num4anova 0.0.1-java → 0.0.2-java

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Files changed (8) hide show
  1. checksums.yaml +4 -4
  2. data/CHANGELOG.md +4 -5
  3. data/Rakefile +2 -0
  4. data/ext/num4anova/MultiComp.java +225 -0
  5. data/ext/num4anova/OneWayLayout.java +0 -1
  6. data/lib/multicomp.rb +73 -0
  7. data/lib/num4anova.rb +2 -1
  8. metadata +4 -2
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data/CHANGELOG.md CHANGED
@@ -2,13 +2,12 @@
2
2
 
3
3
  ## Unreleased
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4
 
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- ## [0.0.2] - 2023-12-12
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+ ## [0.0.2] - 2024-01-23
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6
 
7
- ### change
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- - chg Q-QPlot and kstest
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- - chg from one-side test to two side test.
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+ ### add
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+ - add Multiple Comparisons function.
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9
 
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- ## [0.0.1] - 2023-12-05
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+ ## [0.0.1] - 2024-01-10
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11
 
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12
  ### Fixed
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13
  - fix first fixed.
data/Rakefile CHANGED
@@ -6,3 +6,5 @@ Rake::JavaExtensionTask.new(name='num4anova') do | ext |
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  ext.classpath = jars.map { |x| File.expand_path x }.join ":"
7
7
  end
8
8
  task :default => [:compile]
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+
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+
data/ext/num4anova/MultiComp.java ADDED
@@ -0,0 +1,225 @@
1
+ import org.apache.commons.math3.stat.descriptive.DescriptiveStatistics;
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+ import java.util.Arrays;
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+ import java.util.List;
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+ import java.util.ArrayList;
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+ import org.apache.commons.math3.distribution.TDistribution;
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+
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+ import org.apache.commons.math3.util.Combinations;
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+ public class MultiComp {
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+ public static class ParametrixTest {
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+ private static ParametrixTest paramTest = new ParametrixTest();
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+ public static ParametrixTest getInstance() {
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+ return paramTest;
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+ }
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+ public boolean[][] turkeyTest(double[][] xi, double a) {
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+ HypothesisTest hypoth = new TurkeyTest();
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+
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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[][] bonferronoTest(double[][] xi, double a) {
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+ HypothesisTest hypoth = new BonferroniTest();
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+
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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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+ /*********************************/
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+ /* interface define */
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+ /*********************************/
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+ private interface HypothesisTest {
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+ double[][] calcTestStatistic(double[][] xi);
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+ boolean[][] executeTest(double[][] statistic, double a);
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+ }
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+ /*********************************/
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+ /* Class define */
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+ /*********************************/
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+ // turkey法
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+ private class TurkeyTest implements HypothesisTest {
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+ private int m = 0;
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+ private int n = 0;
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+ public double[][] calcTestStatistic(double[][] xi) {
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+ n = xi.length; // a
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+ m = xi[0].length; // n
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+ double[][] statistic = new double[n][n];
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+ double[] mean = calcStdMean(xi);
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+ double ve = calcVe(xi);
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+
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+ for(int i = 0; i < n; i++) {
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+ for(int j = i; j < n; j++) {
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+ statistic[i][j] =
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+ Math.abs(mean[i] - mean[j]) / Math.sqrt(ve / m);
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+ }
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+ }
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+
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+ return statistic;
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+
56
+ }
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+ public boolean[][] executeTest(double[][] statistic, double a) {
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+ int v = n * (m - 1);
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+ double q = qvalue(n, v, a);
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+ boolean[][] ret = new boolean[n][n];
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+
62
+ for(int i = 0; i < n; i++) {
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+ for(int j = i; j < n; j++) {
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+ ret[i][j] = (statistic[i][j] >= q) ? true : false;
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+ }
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+ }
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+ return ret;
68
+ }
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+
70
+ private double[] calcStdMean(double[][] xi) {
71
+ int n = xi.length;
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+ double[] mean = new double[n];
73
+
74
+ for(int i = 0; i < n; i++) {
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+ DescriptiveStatistics stat = new DescriptiveStatistics();
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+ Arrays.stream(xi[i]).forEach(stat::addValue);
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+
78
+ mean[i] = stat.getMean();
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+ stat.clear();
80
+ }
81
+ return mean;
82
+ }
83
+ private double calcVe(double[][] xi) {
84
+ int n = xi.length;
85
+ int m = xi[0].length;
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+ double na = n * (m - 1);
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+ double sumSq = 0.0;
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+
89
+ for(int i = 0; i < n; i++) {
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+ DescriptiveStatistics stat = new DescriptiveStatistics();
91
+ Arrays.stream(xi[i]).forEach(stat::addValue);
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+ double mean = stat.getMean();
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+ for (int j = 0; j < m; j++) {
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+ double diff = xi[i][j] - mean;
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+ sumSq = sumSq + diff * diff;
