; i++) {
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Arrays.stream(xi[i]).forEach(stat::addValue);
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invSumN += 1.0 / (stat.getN() - 1.0);
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@@ -243,5 +258,127 @@ public class OneWayLayout {
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return (r_val < statistic) ? true : false;
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}
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}
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// 反復測定Plot
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private class ReplicateChartPlot implements ChartPlot {
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public JFreeChart createChart(String title, String dname, Map<String, double[]> vals) {
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CategoryPlot plot = createPlot(dname, vals);
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ChartFactory.setChartTheme(StandardChartTheme.createLegacyTheme());
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JFreeChart chart = new JFreeChart(title, plot);
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ChartUtils.applyCurrentTheme(chart);
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return chart;
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}
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private CategoryPlot createPlot( String dname, Map<String, double[]> vals) {
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CreatePlot plotImpl = new ReplicatePlot();
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return plotImpl.createPlot(dname, vals);
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}
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private class ReplicatePlot implements CreatePlot {
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public CategoryPlot createPlot(String dname, Map<String, double[]> vals) {
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LineAndShapeRenderer renderer = new LineAndShapeRenderer(true, true);
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renderer.setDefaultToolTipGenerator(
|
281
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new StandardCategoryToolTipGenerator()
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);
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CategoryPlot plot = new CategoryPlot();
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plot.setOrientation(PlotOrientation.VERTICAL);
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plot.mapDatasetToRangeAxis(0,0);
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plot.setDatasetRenderingOrder(DatasetRenderingOrder.FORWARD);
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/*--- 横軸 ---*/
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CategoryAxis categoryAxis = new CategoryAxis("因子");
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plot.setDomainAxis(categoryAxis);
|
292
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+
|
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/*--- 縦軸 ---*/
|
294
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+
NumberAxis valueAxis0 = new NumberAxis("推定周辺平均");
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295
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plot.setRangeAxis(valueAxis0);
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plot.setRenderer(0, renderer);
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plot.setDataset(0, createDataset(dname, vals));
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return plot;
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300
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}
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301
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private CategoryDataset createDataset(String dname, Map<String, double[]> vals) {
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302
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DefaultCategoryDataset data = new DefaultCategoryDataset();
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DescriptiveStatistics stat = new DescriptiveStatistics();
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|
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for(Map.Entry<String, double[]> entry : vals.entrySet()) {
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double[] v = entry.getValue();
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+
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Arrays.stream(v).forEach(stat::addValue);
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data.addValue(stat.getMean(), dname, entry.getKey());
|
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stat.clear();
|
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}
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return data;
|
313
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}
|
314
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+
}
|
315
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}
|
316
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private class ReplicateTest implements OneWayAnovaTest {
|
317
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private int a1 = 0;
|
318
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private int b1 = 0;
|
319
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public double calcTestStatistic(double[][] xi) {
|
320
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b1 = xi[0].length;
|
321
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a1 = xi.length;
|
322
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+
double st = calcSt(xi, a1, b1);
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double sa = calcSa(xi, a1, b1);
|
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double sb = calcSb(xi, a1, b1);
|
325
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double se = st - sa - sb;
|
326
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+
double meanSa = sa / (a1 - 1);
|
327
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double meanSe = se / ((a1 - 1) * (b1 - 1));
|
328
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+
|
329
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+
return meanSa / meanSe ;
|
330
|
+
}
|
331
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+
private double calcSt(double[][] xi, int a, int b) {
|
332
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+
DescriptiveStatistics stat = new DescriptiveStatistics();
|
333
|
+
double sumSt1 = 0.0;
|
334
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+
double sumSt2 = 0.0;
|
335
|
+
|
336
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+
for(int i = 0; i < a; i++) {
|
337
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+
Arrays.stream(xi[i]).forEach(stat::addValue);
|
338
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+
sumSt1 += stat.getSumsq();
|
339
|
+
sumSt2 += stat.getSum();
|
340
|
+
stat.clear();
|
341
|
+
}
|
342
|
+
return sumSt1 - sumSt2 * sumSt2 / (a * b);
|
343
|
+
}
|
344
|
+
private double calcSa(double[][] xi, int a, int b) {
