num4anova 0.0.1-java

checksums.yaml

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data/CHANGELOG.md

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+# Change Log
+
+## Unreleased
+
+## [0.0.2] - 2023-12-12
+
+### change
+- chg Q-QPlot and kstest
+- chg from one-side test to two side test.
+
+## [0.0.1] - 2023-12-05
+
+### Fixed
+- fix first fixed.
+

data/Gemfile

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+source "https://rubygems.org"
+
+gemspec

data/LICENSE

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+MIT License
+
+Copyright (c) 2023 siranovel
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

data/Rakefile

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+require  'rake/javaextensiontask'
+
+jars = Dir.glob("lib/*.jar")
+Rake::JavaExtensionTask.new(name='num4anova')  do | ext |
+  ext.release          = '11'
+  ext.classpath        = jars.map { |x| File.expand_path x }.join ":"
+end
+task :default => [:compile]

data/ext/num4anova/OneWayLayout.java

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+import org.jfree.chart.JFreeChart;
+import org.jfree.chart.StandardChartTheme;
+import org.jfree.chart.ChartFactory;
+import org.jfree.data.statistics.BoxAndWhiskerCategoryDataset;
+import org.jfree.data.statistics.DefaultBoxAndWhiskerCategoryDataset;
+import org.jfree.data.statistics.BoxAndWhiskerCalculator;
+import org.jfree.data.statistics.BoxAndWhiskerItem;
+import org.jfree.data.category.CategoryDataset;
+import org.jfree.data.category.DefaultCategoryDataset;
+import org.jfree.chart.plot.CategoryPlot;
+import org.jfree.chart.axis.ValueAxis;
+import org.jfree.chart.renderer.category.BoxAndWhiskerRenderer;
+import org.jfree.chart.labels.BoxAndWhiskerToolTipGenerator;
+import org.jfree.chart.plot.PlotOrientation;
+import org.jfree.chart.plot.DatasetRenderingOrder;
+import org.jfree.chart.axis.CategoryAxis;
+import org.jfree.chart.axis.NumberAxis;
+import org.jfree.chart.renderer.category.LineAndShapeRenderer;
+import org.jfree.chart.labels.StandardCategoryToolTipGenerator;
+import org.jfree.chart.renderer.xy.XYLineAndShapeRenderer;
+
+import org.jfree.chart.ChartUtils;
+import java.io.File;
+import java.io.IOException;
+import java.util.Arrays;
+import java.util.List;
+import java.util.ArrayList;
+
+import org.apache.commons.math3.stat.inference.OneWayAnova;
+import org.apache.commons.math3.stat.descriptive.DescriptiveStatistics;
+import org.apache.commons.math3.distribution.ChiSquaredDistribution;
+import java.util.Map;
+public class OneWayLayout {
+    private static OneWayLayout oneWay = new OneWayLayout();
+    public static OneWayLayout getInstance() {
+        return oneWay;
+    }
+    public void boxWhiskerPlot(String dname, Map<String, double[]> vals) {
+        ChartPlot plot = new BoxWhiskerChartPlot();
+        JFreeChart chart = plot.createChart("箱ひげ図", dname, vals);
+
+        plot.writeJPEG("boxWhisker.jpeg", chart, 500, 300);
+    }
+    public void oneWayScatterPlot(String dname, Map<String, double[]> vals) {
+        ChartPlot plot = new OneWayScatterChartPlot();
+        JFreeChart chart = plot.createChart("一元散布図", dname, vals);
+
+        plot.writeJPEG("scatter.jpeg", chart, 800, 500);
+    }
+    public boolean onewayanova(double[][] xi, double a) {
+        List<double[]> data = new ArrayList<double[]>();
+        OneWayAnova anova = new OneWayAnova();
+
+        Arrays.stream(xi).forEach(data::add);
+        return anova.anovaTest(data, a);
+    }
+    public boolean bartletTest(double[][] xi, double a) {
+        OneWayAnovaTest oneway = new BartletTest();
+
+        double statistic = oneway.calcTestStatistic(xi);
+        return oneway.test(statistic, a);
+    }
+    /*********************************/
+    /* interface define              */
+    /*********************************/
+    private interface ChartPlot {