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+ }
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+ stat.clear();
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+ }
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+ return sumSq / na;
100
+ }
101
+ // スチューデント化された範囲のa点
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+ // v=120
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+ // k=10 q= 4.5595 p2/a=0.016282 1/61.417516276
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+ // k=8 q= 4.3630 p2/a=0.025263 1/39.583580731
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+ // k=6 q= 4.0960 p2/a=0.044883 1/22.280150614
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+ // k=5 q= 3.9169 p2/a=0.065040 1/15.375153752
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+ // k=4 q= 3.6846 p2/a=0.103377 1/9.673331592
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+ // k=3 q= 3.3561 p2/a=0.192270 1/5.2010194
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+ // k=2 q= 2.8000 p2/a=0.500036 1/2
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+ // v=14
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+ // k=10 q= 5.2534 p2/a=0.023091 1/43.306916115
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+ // k=8 q= 4.9903 p2/a=0.033394 1/29.945499191
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+ // k=6 q= 4.6385 p2/a=0.054768 1/18.258837277
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+ // k=5 q= 4.4066 p2/a=0.075883 1/13.178182202
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+ // k=4 q= 4.1105 p2/a=0.114920 1/8.701705534
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+ // k=3 q= 3.7014 p2/a=0.202830 1/4.930237144
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+ // k=2 q= 3.0332 p2/a=0.499991 1/2.000036001
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+ // v=12
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+ // k=10 q= 5.3946 p2/a=0.024637 1/40.58935747
120
+ // k=8 q= 5.1187 p2/a=0.035180 1/28.425241615
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+ // k=6 q= 4.7502 p2/a=0.056858 1/17.587674558
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+ // k=5 q= 4.5077 p2/a=0.078128 1/12.799508499
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+ // k=4 q= 4.1987 p2/a=0.117245 1/8.529148365
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+ // k=3 q= 3.7729 p2/a=0.204923 1/4.879881712
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+ // k=2 q= 3.0813 p2/a=0.500004 1/2
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+ // v=10
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+ // k=10 q= 5.5984 p2/a=0.026922 1/37.144342917
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+ // k=8 q= 5.3042 p2/a=0.037799 1/26.455726342
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+ // k=6 q= 4.9128 p2/a=0.059822 1/16.716258233
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+ // k=5 q= 4.6543 p2/a=0.081351 1/12.292411894
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+ // k=4 q= 4.3266 p2/a=0.120575 1/8.293593199
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+ // k=3 q= 3.8768 p2/a=0.207859 1/4.810953579
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+ // k=2 q= 3.1511 p2/a=0.499979 1/2
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+ // v=9
135
+ // k=10 q= 5.7384 p2/a=0.028519 1/35.06434307
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+ // k=8 q= 5.4312 p2/a=0.039639 1/25.22767981
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+ // k=6 q= 5.0235 p2/a=0.061950 1/16.14205004
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+ // k=5 q= 4.7554 p2/a=0.083549 1/11.969024165
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+ // k=4 q= 4.4149 p2/a=0.122828 1/8.141466115
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+ // k=3 q= 3.9485 p2/a=0.209848 1/4.76535397
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+ // k=2 q= 3.1992 p2/a=0.499985 1/2
142
+ private double qvalue(int k, int v, double a) {
143
+ double den = (k-1) * (2 + k) / 2;
144
+ double p = 1.0 - a / den;
145
+ TDistribution tDist = new TDistribution(v);
146
+ double t =
147
+ tDist.inverseCumulativeProbability(p);
148
+
149
+ return Math.sqrt(2) * t;
150
+ }
151
+ }
152
+ // ボンフェロー法
153
+ private class BonferroniTest implements HypothesisTest {
154
+ private int k = 0;
155
+ private int n = 0;
156
+ private int m = 0;
157
+ public double[][] calcTestStatistic(double[][] xi) {
158
+ n = xi.length;
159
+ m = xi[0].length;
160
+ double[][] statistic = new double[n][n];
161
+ double[] mean = calcStdMean(xi);
162
+ Combinations c = new Combinations(n, 2);
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+ List<int[]> al = new ArrayList<>();
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+ for(int[] iterate : c) {
165
+ al.add(iterate);
166
+ }
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+ k = al.size();
168
+ double ve = calcVe(xi);
169
+ for(int[] array : al) {
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+ int i = array[0];
171
+ int j = array[1];
172
+ int n1 = xi[i].length;
173
+ int n2 = xi[j].length;
174
+
175
+ statistic[i][j] = Math.abs(mean[i] - mean[j])
176
+ / Math.sqrt((1.0 / n1 + 1.0 / n2) * ve);
177
+ }
178
+ return statistic;
179
+ }
180
+ public boolean[][] executeTest(double[][] statistic, double a) {
181
+ boolean[][] ret = new boolean[n][n];
182
+ double na = n * (m - 1);
183
+ TDistribution tDist = new TDistribution(na);
184
+
185
+ double t = tDist.inverseCumulativeProbability(1.0 - a / k);
186
+
187
+ for(int i = 0; i < n; i++) {
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+ for(int j = i; j < n; j++) {
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+ ret[i][j] = (statistic[i][j] >= t) ? true : false;
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+ }
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+ }
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+ return ret;
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+ }
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+ private double[] calcStdMean(double[][] xi) {
195
+ double[] mean = new double[n];
196
+
197
+ for(int i = 0; i < n; i++) {
198
+ DescriptiveStatistics stat = new DescriptiveStatistics();
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+ Arrays.stream(xi[i]).forEach(stat::addValue);
200
+
201
+ mean[i] = stat.getMean();
202
+ stat.clear();
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+ }
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+ return mean;
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+ }
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+ private double calcVe(double[][] xi) {
207
+ double na = n * (m - 1);
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+ double sumSq = 0.0;
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+
210
+ for(int i = 0; i < n; i++) {
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+ DescriptiveStatistics stat = new DescriptiveStatistics();
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+ Arrays.stream(xi[i]).forEach(stat::addValue);
213
+ double mean = stat.getMean();
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+ for (int j = 0; j < m; j++) {
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+ double diff = xi[i][j] - mean;
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+ sumSq = sumSq + diff * diff;
217
+ }
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+ stat.clear();
219
+ }
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+ return sumSq / na;
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+ }
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+ }
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+ }
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+ }
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+
data/ext/num4anova/OneWayLayout.java CHANGED
@@ -17,7 +17,6 @@ import org.jfree.chart.axis.CategoryAxis;
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17
  import org.jfree.chart.axis.NumberAxis;
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  import org.jfree.chart.renderer.category.LineAndShapeRenderer;
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19
  import org.jfree.chart.labels.StandardCategoryToolTipGenerator;
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- import org.jfree.chart.renderer.xy.XYLineAndShapeRenderer;
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20
 