|
345
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+
double sumSa1 = 0.0;
|
346
|
+
double sumSa2 = 0.0;
|
347
|
+
double[] an = new double[a];
|
348
|
+
|
349
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+
for(int i = 0; i < a; i++) {
|
350
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+
for(int j = 0; j < b; j++) {
|
351
|
+
an[i] += xi[i][j];
|
352
|
+
sumSa2 += xi[i][j];
|
353
|
+
}
|
354
|
+
}
|
355
|
+
DescriptiveStatistics stat = new DescriptiveStatistics();
|
356
|
+
Arrays.stream(an).forEach(stat::addValue);
|
357
|
+
sumSa1 = stat.getSumsq() / b;
|
358
|
+
return sumSa1 - sumSa2 * sumSa2 / (a * b);
|
359
|
+
}
|
360
|
+
private double calcSb(double[][] xi, int a, int b) {
|
361
|
+
double[] bn = new double[b];
|
362
|
+
double sumSb1 = 0.0;
|
363
|
+
double sumSb2 = 0.0;
|
364
|
+
|
365
|
+
for(int i = 0; i < a; i++) {
|
366
|
+
for(int j = 0; j < b; j++) {
|
367
|
+
bn[j] += xi[i][j];
|
368
|
+
sumSb2 += xi[i][j];
|
369
|
+
}
|
370
|
+
}
|
371
|
+
DescriptiveStatistics stat = new DescriptiveStatistics();
|
372
|
+
Arrays.stream(bn).forEach(stat::addValue);
|
373
|
+
sumSb1 = stat.getSumsq() / a;
|
374
|
+
return sumSb1 - sumSb2 * sumSb2 / (a * b);
|
375
|
+
}
|
376
|
+
public boolean test(double statistic, double a) {
|
377
|
+
FDistribution fDist = new FDistribution(a1 - 1, (a1 - 1) * (b1 - 1));
|
378
|
+
double f = fDist.inverseCumulativeProbability(1.0 - a);
|
379
|
+
|
380
|
+
return (statistic >= f) ? true : false;
|
381
|
+
}
|
382
|
+
}
|
246
383
|
}
|
247
384
|
|
data/lib/dunnet.rb
ADDED
@@ -0,0 +1,89 @@
|
|
1
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+
# Dunnet検定
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2
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+
# (Apache commoms math3使用)
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3
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+
module DunnetTestLib
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4
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+
# Dunnet検定の両側検定
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5
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+
#
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6
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+
# @overload twoside_test(xi, a)
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7
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+
# @param [array] xi データ(double[][])
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8
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# @param [double] a 有意水準
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9
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+
# @return [Array] 検定結果(boolean[][] true:棄却域内 false:棄却域外)
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10
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+
# @example
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11
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# xi = [
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12
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# [12.2, 18.8, 18.2],
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13
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# [22.2, 20.5, 14.6],
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14
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# [20.8, 19.5, 26.3],
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15
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+
# [26.4, 32.5, 31.3],
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16
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# [24.5, 21.2, 22.4],
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17
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+
# ]
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18
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# paraTest = MultiCompLib::ParametrixTestLib.new
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19
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# paraTest.twoside_test(xi, 0.05)
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20
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# =>
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21
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# res = [
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22
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# [false, false, false, true, false],
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23
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# [false, false, false, true, false],
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24
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# [false, false, false, false, false],
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25
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# [true, true, false, false, false],
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26
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# [false, false, false, false, false],
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27
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# ]
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28
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def twoside_test(xi, a)
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29
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+
ret = @paramTest.twosideTest(xi.to_java(Java::double[]), a)
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30
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+
return ret.to_a
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31
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+
end
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32
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+
# Dunnet検定の右側検定
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33
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#
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34
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+
# @overload rightside_test(xi, a)
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35
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+
# @param [array] xi データ(double[][])
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36
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+
# @param [double] a 有意水準
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37
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+
# @return [Array] 検定結果(boolean[][] true:棄却域内 false:棄却域外)
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38
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+
# @example
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39
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+
# xi = [
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40
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+
# [12.2, 18.8, 18.2],
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41
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+
# [22.2, 20.5, 14.6],
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42
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+