+        JFreeChart createChart(String title, String dname, Map<String, double[]> vals);
+        default void writeJPEG(String fname, JFreeChart chart, int width, int height) {
+            File file = new File(fname);
+            try {
+                ChartUtils.saveChartAsJPEG(file, chart, width, height);
+            } catch (IOException e) {
+                e.printStackTrace();
+            }
+        }
+    }
+    private interface CreatePlot {
+        CategoryPlot createPlot(String dname, Map<String, double[]> xi);
+    }
+    private interface OneWayAnovaTest {
+        double calcTestStatistic(double[][] xi);
+        boolean test(double statistic, double a);
+    }
+    /*********************************/
+    /* class define                  */
+    /*********************************/
+    // 箱ひげ図
+    private class BoxWhiskerChartPlot implements ChartPlot {
+        public JFreeChart createChart(String title, String dname, Map<String, double[]> vals) {
+            CategoryPlot plot = createPlot(dname, vals);
+            ChartFactory.setChartTheme(StandardChartTheme.createLegacyTheme());
+            JFreeChart chart = new JFreeChart(title, plot);
+
+            ChartUtils.applyCurrentTheme(chart);
+            return chart;
+        }
+        private CategoryPlot createPlot(String dname, Map<String, double[]> vals) {
+            CreatePlot plotImpl = new BoxWhiskerPlot();
+
+            return plotImpl.createPlot(dname, vals);
+        }
+        private class BoxWhiskerPlot implements CreatePlot {
+            public CategoryPlot createPlot(String dname, Map<String, double[]> vals) {
+                BoxAndWhiskerRenderer renderer0 = new BoxAndWhiskerRenderer();
+                renderer0.setDefaultToolTipGenerator(new BoxAndWhiskerToolTipGenerator());
+                renderer0.setMaximumBarWidth(0.2);
+
+                CategoryPlot plot = new CategoryPlot();
+                plot.setOrientation(PlotOrientation.VERTICAL);
+                plot.mapDatasetToRangeAxis(0,0);
+	        plot.setDatasetRenderingOrder(DatasetRenderingOrder.FORWARD);
+
+                /*--- 横軸 ---*/
+                CategoryAxis categoryAxis = new CategoryAxis();
+                plot.setDomainAxis(categoryAxis);
+
+                /*--- 縦軸 ---*/
+                NumberAxis valueAxis = new NumberAxis();
+                valueAxis.setAutoRangeIncludesZero(false);
+                plot.setRangeAxis(valueAxis);
+                
+
+                plot.setRenderer(0, renderer0);
+                plot.setDataset(0, createDataset(dname, vals));
+
+                return plot;
+            }
+            private BoxAndWhiskerCategoryDataset createDataset(String dname, Map<String, double[]> vals) {
+                DefaultBoxAndWhiskerCategoryDataset data = 
+                    new DefaultBoxAndWhiskerCategoryDataset();
+                List<Double> values = new ArrayList<Double>();
+                for(Map.Entry<String, double[]> entry : vals.entrySet()) {
+                    double[] v = entry.getValue();
+
+                    Arrays.stream(v).forEach(values::add);
+                    data.add(
+                        BoxAndWhiskerCalculator.calculateBoxAndWhiskerStatistics(values),
+                        dname, entry.getKey()
+                    );
+                    values.clear();
+                }
+                return data;
+            }
+        }
+    }
+    // 一元配置グラフ
+    private class OneWayScatterChartPlot implements ChartPlot {
+        public JFreeChart createChart(String title, String dname, Map<String, double[]> vals) {
+            CategoryPlot plot = createPlot(dname, vals);
+
+            ChartFactory.setChartTheme(StandardChartTheme.createLegacyTheme());
+            JFreeChart chart = new JFreeChart(title, plot);
+
+            ChartUtils.applyCurrentTheme(chart);