22
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  import org.jfree.chart.ChartUtils;
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  import java.io.File;
data/lib/multicomp.rb ADDED
@@ -0,0 +1,73 @@
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+ require 'java'
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+ require 'num4anova.jar'
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+ require 'jfreechart-1.5.4.jar'
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+ require 'commons-math3-3.6.1.jar'
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+
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+ java_import 'MultiComp'
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+ # 多重比較を行う
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+ # (Apache commoms math3使用)
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+ module MultiCompLib
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+ # パラメトリック検定
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+ class ParametrixTestLib
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+ def initialize
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+ @paramTest = MultiComp::ParametrixTest.getInstance()
14
+ end
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+ # turkeyの方法による多重比較
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+ #
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+ # @overload turkey_test(xi, a)
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+ # @param [array] xi データ(double[][])
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+ # @param [double] a 有意水準
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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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+ # @example
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+ # xi = [
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+ # [12.2, 18.8, 18.2],
24
+ # [22.2, 20.5, 14.6],
25
+ # [20.8, 19.5, 26.3],
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+ # [26.4, 32.5, 31.3],
27
+ # [24.5, 21.2, 22.4],
28
+ # ]
29
+ # paraTest.turkey_test(xi, a)
30
+ # =>
31
+ # [
32
+ # [false, false, false, true, false],
33
+ # [false, false, false, true, false],
34
+ # [false, false, false, false, false],
35
+ # [false, false, false, false, false],
36
+ # [false, false, false, false, false],
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+ # ]
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+ def turkey_test(xi, a)
39
+ ret = @paramTest.turkeyTest(xi.to_java(Java::double[]), a)
40
+ return ret.to_a
41
+ end
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+ # ボンフェロー二の不等式による多重比較
43
+ #
44
+ # @overload bonferrono_test(xi, a)
45
+ # @param [array] xi データ(double[][])
46
+ # @param [double] a 有意水準
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+ # @return [Array] 検定結果(boolean[][] true:棄却域内 false:棄却域外)
48
+ # @example
49
+ # xi = [
50
+ # [12.2, 18.8, 18.2],
51
+ # [22.2, 20.5, 14.6],
52
+ # [20.8, 19.5, 26.3],
53
+ # [26.4, 32.5, 31.3],
54
+ # [24.5, 21.2, 22.4],
55
+ # ]
56
+ # paraTest.bonferrono_test(xi, a)
57
+ # =>
58
+ # [
59
+ # [false, false, false, true, false],
60
+ # [false, false, false, true, false],
61
+ # [false, false, false, false, false],
62
+ # [false, false, false, false, false],
63
+ # [false, false, false, false, false],
64
+ # ]
65
+ def bonferrono_test(xi, a)
66
+ ret = @paramTest.bonferronoTest(xi.to_java(Java::double[]), a)
67
+ return ret.to_a
68
+ end
69
+ end
70
+ # ノンパラメトリック検定
71
+ class NonParametrixTestLib
72
+ end
73
+ end
data/lib/num4anova.rb CHANGED
@@ -5,7 +5,8 @@ require 'commons-math3-3.6.1.jar'
5
5
 