# [20.8, 19.5, 26.3],
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43
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+
# [26.4, 32.5, 31.3],
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44
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+
# [24.5, 21.2, 22.4],
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45
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+
# ]
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46
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+
# paraTest = MultiCompLib::ParametrixTestLib.new
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47
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+
# paraTest.rightside_test(xi, 0.05)
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48
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+
# =>
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49
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+
# res = [
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50
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+
# [false, false, true, true, true],
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51
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# [false, false, false, true, false],
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52
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# [false, false, false, true, false],
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53
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# [false, false, false, false, false],
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54
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# [false, false, false, true, false],
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55
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# ]
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56
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def rightside_test(xi, a)
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57
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ret = @paramTest.rightsideTest(xi.to_java(Java::double[]), a)
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58
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return ret.to_a
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59
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+
end
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60
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+
# Dunnet検定の左側検定
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61
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#
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62
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# @overload leftside_test(xi, a)
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63
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# @param [array] xi データ(double[][])
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64
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+
# @param [double] a 有意水準
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65
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+
# @return [Array] 検定結果(boolean[][] true:棄却域内 false:棄却域外)
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66
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+
# @example
|
67
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# xi = [
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68
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# [12.2, 18.8, 18.2],
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69
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+
# [22.2, 20.5, 14.6],
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70
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+
# [20.8, 19.5, 26.3],
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71
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# [26.4, 32.5, 31.3],
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72
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# [24.5, 21.2, 22.4],
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73
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# ]
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74
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# paraTest = MultiCompLib::ParametrixTestLib.new
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75
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# paraTest.leftside_test(xi, 0.05)
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76
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# =>
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77
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# res = [
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78
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# [false, false, false, false, false],
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79
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# [false, false, false, false, false],
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80
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+
# [true, false, false, false, false],
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81
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# [true, true, true, false, true],
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82
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# [true, false, false, false, false],
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83
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# ]
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84
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+
def leftside_test(xi, a)
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85
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+
ret = @paramTest.leftsideTest(xi.to_java(Java::double[]), a)
|
86
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return ret.to_a
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87
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+
end
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88
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+
end
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89
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+
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data/lib/multicomp.rb
CHANGED
@@ -3,12 +3,15 @@ require 'num4anova.jar'
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3
3
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require 'jfreechart-1.5.4.jar'
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4
4
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require 'commons-math3-3.6.1.jar'
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5
5
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6
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+
require_relative('dunnet')
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7
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+
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6
8
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java_import 'MultiComp'
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7
9
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# 多重比較を行う
