[3/5] git commit: Merge remote-tracking branch 'oleersoy/master'

[luc]

Merge remote-tracking branch 'oleersoy/master'

Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/fc7eeb48
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/fc7eeb48
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/fc7eeb48

Branch: refs/heads/master
Commit: fc7eeb4801b1ea7524b9329d5584c2e5ed945913
Parents: a3fdeb4 0dec6e7
Author: Luc Maisonobe 
Authored: Wed Oct 15 09:02:58 2014 +0200
Committer: Luc Maisonobe 
Committed: Wed Oct 15 09:02:58 2014 +0200

--
 .../exception/MathIllegalStateException.java|  5 +++--
 .../AbstractIntegerDistributionTest.java| 21 +++-
 2 files changed, 23 insertions(+), 3 deletions(-)
--

[5/5] git commit: Added Ole Ersoy to the contributors list.

[luc]

Added Ole Ersoy to the contributors list.

Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/d26810c0
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/d26810c0
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/d26810c0

Branch: refs/heads/master
Commit: d26810c0d98bacce22363ad6ec327eebeb1afacf
Parents: f5a8bf3
Author: Luc Maisonobe 
Authored: Wed Oct 15 09:13:36 2014 +0200
Committer: Luc Maisonobe 
Committed: Wed Oct 15 09:13:36 2014 +0200

--
 pom.xml | 3 +++
 1 file changed, 3 insertions(+)
--


http://git-wip-us.apache.org/repos/asf/commons-math/blob/d26810c0/pom.xml
--
diff --git a/pom.xml b/pom.xml
index 3a62e60..8430131 100644
--- a/pom.xml
+++ b/pom.xml
@@ -204,6 +204,9 @@
   Ted Dunning
 
 
+  Ole Ersoy
+
+
   Ajo Fod
 
 

[2/5] git commit: Corrected variance (Thanks Thomas) and added tests for inverseCumulativeProbability

[luc]

Corrected variance (Thanks Thomas) and added tests for 
inverseCumulativeProbability


Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/0dec6e76
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/0dec6e76
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/0dec6e76

Branch: refs/heads/master
Commit: 0dec6e76fb544fa3e8bf5fd17f16314735971dd7
Parents: 4cb944e
Author: Ole 
Authored: Fri Oct 10 17:24:57 2014 -0500
Committer: Ole 
Committed: Fri Oct 10 17:24:57 2014 -0500

--
 .../AbstractIntegerDistributionTest.java| 21 +++-
 1 file changed, 20 insertions(+), 1 deletion(-)
--


http://git-wip-us.apache.org/repos/asf/commons-math/blob/0dec6e76/src/test/java/org/apache/commons/math3/distribution/AbstractIntegerDistributionTest.java
--
diff --git 
a/src/test/java/org/apache/commons/math3/distribution/AbstractIntegerDistributionTest.java
 
b/src/test/java/org/apache/commons/math3/distribution/AbstractIntegerDistributionTest.java
index 97ea5a0..d6f668b 100644
--- 
a/src/test/java/org/apache/commons/math3/distribution/AbstractIntegerDistributionTest.java
+++ 
b/src/test/java/org/apache/commons/math3/distribution/AbstractIntegerDistributionTest.java
@@ -28,6 +28,25 @@ public class AbstractIntegerDistributionTest {
 protected final double p = diceDistribution.probability(1);
 
