From b916ac08e8fb8cc86bbccb7ee20b8b60dfe8a4d7 Mon Sep 17 00:00:00 2001
From: "joseph.lizier" <joseph.lizier@gmail.com>
Date: Wed, 13 Aug 2014 14:53:57 +0000
Subject: [PATCH] Javadocs noted as incomplete, and indeed the code itself
 experimental, for mixed package.

---
 ...MutualInfoCalculatorMultiVariateWithDiscrete.java | 10 ++++++++--
 ...InfoCalculatorMultiVariateWithDiscreteSource.java | 10 ++++++++--
 ...lculatorMultiVariateWithDiscreteSourceCommon.java |  9 ++++++++-
 ...MutualInfoCalculatorMultiVariateWithDiscrete.java | 10 ++++++++--
 ...ulatorMultiVariateWithDiscreteSourceGaussian.java | 12 +++++++++---
 ...foCalculatorMultiVariateWithDiscreteGaussian.java | 12 +++++++++---
 ...InfoCalculatorMultiVariateWithDiscreteKernel.java | 10 ++++++++++
 ...nfoCalculatorMultiVariateWithDiscreteKraskov.java | 10 +++++++---
 ...nfoCalculatorMultiVariateWithDiscreteKraskov.java | 10 +++++++---
 ...foCalculatorMultiVariateWithDiscreteSymbolic.java | 10 ++++++++++
 ...foCalculatorMultiVariateWithDiscreteSymbolic.java | 10 ++++++++++
 11 files changed, 94 insertions(+), 19 deletions(-)

diff --git a/java/source/infodynamics/measures/mixed/ConditionalMutualInfoCalculatorMultiVariateWithDiscrete.java b/java/source/infodynamics/measures/mixed/ConditionalMutualInfoCalculatorMultiVariateWithDiscrete.java
index 663d94f..2482d88 100755
--- a/java/source/infodynamics/measures/mixed/ConditionalMutualInfoCalculatorMultiVariateWithDiscrete.java
+++ b/java/source/infodynamics/measures/mixed/ConditionalMutualInfoCalculatorMultiVariateWithDiscrete.java
@@ -19,13 +19,19 @@
 package infodynamics.measures.mixed;
 
 import infodynamics.utils.EmpiricalMeasurementDistribution;
+import infodynamics.measures.continuous.ConditionalMutualInfoCalculatorMultiVariate;
 
 /**
  * A conditional mutual information calculator between a joint set of continuous variables, 
  *  and a discrete variable, conditioned on another discrete variable. 
  * 
- * @author Joseph Lizier, joseph.lizier at gmail.com
- *
+ * <p>These calculators are <b>EXPERIMENTAL</b> -- not properly tested,
+ * and not well documented. The intended calling pattern is similar to
+ * {@link ConditionalMutualInfoCalculatorMultiVariate}
+ * </p>
+ * 
+ * @author Joseph Lizier (<a href="joseph.lizier at gmail.com">email</a>,
+ * <a href="http://lizier.me/joseph/">www</a>)
  */
 public interface ConditionalMutualInfoCalculatorMultiVariateWithDiscrete {
 
diff --git a/java/source/infodynamics/measures/mixed/ConditionalMutualInfoCalculatorMultiVariateWithDiscreteSource.java b/java/source/infodynamics/measures/mixed/ConditionalMutualInfoCalculatorMultiVariateWithDiscreteSource.java
index 732507a..579a35a 100755
--- a/java/source/infodynamics/measures/mixed/ConditionalMutualInfoCalculatorMultiVariateWithDiscreteSource.java
+++ b/java/source/infodynamics/measures/mixed/ConditionalMutualInfoCalculatorMultiVariateWithDiscreteSource.java
@@ -18,14 +18,20 @@
 
 package infodynamics.measures.mixed;
 
