From bc40fb41251071657c0ad597d96146b1ca533793 Mon Sep 17 00:00:00 2001
From: "joseph.lizier" <joseph.lizier@gmail.com>
Date: Wed, 13 Aug 2014 02:41:25 +0000
Subject: [PATCH] Kraskov estimators switched to use 4 nearest neighbours by
 default (as recommended by Kraskov et al.)

---
 ...ConditionalMutualInfoCalculatorMultiVariateKraskov.java | 7 +++----
 .../continuous/kraskov/MultiInfoCalculatorKraskov.java     | 7 +++----
 .../kraskov/MutualInfoCalculatorMultiVariateKraskov.java   | 6 +++---
 3 files changed, 9 insertions(+), 11 deletions(-)

diff --git a/java/source/infodynamics/measures/continuous/kraskov/ConditionalMutualInfoCalculatorMultiVariateKraskov.java b/java/source/infodynamics/measures/continuous/kraskov/ConditionalMutualInfoCalculatorMultiVariateKraskov.java
index 6851dba..72322a4 100755
--- a/java/source/infodynamics/measures/continuous/kraskov/ConditionalMutualInfoCalculatorMultiVariateKraskov.java
+++ b/java/source/infodynamics/measures/continuous/kraskov/ConditionalMutualInfoCalculatorMultiVariateKraskov.java
@@ -73,7 +73,7 @@ public abstract class ConditionalMutualInfoCalculatorMultiVariateKraskov
 	/**
 	 * we compute distances to the kth neighbour in the joint space
 	 */
-	protected int k;
+	protected int k = 4;
 		
 	/**
 	 * Calculator for the norm between data points
@@ -104,7 +104,7 @@ public abstract class ConditionalMutualInfoCalculatorMultiVariateKraskov
 	
 	/**
 	 * Property name for the number of K nearest neighbours used in
-	 * the KSG algorithm in the full joint space.
+	 * the KSG algorithm in the full joint space (default 4).
 	 */
 	public final static String PROP_K = "k";
 	/**
@@ -120,7 +120,6 @@ public abstract class ConditionalMutualInfoCalculatorMultiVariateKraskov
 	 */
 	public ConditionalMutualInfoCalculatorMultiVariateKraskov() {
 		super();
-		k = 1; // by default
 		normCalculator = new EuclideanUtils(EuclideanUtils.NORM_MAX_NORM);
 	}
 
@@ -142,7 +141,7 @@ public abstract class ConditionalMutualInfoCalculatorMultiVariateKraskov
 	 * values should represent, include:</p>
 	 * <ul>
 	 *  <li>{@link #PROP_K} -- number of k nearest neighbours to use in joint kernel space
-	 *      in the KSG algorithm (default is 1).</li>
+	 *      in the KSG algorithm (default is 4).</li>
 	 * 	<li>{@link #PROP_NORM_TYPE}</li> -- normalization type to apply to 
 	 * 		working out the norms between the points in each marginal space.
 	 * 		Options are defined by {@link EuclideanUtils#setNormToUse(String)} -
diff --git a/java/source/infodynamics/measures/continuous/kraskov/MultiInfoCalculatorKraskov.java b/java/source/infodynamics/measures/continuous/kraskov/MultiInfoCalculatorKraskov.java
index 2b887fe..4b04fbd 100755
--- a/java/source/infodynamics/measures/continuous/kraskov/MultiInfoCalculatorKraskov.java
+++ b/java/source/infodynamics/measures/continuous/kraskov/MultiInfoCalculatorKraskov.java
@@ -63,7 +63,7 @@ public abstract class MultiInfoCalculatorKraskov implements
 	/**
 	 * we compute distances to the kth nearest neighbour
 	 */
-	protected int k;
+	protected int k = 4;
 	/**
 	 * Cached observations
 	 */
@@ -109,7 +109,7 @@ public abstract class MultiInfoCalculatorKraskov implements
 	
 	/**
 	 * Property name for the number of K nearest neighbours used in
-	 * the KSG algorithm (default 1).
+	 * the KSG algorithm (default 4).
 	 */
 	public final static String PROP_K = "k";
 	/**
@@ -133,7 +133,6 @@ public abstract class MultiInfoCalculatorKraskov implements
 	 */
 	public MultiInfoCalculatorKraskov() {
 		super();
-		k = 1; // by default
 		normCalculator = new EuclideanUtils(EuclideanUtils.NORM_MAX_NORM);
 	}
 
@@ -155,7 +154,7 @@ public abstract class MultiInfoCalculatorKraskov implements
 	 * values should represent, include:</p>
 	 * <ul>
 	 *  <li>{@link #PROP_K} -- number of k nearest neighbours to use in joint kernel space
-	 *      in the KSG algorithm (default is 1).</li>
+	 *      in the KSG algorithm (default is 4).</li>
 	 * 	<li>{@link #PROP_NORM_TYPE}</li> -- normalization type to apply to 
 	 * 		working out the norms between the points in each marginal space.
 	 * 		Options are defined by {@link EuclideanUtils#setNormToUse(String)} -
diff --git a/java/source/infodynamics/measures/continuous/kraskov/MutualInfoCalculatorMultiVariateKraskov.java b/java/source/infodynamics/measures/continuous/kraskov/MutualInfoCalculatorMultiVariateKraskov.java
index ebff3be..2d19305 100755
--- a/java/source/infodynamics/measures/continuous/kraskov/MutualInfoCalculatorMultiVariateKraskov.java
+++ b/java/source/infodynamics/measures/continuous/kraskov/MutualInfoCalculatorMultiVariateKraskov.java
@@ -65,7 +65,7 @@ public abstract class MutualInfoCalculatorMultiVariateKraskov
 	/**
 	 * we compute distances to the kth nearest neighbour
 	 */
-	protected int k = 1;
+	protected int k = 4;
 	
 	/**
 	 * Calculator for the norm between data points
@@ -92,7 +92,7 @@ public abstract class MutualInfoCalculatorMultiVariateKraskov
 	
 	/**
 	 * Property name for the number of K nearest neighbours used in
-	 * the KSG algorithm in the full joint space.
+	 * the KSG algorithm in the full joint space (default 4).
 	 */
 	public final static String PROP_K = "k";
 	/**
@@ -149,7 +149,7 @@ public abstract class MutualInfoCalculatorMultiVariateKraskov
 	 * values should represent, include:</p>
 	 * <ul>
 	 *  <li>{@link #PROP_K} -- number of k nearest neighbours to use in joint kernel space
-	 *      in the KSG algorithm (default is 1).</li>
+	 *      in the KSG algorithm (default is 4).</li>
 	 * 	<li>{@link #PROP_NORM_TYPE}</li> -- normalization type to apply to 
 	 * 		working out the norms between the points in each marginal space.
 	 * 		Options are defined by {@link EuclideanUtils#setNormToUse(String)} -