 @Test
+public void testInverseCumulativeProbabilityMethod()
+{
+   double precision = 0.001;
+   Assert.assertEquals(1, 
diceDistribution.inverseCumulativeProbability(0));
+   Assert.assertEquals(1, 
diceDistribution.inverseCumulativeProbability((1d-Double.MIN_VALUE)/6d));
+   Assert.assertEquals(2, 
diceDistribution.inverseCumulativeProbability((1d+precision)/6d));
+   Assert.assertEquals(2, 
diceDistribution.inverseCumulativeProbability((2d-Double.MIN_VALUE)/6d));
+   Assert.assertEquals(3, 
diceDistribution.inverseCumulativeProbability((2d+precision)/6d));
+   Assert.assertEquals(3, 
diceDistribution.inverseCumulativeProbability((3d-Double.MIN_VALUE)/6d));
+   Assert.assertEquals(4, 
diceDistribution.inverseCumulativeProbability((3d+precision)/6d));
+   Assert.assertEquals(4, 
diceDistribution.inverseCumulativeProbability((4d-Double.MIN_VALUE)/6d));
+   Assert.assertEquals(5, 
diceDistribution.inverseCumulativeProbability((4d+precision)/6d));
+   Assert.assertEquals(5, 
diceDistribution.inverseCumulativeProbability((5d-precision)/6d));//Can't use 
Double.MIN
+   Assert.assertEquals(6, 
diceDistribution.inverseCumulativeProbability((5d+precision)/6d));
+   Assert.assertEquals(6, 
diceDistribution.inverseCumulativeProbability((6d-precision)/6d));//Can't use 
Double.MIN
+   Assert.assertEquals(6, 
diceDistribution.inverseCumulativeProbability((6d)/6d));
+}
+
+@Test
 public void testCumulativeProbabilitiesSingleArguments() {
 for (int i = 1; i < 7; i++) {
 Assert.assertEquals(p * i,
@@ -90,7 +109,7 @@ public class AbstractIntegerDistributionTest {
 }
 
 public double getNumericalVariance() {
-return 12.5 - 3.5 * 3.5;  // E(X^2) - E(X)^2
+return 70/24;  // E(X^2) - E(X)^2
 }
 
 public int getSupportLowerBound() {

[1/5] git commit: Updated the class description

[luc]

Repository: commons-math
Updated Branches:
  refs/heads/master a3fdeb4da -> d26810c0d


Updated the class description


Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/4cb944ea
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/4cb944ea
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/4cb944ea

Branch: refs/heads/master
Commit: 4cb944ea687d84a54d679fc3f5362e2950551ff3
Parents: 69273dc
Author: Ole 
Authored: Thu Oct 9 10:13:31 2014 -0500
Committer: Ole 
Committed: Thu Oct 9 10:13:31 2014 -0500

--
 .../commons/math3/exception/MathIllegalStateException.java  | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)
--


http://git-wip-us.apache.org/repos/asf/commons-math/blob/4cb944ea/src/main/java/org/apache/commons/math3/exception/MathIllegalStateException.java
--
diff --git 
a/src/main/java/org/apache/commons/math3/exception/MathIllegalStateException.java
 
b/src/main/java/org/apache/commons/math3/exception/MathIllegalStateException.java
index 22f8812..f47359c 100644
--- 
a/src/main/java/org/apache/commons/math3/exception/MathIllegalStateException.java
+++ 
b/src/main/java/org/apache/commons/math3/exception/MathIllegalStateException.java
@@ -22,8 +22,9 @@ import 
org.apache.commons.math3.exception.util.ExceptionContext;
 import org.apache.commons.math3.exception.util.ExceptionContextProvider;
 
 /**
- * Base class for all exceptions that signal a mismatch between the
- * current state and the user's expectations.
+ * Base class for all exceptions that signal that the process 
+ * throwing the exception is in a state that does not comply with
+ * the set of states the it is designed to be in.
  *
  * @since 2.2
  */

[4/5] git commit: Whitespace.

[luc]

Whitespace.

Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/f5a8bf39
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/f5a8bf39
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/f5a8bf39

Branch: refs/heads/master
Commit: f5a8bf398c84bd4cdeea740c1a5b7b39cac4f777
Parents: fc7eeb4
Author: Luc Maisonobe 
Authored: Wed Oct 15 09:05:22 2014 +0200
Committer: Luc Maisonobe 
Committed: Wed Oct 15 09:05:22 2014 +0200