+import infodynamics.measures.continuous.ConditionalMutualInfoCalculatorMultiVariate;
 import infodynamics.utils.EmpiricalMeasurementDistribution;
 
 /**
  * A conditional mutual information calculator between a joint set of continuous variables, 
  *  and a discrete variable, conditioned on another continuous variable vector. 
  * 
- * @author Joseph Lizier, joseph.lizier at gmail.com
- *
+ * <p>These calculators are <b>EXPERIMENTAL</b> -- not properly tested,
+ * and not well documented. The intended calling pattern is similar to
+ * {@link ConditionalMutualInfoCalculatorMultiVariate}
+ * </p>
+ * 
+ * @author Joseph Lizier (<a href="joseph.lizier at gmail.com">email</a>,
+ * <a href="http://lizier.me/joseph/">www</a>)
  */
 public interface ConditionalMutualInfoCalculatorMultiVariateWithDiscreteSource {
 
diff --git a/java/source/infodynamics/measures/mixed/ConditionalMutualInfoCalculatorMultiVariateWithDiscreteSourceCommon.java b/java/source/infodynamics/measures/mixed/ConditionalMutualInfoCalculatorMultiVariateWithDiscreteSourceCommon.java
index b518f5d..8e249c4 100755
--- a/java/source/infodynamics/measures/mixed/ConditionalMutualInfoCalculatorMultiVariateWithDiscreteSourceCommon.java
+++ b/java/source/infodynamics/measures/mixed/ConditionalMutualInfoCalculatorMultiVariateWithDiscreteSourceCommon.java
@@ -18,6 +18,7 @@
 
 package infodynamics.measures.mixed;
 
+import infodynamics.measures.continuous.ConditionalMutualInfoCalculatorMultiVariate;
 import infodynamics.measures.mixed.ConditionalMutualInfoCalculatorMultiVariateWithDiscreteSource;
 import infodynamics.utils.MatrixUtils;
 import infodynamics.utils.EmpiricalMeasurementDistribution;
@@ -31,7 +32,13 @@ import infodynamics.utils.RandomGenerator;
  *  conditioned on another vector of continuous variables Z.
  *  It implements common methods for child classes to build on</p>
  *  
- * @author Joseph Lizier
+ * <p>These calculators are <b>EXPERIMENTAL</b> -- not properly tested,
+ * and not well documented. The intended calling pattern is similar to
+ * {@link ConditionalMutualInfoCalculatorMultiVariate}
+ * </p>
+ * 
+ * @author Joseph Lizier (<a href="joseph.lizier at gmail.com">email</a>,
+ * <a href="http://lizier.me/joseph/">www</a>)
  */
 public abstract class ConditionalMutualInfoCalculatorMultiVariateWithDiscreteSourceCommon
 	implements ConditionalMutualInfoCalculatorMultiVariateWithDiscreteSource {
diff --git a/java/source/infodynamics/measures/mixed/MutualInfoCalculatorMultiVariateWithDiscrete.java b/java/source/infodynamics/measures/mixed/MutualInfoCalculatorMultiVariateWithDiscrete.java
index c85864e..424647a 100755
--- a/java/source/infodynamics/measures/mixed/MutualInfoCalculatorMultiVariateWithDiscrete.java
+++ b/java/source/infodynamics/measures/mixed/MutualInfoCalculatorMultiVariateWithDiscrete.java
@@ -18,6 +18,7 @@
 
 package infodynamics.measures.mixed;
 
+import infodynamics.measures.continuous.MutualInfoCalculatorMultiVariate;
 import infodynamics.utils.EmpiricalMeasurementDistribution;
 