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8
10
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# (Apache commoms math3使用)
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9
11
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module MultiCompLib
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10
12
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# パラメトリック検定
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11
13
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class ParametrixTestLib
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14
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+
include DunnetTestLib
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12
15
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def initialize
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13
16
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@paramTest = MultiComp::ParametrixTest.getInstance()
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14
17
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end
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@@ -26,7 +29,8 @@ module MultiCompLib
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26
29
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# [26.4, 32.5, 31.3],
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27
30
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# [24.5, 21.2, 22.4],
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28
31
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# ]
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29
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-
# paraTest.
|
32
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+
# paraTest = MultiCompLib::ParametrixTestLib.new
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33
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+
# paraTest.turkey_test(xi, 0.05)
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30
34
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# =>
|
31
35
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# [
|
32
36
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# [false, false, false, true, false],
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@@ -53,7 +57,8 @@ module MultiCompLib
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53
57
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# [26.4, 32.5, 31.3],
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54
58
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# [24.5, 21.2, 22.4],
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55
59
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# ]
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56
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-
# paraTest.
|
60
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+
# paraTest = MultiCompLib::ParametrixTestLib.new
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61
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+
# paraTest.bonferrono_test(xi, 0.05)
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57
62
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# =>
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58
63
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# [
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59
64
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# [false, false, false, true, false],
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data/lib/num4anova.rb
CHANGED
@@ -72,13 +72,13 @@ module Num4AnovaLib
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|
72
72
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# @param [double] a 有意水準
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73
73
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# @return [boolean] 検定結果(true:棄却域内 false:棄却域外)
|
74
74
|
# @example
|
75
|
-
#
|
76
|
-
#
|
77
|
-
#
|
78
|
-
#
|
79
|
-
#
|
80
|
-
#
|
81
|
-
#
|
75
|
+
# xi = [
|
76
|
+
# [12.2, 18.8, 18.2],
|
77
|
+
# [22.2, 20.5, 14.6],
|
78
|
+
# [20.8, 19.5, 26.3],
|
79
|
+
# [26.4, 32.5, 31.3],
|
80
|
+
# [24.5, 21.2, 22.4],
|
81
|
+
# ]
|
82
82
|
# oneWay = Num4AnovaLib::OneWayLayoutLib.new
|
83
83
|
# oneWay.oneWay.oneway_anova(xi, 0.05)
|
84
84
|
# => true
|
@@ -92,19 +92,63 @@ module Num4AnovaLib
|
|
92
92
|
# @param [double] a 有意水準
|
93
93
|
# @return [boolean] 検定結果(true:棄却域内 false:棄却域外)
|
94
94
|
# @example
|
95
|
-
#
|
96
|
-
#
|
97
|
-
#
|
98
|
-
#
|
99
|
-
#
|
100
|
-
#
|
101
|
-
#
|
95
|
+
# xi = [
|
96
|
+
# [12.2, 18.8, 18.2],
|
97
|
+
# [22.2, 20.5, 14.6],
|
98
|
+
# [20.8, 19.5, 26.3],
|
99
|
+
# [26.4, 32.5, 31.3],
|
100
|
+
# [24.5, 21.2, 22.4],
|
101
|
+
# ]
|
102
102
|
# oneWay = Num4AnovaLib::OneWayLayoutLib.new
|
103
103
|
# oneWay.bartlet(xi, 0.05)
|
104
104
|
# => true
|
105
105
|
def bartlet(xi, a)
|
106
106
|
return @oneWay.bartletTest(xi.to_java(Java::double[]), a)
|
107
107
|
end
|
108
|
+
# 反復測定Plot
|
109
|
+
#
|
110
|
+
# @overload replicate_plot(dname, vals)
|
111
|
+
# @param [String] dname データ名
|
112
|
+
# @param [Hash] vals Hash(String, double[])
|
113
|
+
# @return [void] replicate.jpegファイルを出力
|
114
|
+
# @example
|
115
|
+
# vals = {
|
116
|
+
# "stageA1" => [27, 52, 18, 21, 32],
|
117
|
+
# "stageA2" => [52, 72, 31, 50, 45],
|
118
|
+
# "stageA3" => [47, 54, 29, 43, 32],
|
119
|
+
# "stageA4" => [28, 50, 22, 26, 29],
|
120
|
+
# }
|
121
|
+
# oneWay = Num4AnovaLib::OneWayLayoutLib.new
|
122
|
+
# oneWay.replicate_plot("LDH", vals)
|
123
|
+
# => replicate.jpeg
|
124
|
+
# @note
|
125
|
+
# グラフは、jfreechartを使用
|
126
|
+
def replicate_plot(dname, vals)
|
127
|
+
o = HashMap.new
|
128
|
+
vals.each{|k, v|
|
129
|
+
o[k] = v.to_java(Java::double)
|
130
|
+
}
|
131
|
+
return @oneWay.replicatePlot(dname, o)
|
132
|
+
end
|
133
|
+
# 反復測定検定
|
134
|
+
#
|
135
|
+
# @overload replicate_test(xi, a)
|
136
|
+
# @param [array] xi データ(double[][])
|
137
|
+
# @param [double] a 有意水準
|
138
|
+
# @return [boolean] 検定結果(true:棄却域内 false:棄却域外)
|
139
|
+
# @example
|
140
|
+
# xi = [
|
141
|
+
# [27, 52, 18, 21, 32],
|
142
|
+
# [52, 72, 31, 50, 45],
|
143
|
+
# [47, 54, 29, 43, 32],
|
144
|
+
# [28, 50, 22, 26, 29],
|
145
|
+
# ]
|
146
|
+
# oneWay = Num4AnovaLib::OneWayLayoutLib.new
|
147
|
+
# oneWay.replicate_test("LDH", vals)
|
148
|
+
# => true
|
149
|
+
def replicate_test(xi, a)
|
150
|
+
return @oneWay.replicateTest(xi.to_java(Java::double[]), a)
|
151
|
+
end
|
108
152
|
end
|
109
153
|
end
|
110
154
|
|
metadata
CHANGED
@@ -1,14 +1,14 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: num4anova
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 0.0.
|
4
|
+
version: 0.0.4
|
5
5
|
platform: java
|
6
6
|
authors:
|
7
7
|
- siranovel
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date: 2024-01-
|
11
|
+
date: 2024-01-30 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: rake
|
@@ -64,6 +64,7 @@ files:
|
|
64
64
|
- ext/num4anova/MultiComp.java
|
65
65
|
- ext/num4anova/OneWayLayout.java
|
66
66
|
- lib/commons-math3-3.6.1.jar
|
67
|
+
- lib/dunnet.rb
|
67
68
|
- lib/jcommon-1.0.23.jar
|
68
69
|
- lib/jfreechart-1.5.4.jar
|
69
70
|
- lib/multicomp.rb
|