+            return chart;
+        }
+        private CategoryPlot createPlot(String dname, Map<String, double[]> vals) {
+            CreatePlot plotImpl = new OneWayScatterPlot();
+
+            return plotImpl.createPlot(dname, vals);
+        }
+        private class OneWayScatterPlot implements CreatePlot {
+            public CategoryPlot createPlot(String dname, Map<String, double[]> vals) {
+                LineAndShapeRenderer renderer = new LineAndShapeRenderer(false, true);
+                renderer.setDefaultToolTipGenerator(
+                    new StandardCategoryToolTipGenerator());
+
+                CategoryPlot plot = new CategoryPlot();
+                plot.setOrientation(PlotOrientation.VERTICAL);
+                plot.mapDatasetToRangeAxis(0,0);
+	        plot.setDatasetRenderingOrder(DatasetRenderingOrder.FORWARD);
+
+                /*--- 横軸 ---*/
+                CategoryAxis categoryAxis = new CategoryAxis();
+                plot.setDomainAxis(categoryAxis);
+
+                /*--- 縦軸 ---*/
+                NumberAxis valueAxis0 = new NumberAxis();
+                plot.setRangeAxis(valueAxis0);
+
+                plot.setRenderer(0, renderer);
+                plot.setDataset(0, createDataset(dname, vals));
+                return plot;
+            }
+
+            private CategoryDataset createDataset(String dname, Map<String, double[]> vals) {
+                DefaultCategoryDataset data = new DefaultCategoryDataset();
+                for(Map.Entry<String, double[]> entry : vals.entrySet()) {
+                    double[] v = entry.getValue();
+                    for(int i = 0; i < v.length; i++) {
+                        String rowKey = String.format("dt%02d", i);
+
+                        data.addValue(v[i], rowKey, entry.getKey());
+                    }
+                }
+                return data;
+            }
+        }
+    }
+    private class BartletTest implements OneWayAnovaTest {
+        private int n = 0;
+        public double calcTestStatistic(double[][] xi) {
+            n = xi.length;
+            double ln2L = logL(xi);
+
+            return calcB(ln2L, xi);
+        }
+        private double logL(double[][] xi) {
+            double[] si = new double[n];
+            DescriptiveStatistics stat = new DescriptiveStatistics();
+            double nisi2 = 0.0;    // (Ni - 1)*si^2の合計
+            double nilogsi2 = 0.0; // (Ni - 1)*log(si^2)の合計
+            int sumN = 0;
+
+            for(int i = 0; i < n; i++) {
+                Arrays.stream(xi[i]).forEach(stat::addValue);
+                sumN += stat.getN();
+                si[i] = stat.getVariance();
+                nisi2 += (stat.getN() - 1) * si[i];
+                nilogsi2 += (stat.getN() - 1) * Math.log(si[i]);
+                stat.clear();
+            }
+            double sumNin = sumN - n;
+            return sumNin * (Math.log(nisi2 / sumNin) - nilogsi2 / sumNin);
+        }
+        private double calcB(double ln2L, double[][] xi) {
+            double invSumN = 0.0;
+            int sumN = 0;
+            DescriptiveStatistics stat = new DescriptiveStatistics();
+            for(int i = 0; i < n; i++) {
+                Arrays.stream(xi[i]).forEach(stat::addValue);
+                invSumN += 1.0 / (stat.getN() - 1.0);
+                sumN += stat.getN();
+                stat.clear();
+            }
+            double deno = 1 + 1.0 / (3 * (n - 1))
+                        * (invSumN - 1.0 / (sumN - n));
+            return ln2L / deno;
+        }
+        public boolean test(double statistic, double a) {
+            ChiSquaredDistribution chi2Dist = new ChiSquaredDistribution(n - 1);
+            double r_val = chi2Dist.inverseCumulativeProbability(1.0 - a);
+
+            return (r_val < statistic) ? true : false;
+        }
+    }
+}
+