 /**
@@ -43,8 +44,13 @@ import infodynamics.utils.EmpiricalMeasurementDistribution;
  * 	</ol>
  * </p>
  * 
- * @author Joseph Lizier joseph.lizier_at_gmail.com
- *
+ * <p>These calculators are <b>EXPERIMENTAL</b> -- not properly tested,
+ * and not well documented. The intended calling pattern is similar to
+ * {@link MutualInfoCalculatorMultiVariate}
+ * </p>
+ * 
+ * @author Joseph Lizier (<a href="joseph.lizier at gmail.com">email</a>,
+ * <a href="http://lizier.me/joseph/">www</a>)
  */
 public interface MutualInfoCalculatorMultiVariateWithDiscrete {
 
diff --git a/java/source/infodynamics/measures/mixed/gaussian/ConditionalMutualInfoCalculatorMultiVariateWithDiscreteSourceGaussian.java b/java/source/infodynamics/measures/mixed/gaussian/ConditionalMutualInfoCalculatorMultiVariateWithDiscreteSourceGaussian.java
index 4043877..354db2b 100755
--- a/java/source/infodynamics/measures/mixed/gaussian/ConditionalMutualInfoCalculatorMultiVariateWithDiscreteSourceGaussian.java
+++ b/java/source/infodynamics/measures/mixed/gaussian/ConditionalMutualInfoCalculatorMultiVariateWithDiscreteSourceGaussian.java
@@ -19,6 +19,7 @@
 package infodynamics.measures.mixed.gaussian;
 
 import infodynamics.measures.mixed.ConditionalMutualInfoCalculatorMultiVariateWithDiscreteSourceCommon;
+import infodynamics.measures.continuous.ConditionalMutualInfoCalculatorMultiVariate;
 import infodynamics.measures.continuous.ConditionalMutualInfoMultiVariateCommon;
 import infodynamics.measures.continuous.gaussian.EntropyCalculatorMultiVariateGaussian;
 import infodynamics.utils.MatrixUtils;
@@ -43,7 +44,12 @@ import infodynamics.utils.MatrixUtils;
  * as we would normally expect a mutual information calculation: if we add more
  * continuous variables in, it may increase in spite of redundancy between these
  * variables. TODO Further exploration should take place here ...</p>
- *  
+ * 
+ * <p>These calculators are <b>EXPERIMENTAL</b> -- not properly tested,
+ * and not well documented. The intended calling pattern is similar to
+ * {@link ConditionalMutualInfoCalculatorMultiVariate}
+ * </p>
+ * 
  * <p>
  * Usage:
  * 	<ol>
@@ -75,8 +81,8 @@ import infodynamics.utils.MatrixUtils;
  * @see <a href="http://mathworld.wolfram.com/DifferentialEntropy.html">Differential entropy for Gaussian random variables at Mathworld</a>
  * @see <a href="http://en.wikipedia.org/wiki/Differential_entropy">Differential entropy for Gaussian random variables at Wikipedia</a>
  * @see <a href="http://en.wikipedia.org/wiki/Multivariate_normal_distribution">Multivariate normal distribution on Wikipedia</a>
- * @author Joseph Lizier joseph.lizier_at_gmail.com
- * 
+ * @author Joseph Lizier (<a href="joseph.lizier at gmail.com">email</a>,
+ * <a href="http://lizier.me/joseph/">www</a>)
  */
 public class ConditionalMutualInfoCalculatorMultiVariateWithDiscreteSourceGaussian
 		extends	ConditionalMutualInfoCalculatorMultiVariateWithDiscreteSourceCommon 
diff --git a/java/source/infodynamics/measures/mixed/gaussian/MutualInfoCalculatorMultiVariateWithDiscreteGaussian.java b/java/source/infodynamics/measures/mixed/gaussian/MutualInfoCalculatorMultiVariateWithDiscreteGaussian.java
index 0074cfd..72ce2bc 100755
--- a/java/source/infodynamics/measures/mixed/gaussian/MutualInfoCalculatorMultiVariateWithDiscreteGaussian.java
+++ b/java/source/infodynamics/measures/mixed/gaussian/MutualInfoCalculatorMultiVariateWithDiscreteGaussian.java
@@ -18,6 +18,7 @@
 
 package infodynamics.measures.mixed.gaussian;
 
