Change distributions from o.a.c.math3 to o.a.c.statistics

aherbert · Jul 20, 2023 · 6ec7fb3 · 6ec7fb3
1 parent 842afe7
commit 6ec7fb3
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Showing 5 changed files with 20 additions and 16 deletions.
diff --git a/gdsc-core/pom.xml b/gdsc-core/pom.xml
@@ -88,6 +88,10 @@ GDSC SMLM ImageJ Plugins - Single molecule localisation microscopy (SMLM)
       <groupId>org.apache.commons</groupId>
       <artifactId>commons-rng-core</artifactId>
     </dependency>
+    <dependency>
+      <groupId>org.apache.commons</groupId>
+      <artifactId>commons-statistics-distribution</artifactId>
+    </dependency>
     <!-- Prevent logging from QuickHull3D -->
     <dependency>
       <groupId>org.slf4j</groupId>

diff --git a/gdsc-core/src/main/java/uk/ac/sussex/gdsc/core/utils/RegressionUtils.java b/gdsc-core/src/main/java/uk/ac/sussex/gdsc/core/utils/RegressionUtils.java
@@ -28,7 +28,7 @@
 
 package uk.ac.sussex.gdsc.core.utils;
 
-import org.apache.commons.math3.distribution.FDistribution;
+import org.apache.commons.statistics.distribution.FDistribution;
 
 /**
  * Contains utilities for working with regression data.
@@ -120,10 +120,9 @@ public static double residualsFTest(double residualSumSquares1, int numberOfPara
     if (f == Double.POSITIVE_INFINITY) {
       return 0;
     }
-    // pass a null rng to avoid unneeded overhead as we will not sample from this distribution
-    final FDistribution distribution = new FDistribution(null,
-        numberOfParameters2 - numberOfParameters1, numberOfPoints - numberOfParameters2);
-    return 1.0 - distribution.cumulativeProbability(f);
+    final FDistribution distribution = FDistribution.of(numberOfParameters2 - numberOfParameters1,
+        numberOfPoints - numberOfParameters2);
+    return distribution.survivalProbability(f);
   }
 
   /**

diff --git a/gdsc-core/src/main/java/uk/ac/sussex/gdsc/core/utils/Statistics.java b/gdsc-core/src/main/java/uk/ac/sussex/gdsc/core/utils/Statistics.java
@@ -28,7 +28,7 @@
 
 package uk.ac.sussex.gdsc.core.utils;
 
-import org.apache.commons.math3.distribution.TDistribution;
+import org.apache.commons.statistics.distribution.TDistribution;
 
 /**
  * Simple class to calculate the mean and standard deviation of data.
@@ -472,10 +472,11 @@ public double getConfidenceInterval(double confidenceLevel) {
       throw new IllegalArgumentException("Confidence level must be in the range 0-1");
     }
     final double se = getStandardError();
-    final double alpha = 1 - (1 - confidenceLevel) * 0.5; // Two-sided, e.g. 0.95 -> 0.975
+    final double alpha = (1 - confidenceLevel) * 0.5; // Two-sided, e.g. 0.95 -> 0.975
     final int degreesOfFreedom = size - 1;
-    final TDistribution t = new TDistribution(degreesOfFreedom);
-    return t.inverseCumulativeProbability(alpha) * se;
+    final TDistribution t = TDistribution.of(degreesOfFreedom);
+    // Add to zero to workaround alpha=0 returning -0.0
+    return 0.0 + t.inverseSurvivalProbability(alpha) * se;
   }
 
   /**

diff --git a/...k/ac/sussex/gdsc/core/utils/rng/BinomialDiscreteInverseCumulativeProbabilityFunction.java b/...k/ac/sussex/gdsc/core/utils/rng/BinomialDiscreteInverseCumulativeProbabilityFunction.java
@@ -28,10 +28,10 @@
 
 package uk.ac.sussex.gdsc.core.utils.rng;
 
-import org.apache.commons.math3.distribution.BinomialDistribution;
 import org.apache.commons.math3.exception.NotPositiveException;
 import org.apache.commons.math3.exception.OutOfRangeException;
 import org.apache.commons.rng.sampling.distribution.DiscreteInverseCumulativeProbabilityFunction;
+import org.apache.commons.statistics.distribution.BinomialDistribution;
 
 /**
  * Provides the inverse cumulative probability of the Binomial distribution.
@@ -90,7 +90,7 @@ public void updateDistribution(int trials, double probabilityOfSuccess) {
   }
 
   private void update(int trials, double probabilityOfSuccess) {
-    bd = new BinomialDistribution(null, trials, probabilityOfSuccess);
+    bd = BinomialDistribution.of(trials, probabilityOfSuccess);
   }
 
   @Override

diff --git a/.../sussex/gdsc/core/utils/rng/BinomialDiscreteInverseCumulativeProbabilityFunctionTest.java b/.../sussex/gdsc/core/utils/rng/BinomialDiscreteInverseCumulativeProbabilityFunctionTest.java
@@ -28,7 +28,7 @@
 
 package uk.ac.sussex.gdsc.core.utils.rng;
 
-import org.apache.commons.math3.distribution.BinomialDistribution;
+import org.apache.commons.statistics.distribution.BinomialDistribution;
 import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.Test;
 
@@ -38,7 +38,7 @@ class BinomialDiscreteInverseCumulativeProbabilityFunctionTest {
   void testInverseCumulativeProbabiity() {
     final int trials = 13;
     final double probabilityOfSuccess = 0.02;
-    final BinomialDistribution bd = new BinomialDistribution(trials, probabilityOfSuccess);
+    final BinomialDistribution bd = BinomialDistribution.of(trials, probabilityOfSuccess);
     final BinomialDiscreteInverseCumulativeProbabilityFunction fun =
         new BinomialDiscreteInverseCumulativeProbabilityFunction(trials, probabilityOfSuccess);
     for (int i = 0; i <= 10; i++) {
@@ -52,7 +52,7 @@ void testInverseCumulativeProbabiity() {
   void testSetTrials() {
     final int trials = 13;
     final double probabilityOfSuccess = 0.02;
-    final BinomialDistribution bd = new BinomialDistribution(trials, probabilityOfSuccess);
+    final BinomialDistribution bd = BinomialDistribution.of(trials, probabilityOfSuccess);
     final BinomialDiscreteInverseCumulativeProbabilityFunction fun =
         new BinomialDiscreteInverseCumulativeProbabilityFunction(trials - 1, probabilityOfSuccess);
 
@@ -69,7 +69,7 @@ void testSetTrials() {
   void testSetProbabilityOfSuccess() {
     final int trials = 13;
     final double probabilityOfSuccess = 0.02;
-    final BinomialDistribution bd = new BinomialDistribution(trials, probabilityOfSuccess);
+    final BinomialDistribution bd = BinomialDistribution.of(trials, probabilityOfSuccess);
     final BinomialDiscreteInverseCumulativeProbabilityFunction fun =
         new BinomialDiscreteInverseCumulativeProbabilityFunction(trials,
             probabilityOfSuccess + 0.1);
@@ -87,7 +87,7 @@ void testSetProbabilityOfSuccess() {
   void testUpdateDistribution() {
     final int trials = 13;
     final double probabilityOfSuccess = 0.02;
-    final BinomialDistribution bd = new BinomialDistribution(trials, probabilityOfSuccess);
+    final BinomialDistribution bd = BinomialDistribution.of(trials, probabilityOfSuccess);
     final BinomialDiscreteInverseCumulativeProbabilityFunction fun =
         new BinomialDiscreteInverseCumulativeProbabilityFunction(trials - 1,
             probabilityOfSuccess + 0.1);