data/lib/num4anova.rb

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+require 'java'
+require 'num4anova.jar'
+require 'jfreechart-1.5.4.jar'
+require 'commons-math3-3.6.1.jar'
+
+java_import 'OneWayLayout'
+java_import 'java.util.HashMap'
+# 数値計算による分散分析を行う
+module Num4AnovaLib
+    # 一元配置の分散分析
+    class OneWayLayoutLib
+        def initialize
+            @oneWay = OneWayLayout.getInstance()
+        end
+        # 箱ひげ図
+        #
+        # @overload boxWhiskerPlot(dname, vals)
+        #   @param [String] dname データ名
+        #   @param [Hash] vals Hash(String, double[])
+        #   @return [void]  boxWhisker.jpegファイルを出力
+        # @example
+        #   vals = {
+        #         "stage51" => [12.2, 18.8, 18.2],
+        #         "stage55" => [22.2, 20.5, 14.6],
+        #         "stage57" => [20.8, 19.5, 26.3],
+        #         "stage59" => [26.4, 32.5, 31.3],
+        #         "stage61" => [24.5, 21.2, 22.4],
+        #       }
+        #   oneWay = Num4AnovaLib::OneWayLayoutLib.new 
+        #   oneWay.boxWhiskerPlot("LDH", vals)
+        #   => boxWhisker.jpeg
+        # @note
+        #   グラフは、jfreechartを使用
+        def boxWhiskerPlot(dname, vals)
+            o = HashMap.new
+            vals.each{|k, v|
+                o[k] = v.to_java(Java::double)
+            }
+            @oneWay.boxWhiskerPlot(dname, o)
+        end
+        # 一元散布図
+        #
+        # @overload oneway_scatter_plot(dname, vals)
+        #   @param [String] dname データ名
+        #   @param [Hash] vals Hash(String, double[])
+        #   @return [void]  scatter.jpegファイルを出力
+        # @example
+        #   vals = {
+        #         "stage51" => [12.2, 18.8, 18.2],
+        #         "stage55" => [22.2, 20.5, 14.6],
+        #         "stage57" => [20.8, 19.5, 26.3],
+        #         "stage59" => [26.4, 32.5, 31.3],
+        #         "stage61" => [24.5, 21.2, 22.4],
+        #       }
+        #   oneWay = Num4AnovaLib::OneWayLayoutLib.new 
+        #   oneWay.oneway_scatter_plot("LDH", vals)
+        #   => scatter.jpeg
+        # @note
+        #   グラフは、jfreechartを使用
+        def oneway_scatter_plot(dname, vals)
+            o = HashMap.new
+            vals.each{|k, v|
+                o[k] = v.to_java(Java::double)
+            }
+            @oneWay.oneWayScatterPlot(dname, o)
+        end
+        # 一元配置分散分析
+        #
+        # @overload oneway_anova(xi, a)
+        #   @param [array]  xi データ(double[][])
+        #   @param [double] a         有意水準
+        #   @return [boolean] 検定結果(true:棄却域内 false:棄却域外)
+        # @example
+        #    xi = [
+        #        [12.2, 18.8, 18.2],
+        #        [22.2, 20.5, 14.6],
+        #        [20.8, 19.5, 26.3],
+        #        [26.4, 32.5, 31.3],
+        #        [24.5, 21.2, 22.4],
+        #    ]
+        #   oneWay = Num4AnovaLib::OneWayLayoutLib.new 
+        #   oneWay.oneWay.oneway_anova(xi, 0.05)
+        #   => true
+        def oneway_anova(xi, a)
+            return @oneWay.onewayanova(xi.to_java(Java::double[]), a)
+        end
+        # バートレット検定
+        #
+        # @overload bartlet(xi, a)
+        #   @param [array]  xi データ(double[][])
+        #   @param [double] a         有意水準
+        #   @return [boolean] 検定結果(true:棄却域内 false:棄却域外)
+        # @example
+        #    xi = [
+        #        [12.2, 18.8, 18.2],
+        #        [22.2, 20.5, 14.6],
+        #        [20.8, 19.5, 26.3],
+        #        [26.4, 32.5, 31.3],
+        #        [24.5, 21.2, 22.4],
+        #    ]
+        #   oneWay = Num4AnovaLib::OneWayLayoutLib.new 
+        #   oneWay.bartlet(xi, 0.05)
+        #   => true
+        def bartlet(xi, a)
+            return @oneWay.bartletTest(xi.to_java(Java::double[]), a)
+        end
+    end
+end
+

metadata

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+--- !ruby/object:Gem::Specification
+name: num4anova
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+platform: java
+authors:
+- siranovel
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2024-01-09 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '12.3'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 12.3.3
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '12.3'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 12.3.3
+- !ruby/object:Gem::Dependency
+  name: rake-compiler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.2'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.2.5
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.2'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.2.5
+description: numerical solution for analysis of variance.
+email: siranovel@gmail.com
+executables: []
+extensions:
+- Rakefile
+extra_rdoc_files: []
+files:
+- CHANGELOG.md
+- Gemfile
+- LICENSE
+- Rakefile
+- ext/num4anova/OneWayLayout.java
+- lib/commons-math3-3.6.1.jar
+- lib/jcommon-1.0.23.jar
+- lib/jfreechart-1.5.4.jar
+- lib/num4anova.rb
+homepage: http://github.com/siranovel/num4varanly
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubygems_version: 3.3.7
+signing_key: 
+specification_version: 4
+summary: num for variance analysis
+test_files: []