+import infodynamics.measures.continuous.ConditionalMutualInfoCalculatorMultiVariate;
 import infodynamics.measures.continuous.gaussian.EntropyCalculatorMultiVariateGaussian;
 import infodynamics.measures.mixed.MutualInfoCalculatorMultiVariateWithDiscrete;
 import infodynamics.utils.EmpiricalMeasurementDistribution;
@@ -42,7 +43,12 @@ import infodynamics.utils.RandomGenerator;
  * as we would normally expect a mutual information calculation: if we add more
  * continuous variables in, it increases in spite of redundancy between these
  * variables. TODO Further exploration should take place here ...</p>
- *  
+ * 
+ * <p>These calculators are <b>EXPERIMENTAL</b> -- not properly tested,
+ * and not well documented. The intended calling pattern is similar to
+ * {@link ConditionalMutualInfoCalculatorMultiVariate}
+ * </p>
+ * 
  * <p>
  * Usage:
  * 	<ol>
@@ -62,8 +68,8 @@ import infodynamics.utils.RandomGenerator;
  * 
  * @see Differential entropy for Gaussian random variables defined at 
  *      {@link http://mathworld.wolfram.com/DifferentialEntropy.html}
- * @author Joseph Lizier joseph.lizier_at_gmail.com
- *
+ * @author Joseph Lizier (<a href="joseph.lizier at gmail.com">email</a>,
+ * <a href="http://lizier.me/joseph/">www</a>)
  */
 public class MutualInfoCalculatorMultiVariateWithDiscreteGaussian implements
 		MutualInfoCalculatorMultiVariateWithDiscrete, Cloneable {
diff --git a/java/source/infodynamics/measures/mixed/kernel/MutualInfoCalculatorMultiVariateWithDiscreteKernel.java b/java/source/infodynamics/measures/mixed/kernel/MutualInfoCalculatorMultiVariateWithDiscreteKernel.java
index 9414a66..afbbfac 100755
--- a/java/source/infodynamics/measures/mixed/kernel/MutualInfoCalculatorMultiVariateWithDiscreteKernel.java
+++ b/java/source/infodynamics/measures/mixed/kernel/MutualInfoCalculatorMultiVariateWithDiscreteKernel.java
@@ -20,12 +20,22 @@ package infodynamics.measures.mixed.kernel;
 
 import java.util.Arrays;
 
+import infodynamics.measures.continuous.MutualInfoCalculatorMultiVariate;
 import infodynamics.measures.continuous.kernel.KernelEstimatorMultiVariate;
 import infodynamics.measures.mixed.MutualInfoCalculatorMultiVariateWithDiscrete;
 import infodynamics.utils.MatrixUtils;
 import infodynamics.utils.EmpiricalMeasurementDistribution;
 import infodynamics.utils.RandomGenerator;
 
+/**
+ * <p>These calculators are <b>EXPERIMENTAL</b> -- not properly tested,
+ * and not well documented. The intended calling pattern is similar to
+ * {@link MutualInfoCalculatorMultiVariate}
+ * </p>
+ * 
+ * @author Joseph Lizier (<a href="joseph.lizier at gmail.com">email</a>,
+ * <a href="http://lizier.me/joseph/">www</a>)
+ */
 public class MutualInfoCalculatorMultiVariateWithDiscreteKernel implements
 	MutualInfoCalculatorMultiVariateWithDiscrete {
 
diff --git a/java/source/infodynamics/measures/mixed/kraskov/ConditionalMutualInfoCalculatorMultiVariateWithDiscreteKraskov.java b/java/source/infodynamics/measures/mixed/kraskov/ConditionalMutualInfoCalculatorMultiVariateWithDiscreteKraskov.java
index c5206a4..a531b72 100755
--- a/java/source/infodynamics/measures/mixed/kraskov/ConditionalMutualInfoCalculatorMultiVariateWithDiscreteKraskov.java
+++ b/java/source/infodynamics/measures/mixed/kraskov/ConditionalMutualInfoCalculatorMultiVariateWithDiscreteKraskov.java
@@ -18,6 +18,7 @@
 
 package infodynamics.measures.mixed.kraskov;
 
+import infodynamics.measures.continuous.ConditionalMutualInfoCalculatorMultiVariate;
 import infodynamics.measures.mixed.ConditionalMutualInfoCalculatorMultiVariateWithDiscreteSourceCommon;
 import infodynamics.utils.EuclideanUtils;
 import infodynamics.utils.MathsUtils;
@@ -34,10 +35,13 @@ import infodynamics.utils.MatrixUtils;
  * follows {#link ConditionalMutualInfoCalculatorMultiVariateKraskov2}.
  * </p>
  * 
- * @see "Estimating mutual information", Kraskov, A., Stogbauer, H., Grassberger, P., Physical Review E 69, (2004) 066138
- * @see http://dx.doi.org/10.1103/PhysRevE.69.066138
+ * <p>These calculators are <b>EXPERIMENTAL</b> -- not properly tested,
+ * and not well documented. The intended calling pattern is similar to
+ * {@link ConditionalMutualInfoCalculatorMultiVariate}
+ * </p>
  * 
- * @author Joseph Lizier
+ * @author Joseph Lizier (<a href="joseph.lizier at gmail.com">email</a>,
+ * <a href="http://lizier.me/joseph/">www</a>)
  */
 public class ConditionalMutualInfoCalculatorMultiVariateWithDiscreteKraskov
 	extends ConditionalMutualInfoCalculatorMultiVariateWithDiscreteSourceCommon
diff --git a/java/source/infodynamics/measures/mixed/kraskov/MutualInfoCalculatorMultiVariateWithDiscreteKraskov.java b/java/source/infodynamics/measures/mixed/kraskov/MutualInfoCalculatorMultiVariateWithDiscreteKraskov.java
index 7bf5fbf..d8eee06 100755
--- a/java/source/infodynamics/measures/mixed/kraskov/MutualInfoCalculatorMultiVariateWithDiscreteKraskov.java
+++ b/java/source/infodynamics/measures/mixed/kraskov/MutualInfoCalculatorMultiVariateWithDiscreteKraskov.java
@@ -18,6 +18,7 @@
 
 package infodynamics.measures.mixed.kraskov;
 
+import infodynamics.measures.continuous.MutualInfoCalculatorMultiVariate;
 import infodynamics.measures.mixed.MutualInfoCalculatorMultiVariateWithDiscrete;
 import infodynamics.utils.EuclideanUtils;
 import infodynamics.utils.MathsUtils;
@@ -35,10 +36,13 @@ import infodynamics.utils.RandomGenerator;
  * where small K is used (e.g. for binary data splitting continuous into
  * two distinct groups, 1400 observations, K=4 has bias ~ -.35)</p>
  * 
- * @see "Estimating mutual information", Kraskov, A., Stogbauer, H., Grassberger, P., Physical Review E 69, (2004) 066138
- * @see http://dx.doi.org/10.1103/PhysRevE.69.066138
+ * <p>These calculators are <b>EXPERIMENTAL</b> -- not properly tested,
+ * and not well documented. The intended calling pattern is similar to
+ * {@link MutualInfoCalculatorMultiVariate}
+ * </p>
  * 
- * @author Joseph Lizier
+ * @author Joseph Lizier (<a href="joseph.lizier at gmail.com">email</a>,
+ * <a href="http://lizier.me/joseph/">www</a>)
  */
 public class MutualInfoCalculatorMultiVariateWithDiscreteKraskov implements MutualInfoCalculatorMultiVariateWithDiscrete {
 
