Use Commons Statistics for significance testing

aherbert · Aug 22, 2024 · 427c7ff · 427c7ff
1 parent 8d97de8
commit 427c7ff
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Showing 5 changed files with 16 additions and 19 deletions.
diff --git a/gdsc-test-rng/pom.xml b/gdsc-test-rng/pom.xml
@@ -46,8 +46,7 @@ Contains utilities for use with Commons RNG for random tests.
     </dependency>
     <dependency>
       <groupId>org.apache.commons</groupId>
-      <artifactId>commons-math3</artifactId>
-      <version>3.6.1</version>
+      <artifactId>commons-statistics-inference</artifactId>
       <scope>test</scope>
     </dependency>
   </dependencies>

diff --git a/...-test-rng/src/test/java/uk/ac/sussex/gdsc/test/rng/BaseLongUniformRandomProviderTest.java b/...-test-rng/src/test/java/uk/ac/sussex/gdsc/test/rng/BaseLongUniformRandomProviderTest.java
@@ -24,10 +24,11 @@
 
 import java.util.Arrays;
 import java.util.stream.Stream;
-import org.apache.commons.math3.stat.inference.ChiSquareTest;
 import org.apache.commons.rng.RandomProviderState;
 import org.apache.commons.rng.RestorableUniformRandomProvider;
 import org.apache.commons.rng.UniformRandomProvider;
+import org.apache.commons.statistics.inference.ChiSquareTest;
+import org.apache.commons.statistics.inference.SignificanceResult;
 import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.RepeatedTest;
 import org.junit.jupiter.api.TestInstance;
@@ -230,9 +231,8 @@ void testNextIntInRange(UniformRandomProvider rng, int limit, int bins) {
     }
     final double[] expected = new double[bins];
     Arrays.fill(expected, (double) samples / bins);
-    final ChiSquareTest test = new ChiSquareTest();
-    final double pvalue = test.chiSquareTest(expected, observed);
-    Assertions.assertFalse(pvalue < 0.01, "P-value = " + pvalue);
+    final SignificanceResult r = ChiSquareTest.withDefaults().test(expected, observed);
+    Assertions.assertFalse(r.reject(0.01), () -> "p-value = " + r.getPValue());
   }
 
   @ParameterizedTest
@@ -248,9 +248,8 @@ void testNextLongInRange(UniformRandomProvider rng, long limit, int bins) {
     }
     final double[] expected = new double[bins];
     Arrays.fill(expected, (double) samples / bins);
-    final ChiSquareTest test = new ChiSquareTest();
-    final double pvalue = test.chiSquareTest(expected, observed);
-    Assertions.assertFalse(pvalue < 0.01, "P-value = " + pvalue);
+    final SignificanceResult r = ChiSquareTest.withDefaults().test(expected, observed);
+    Assertions.assertFalse(r.reject(0.01), () -> "p-value = " + r.getPValue());
   }
 
   @ParameterizedTest

diff --git a/gdsc-test-rng/src/test/java/uk/ac/sussex/gdsc/test/rng/RngFactoryTest.java b/gdsc-test-rng/src/test/java/uk/ac/sussex/gdsc/test/rng/RngFactoryTest.java
@@ -25,8 +25,9 @@
 import java.util.Arrays;
 import java.util.SplittableRandom;
 import java.util.concurrent.ThreadLocalRandom;
-import org.apache.commons.math3.stat.inference.ChiSquareTest;
 import org.apache.commons.rng.UniformRandomProvider;
+import org.apache.commons.statistics.inference.ChiSquareTest;
+import org.apache.commons.statistics.inference.SignificanceResult;
 import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.Test;
 import org.junit.jupiter.params.ParameterizedTest;
@@ -184,8 +185,7 @@ void testCreateIncrement(long seed) {
     }
     final double[] expected = new double[16];
     Arrays.fill(expected, 1.0 / 16);
-    final ChiSquareTest test = new ChiSquareTest();
-    final double pvalue = test.chiSquareTest(expected, observed);
-    Assertions.assertFalse(pvalue < 0.01, "P-value = " + pvalue);
+    final SignificanceResult r = ChiSquareTest.withDefaults().test(expected, observed);
+    Assertions.assertFalse(r.reject(0.01), () -> "p-value = " + r.getPValue());
   }
 }
diff --git a/gdsc-test-utils/pom.xml b/gdsc-test-utils/pom.xml
@@ -41,8 +41,7 @@ Contains utilities for use with test frameworks.
     </dependency>
     <dependency>
       <groupId>org.apache.commons</groupId>
-      <artifactId>commons-math3</artifactId>
-      <version>3.6.1</version>
+      <artifactId>commons-statistics-inference</artifactId>
       <scope>test</scope>
     </dependency>
   </dependencies>

diff --git a/gdsc-test-utils/src/test/java/uk/ac/sussex/gdsc/test/utils/ByteScramblerTest.java b/gdsc-test-utils/src/test/java/uk/ac/sussex/gdsc/test/utils/ByteScramblerTest.java
@@ -24,9 +24,10 @@
 
 import java.util.Arrays;
 import java.util.stream.DoubleStream;
-import org.apache.commons.math3.stat.inference.ChiSquareTest;
 import org.apache.commons.rng.UniformRandomProvider;
 import org.apache.commons.rng.simple.RandomSource;
+import org.apache.commons.statistics.inference.ChiSquareTest;
+import org.apache.commons.statistics.inference.SignificanceResult;
 import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.Test;
 
@@ -71,9 +72,8 @@ void testBitScramblerIsUniform() {
       }
     }
     // Do a chi-square test
-    final ChiSquareTest chiSq = new ChiSquareTest();
     final double[] expected = DoubleStream.generate(() -> 1.0 / 256).limit(256).toArray();
-    final double pValue = chiSq.chiSquareTest(expected, histogram);
-    Assertions.assertFalse(pValue < 0.01);
+    final SignificanceResult r = ChiSquareTest.withDefaults().test(expected, histogram);
+    Assertions.assertFalse(r.reject(0.01), () -> "p-value = " + r.getPValue());
   }
 }