6
6
  java_import 'OneWayLayout'
7
7
  java_import 'java.util.HashMap'
8
- # 数値計算による分散分析を行う
8
+ # 分散分析を行う
9
+ # (Apache commoms math3使用)
9
10
  module Num4AnovaLib
10
11
  # 一元配置の分散分析
11
12
  class OneWayLayoutLib
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: 0.0.1
4
+ version: 0.0.2
5
5
  platform: java
6
6
  authors:
7
7
  - siranovel
8
8
  autorequire:
9
9
  bindir: bin
10
10
  cert_chain: []
11
- date: 2024-01-09 00:00:00.000000000 Z
11
+ date: 2024-01-23 00:00:00.000000000 Z
12
12
  dependencies:
13
13
  - !ruby/object:Gem::Dependency
14
14
  name: rake
@@ -61,10 +61,12 @@ files:
61
61
  - Gemfile
62
62
  - LICENSE
63
63
  - Rakefile
64
+ - ext/num4anova/MultiComp.java
64
65
  - ext/num4anova/OneWayLayout.java
65
66
  - lib/commons-math3-3.6.1.jar
66
67
  - lib/jcommon-1.0.23.jar
67
68
  - lib/jfreechart-1.5.4.jar
69
+ - lib/multicomp.rb
68
70
  - lib/num4anova.rb
69
71
  homepage: http://github.com/siranovel/num4varanly
70
72
  licenses: