1 files changed, 149 insertions, 0 deletions
diff --git a/src/de/lmu/ifi/dbs/elki/distance/distancefunction/BrayCurtisDistanceFunction.java b/src/de/lmu/ifi/dbs/elki/distance/distancefunction/BrayCurtisDistanceFunction.java
new file mode 100644
index 00000000..20a989fc
--- /dev/null
+++ b/src/de/lmu/ifi/dbs/elki/distance/distancefunction/BrayCurtisDistanceFunction.java
@@ -0,0 +1,149 @@
+package de.lmu.ifi.dbs.elki.distance.distancefunction;
+
+/*
+ This file is part of ELKI:
+ Environment for Developing KDD-Applications Supported by Index-Structures
+
+ Copyright (C) 2013
+ Ludwig-Maximilians-Universität München
+ Lehr- und Forschungseinheit für Datenbanksysteme
+ ELKI Development Team
+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Affero General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ GNU Affero General Public License for more details.
+
+ You should have received a copy of the GNU Affero General Public License
+ along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+import de.lmu.ifi.dbs.elki.data.NumberVector;
+import de.lmu.ifi.dbs.elki.data.spatial.SpatialComparable;
+import de.lmu.ifi.dbs.elki.utilities.Alias;
+import de.lmu.ifi.dbs.elki.utilities.documentation.Reference;
+import de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizer;
+
+/**
+ * Bray-Curtis distance function / Sørensen–Dice coefficient for continuous
+ * spaces.
+ * 
+ * Reference:
+ * <p>
+ * J. R. Bray and J. T. Curtis<br />
+ * An ordination of the upland forest communities of southern Wisconsin<br />
+ * Ecological monographs 27.4
+ * </p>
+ * Also:
+ * <p>
+ * T. Sørensen<br />
+ * A method of establishing groups of equal amplitude in plant sociology based
+ * on similarity of species and its application to analyses of the vegetation on
+ * Danish commons<br />
+ * Kongelige Danske Videnskabernes Selskab 5 (4)
+ * </p>
+ * and:
+ * <p>
+ * L. R. Dice<br />
+ * Measures of the Amount of Ecologic Association Between Species<br />
+ * Ecology 26 (3)
+ * </p>
+ * 
+ * 
+ * Note: we modified the usual definition of Bray-Curtis for use with negative
+ * values. In essence, this function is defined as:
+ * 
+ * ManhattanDistance(v1, v2) / (ManhattanNorm(v1) + ManhattanNorm(v2))
+ * 
+ * This obviously limits the usefulness of this distance function for cases
+ * where this kind of normalization is desired. In particular in low dimensional
+ * data it should be used with care.
+ * 
+ * TODO: add a version optimized for sparse vectors / binary data.
+ * 
+ * @author Erich Schubert
+ */
+@Alias({ "bray-curtis", "braycurtis", "sorensen", "dice", "sorensen-dice" })
+@Reference(authors = "J. R. Bray and J. T. Curtis", title = "An ordination of the upland forest communities of southern Wisconsin", booktitle = "Ecological monographs 27.4", url = "http://dx.doi.org/10.2307/1942268")
+public class BrayCurtisDistanceFunction extends AbstractSpatialDoubleDistanceFunction {
+  /**
+   * Static instance.
+   */
+  public static final BrayCurtisDistanceFunction STATIC_CONTINUOUS = new BrayCurtisDistanceFunction();
+
+  /**
+   * Constructor.
+   * 
+   * @deprecated Use {@link #STATIC_CONTINUOUS} instance instead.
+   */
+  @Deprecated
+  public BrayCurtisDistanceFunction() {
+    super();
+  }
+
+  /**
+   * Dummy method, just to attach a second reference.
+   */
+  @Reference(authors = "T. Sørensen", title = "A method of establishing groups of equal amplitude in plant sociology based on similarity of species and its application to analyses of the vegetation on Danish commons", booktitle = "Kongelige Danske Videnskabernes Selskab 5 (4)")
+  static void secondReference() {
+    // Empty, just to attach a second reference
+  };
+
+  /**
+   * Dummy method, just to attach a third reference.
+   */
+  @Reference(authors = "L. R. Dice", title = "Measures of the Amount of Ecologic Association Between Species", booktitle = "Ecology 26 (3)")
+  static void thirdReference() {
+    // Empty, just to attach a second reference
+  };
+
+  @Override
+  public double doubleDistance(NumberVector<?> v1, NumberVector<?> v2) {
+    final int dim = dimensionality(v1, v2);
+    double sumdiff = 0., sumsum = 0.;
+    for (int d = 0; d < dim; d++) {
+      double xd = v1.doubleValue(d), yd = v2.doubleValue(d);
+      sumdiff += Math.abs(xd - yd);
+      sumsum += Math.abs(xd) + Math.abs(yd);
+    }
+    return sumdiff / sumsum;
+  }
+
+  @Override
+  public double doubleMinDist(SpatialComparable mbr1, SpatialComparable mbr2) {
+    final int dim = dimensionality(mbr1, mbr2);
+    double sumdiff = 0., sumsum = 0.;
+    for (int d = 0; d < dim; d++) {
+      final double min1 = mbr1.getMin(d), max1 = mbr1.getMax(d);
+      final double min2 = mbr2.getMin(d), max2 = mbr2.getMax(d);
+      if (max1 < min2) {
+        sumdiff += min2 - max1;
+      } else if (min1 > max2) {
+        sumdiff += min1 - max2;
+      } else {
+        // Minimum difference is 0
+      }
+      sumsum += Math.max(-min1, max1) + Math.max(-min2, max2);
+    }
+    return sumdiff / sumsum;
+  }
+
+  /**
+   * Parameterization class.
+   * 
+   * @author Erich Schubert
+   * 
+   * @apiviz.exclude
+   */
+  public static class Parameterizer extends AbstractParameterizer {
+    @Override
+    protected BrayCurtisDistanceFunction makeInstance() {
+      return BrayCurtisDistanceFunction.STATIC_CONTINUOUS;
+    }
+  }
+}