diff --git a/java/source/infodynamics/measures/mixed/symbolic/ConditionalMutualInfoCalculatorMultiVariateWithDiscreteSymbolic.java b/java/source/infodynamics/measures/mixed/symbolic/ConditionalMutualInfoCalculatorMultiVariateWithDiscreteSymbolic.java
index a953866..3440d7e 100755
--- a/java/source/infodynamics/measures/mixed/symbolic/ConditionalMutualInfoCalculatorMultiVariateWithDiscreteSymbolic.java
+++ b/java/source/infodynamics/measures/mixed/symbolic/ConditionalMutualInfoCalculatorMultiVariateWithDiscreteSymbolic.java
@@ -19,6 +19,7 @@
 package infodynamics.measures.mixed.symbolic;
 
 import infodynamics.measures.mixed.ConditionalMutualInfoCalculatorMultiVariateWithDiscrete;
+import infodynamics.measures.continuous.ConditionalMutualInfoCalculatorMultiVariate;
 import infodynamics.measures.discrete.ConditionalMutualInformationCalculator;
 import infodynamics.utils.FirstIndexComparatorDouble;
 import infodynamics.utils.MathsUtils;
@@ -26,6 +27,15 @@ import infodynamics.utils.MatrixUtils;
 import infodynamics.utils.EmpiricalMeasurementDistribution;
 import infodynamics.utils.RandomGenerator;
 
+/**
+ * <p>These calculators are <b>EXPERIMENTAL</b> -- not properly tested,
+ * and not well documented. The intended calling pattern is similar to
+ * {@link ConditionalMutualInfoCalculatorMultiVariate}
+ * </p>
+ * 
+ * @author Joseph Lizier (<a href="joseph.lizier at gmail.com">email</a>,
+ * <a href="http://lizier.me/joseph/">www</a>)
+ */
 public class ConditionalMutualInfoCalculatorMultiVariateWithDiscreteSymbolic implements
 		ConditionalMutualInfoCalculatorMultiVariateWithDiscrete {
 
diff --git a/java/source/infodynamics/measures/mixed/symbolic/MutualInfoCalculatorMultiVariateWithDiscreteSymbolic.java b/java/source/infodynamics/measures/mixed/symbolic/MutualInfoCalculatorMultiVariateWithDiscreteSymbolic.java
index e5f4406..fd57c87 100755
--- a/java/source/infodynamics/measures/mixed/symbolic/MutualInfoCalculatorMultiVariateWithDiscreteSymbolic.java
+++ b/java/source/infodynamics/measures/mixed/symbolic/MutualInfoCalculatorMultiVariateWithDiscreteSymbolic.java
@@ -19,6 +19,7 @@
 package infodynamics.measures.mixed.symbolic;
 
 import infodynamics.measures.mixed.MutualInfoCalculatorMultiVariateWithDiscrete;
+import infodynamics.measures.continuous.MutualInfoCalculatorMultiVariate;
 import infodynamics.measures.discrete.MutualInformationCalculator;
 import infodynamics.utils.FirstIndexComparatorDouble;
 import infodynamics.utils.MathsUtils;
@@ -26,6 +27,15 @@ import infodynamics.utils.MatrixUtils;
 import infodynamics.utils.EmpiricalMeasurementDistribution;
 import infodynamics.utils.RandomGenerator;
 
+/**
+ * <p>These calculators are <b>EXPERIMENTAL</b> -- not properly tested,
+ * and not well documented. The intended calling pattern is similar to
+ * {@link MutualInfoCalculatorMultiVariate}
+ * </p>
+ * 
+ * @author Joseph Lizier (<a href="joseph.lizier at gmail.com">email</a>,
+ * <a href="http://lizier.me/joseph/">www</a>)
+ */
 public class MutualInfoCalculatorMultiVariateWithDiscreteSymbolic implements
 		MutualInfoCalculatorMultiVariateWithDiscrete {