--
 .../apache/commons/math3/exception/MathIllegalStateException.java  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)
--


http://git-wip-us.apache.org/repos/asf/commons-math/blob/f5a8bf39/src/main/java/org/apache/commons/math3/exception/MathIllegalStateException.java
--
diff --git 
a/src/main/java/org/apache/commons/math3/exception/MathIllegalStateException.java
 
b/src/main/java/org/apache/commons/math3/exception/MathIllegalStateException.java
index f47359c..2bb4a71 100644
--- 
a/src/main/java/org/apache/commons/math3/exception/MathIllegalStateException.java
+++ 
b/src/main/java/org/apache/commons/math3/exception/MathIllegalStateException.java
@@ -22,7 +22,7 @@ import 
org.apache.commons.math3.exception.util.ExceptionContext;
 import org.apache.commons.math3.exception.util.ExceptionContextProvider;
 
 /**
- * Base class for all exceptions that signal that the process 
+ * Base class for all exceptions that signal that the process
  * throwing the exception is in a state that does not comply with
  * the set of states the it is designed to be in.
  *

[8/8] git commit: Merge branch 'master' of https://l...@git-wip-us.apache.org/repos/asf/commons-math.git

[luc]

Merge branch 'master' of 
https://l...@git-wip-us.apache.org/repos/asf/commons-math.git

Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/b5e155e7
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/b5e155e7
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/b5e155e7

Branch: refs/heads/master
Commit: b5e155e7d0448a100e9d4ff7d178a2fb9ea9f659
Parents: 4a339cd a51908a
Author: Luc Maisonobe 
Authored: Fri Oct 17 10:40:35 2014 +0200
Committer: Luc Maisonobe 
Committed: Fri Oct 17 10:40:35 2014 +0200

--
 .../apache/commons/math3/exception/MathIllegalStateException.java  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)
--

[5/8] git commit: Fixed end of line encoding problems.

[luc]

Fixed end of line encoding problems.

Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/f44d4852
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/f44d4852
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/f44d4852

Branch: refs/heads/master
Commit: f44d4852ab758cdf0011efa028c85c68b8b36bee
Parents: bf88cac
Author: Luc Maisonobe 
Authored: Fri Oct 17 10:23:23 2014 +0200
Committer: Luc Maisonobe 
Committed: Fri Oct 17 10:23:23 2014 +0200

--
 .../interpolation/AkimaSplineInterpolator.java  | 450 +-
 .../AkimaSplineInterpolatorTest.java| 454 +--
 2 files changed, 452 insertions(+), 452 deletions(-)
--


http://git-wip-us.apache.org/repos/asf/commons-math/blob/f44d4852/src/main/java/org/apache/commons/math3/analysis/interpolation/AkimaSplineInterpolator.java
--
diff --git 
a/src/main/java/org/apache/commons/math3/analysis/interpolation/AkimaSplineInterpolator.java
 
b/src/main/java/org/apache/commons/math3/analysis/interpolation/AkimaSplineInterpolator.java
index 8fb896c..260cbfb 100644
--- 
a/src/main/java/org/apache/commons/math3/analysis/interpolation/AkimaSplineInterpolator.java
+++ 
b/src/main/java/org/apache/commons/math3/analysis/interpolation/AkimaSplineInterpolator.java
@@ -1,225 +1,225 @@
-/*
- * Licensed to the Apache Software Foundation (ASF) under one or more
- * contributor license agreements.  See the NOTICE file distributed with
- * this work for additional information regarding copyright ownership.
- * The ASF licenses this file to You under the Apache License, Version 2.0
- * (the "License"); you may not use this file except in compliance with
- * the License.  You may obtain a copy of the License at
- *
- *  http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-package org.apache.commons.math3.analysis.interpolation;
-
-import org.apache.commons.math3.analysis.polynomials.PolynomialFunction;
-import org.apache.commons.math3.analysis.polynomials.PolynomialSplineFunction;
-import org.apache.commons.math3.exception.DimensionMismatchException;
-import org.apache.commons.math3.exception.NonMonotonicSequenceException;
-import org.apache.commons.math3.exception.NullArgumentException;
-import org.apache.commons.math3.exception.NumberIsTooSmallException;
-import org.apache.commons.math3.exception.util.LocalizedFormats;
-import org.apache.commons.math3.util.FastMath;
-import org.apache.commons.math3.util.MathArrays;
-import org.apache.commons.math3.util.Precision;
-
-/**
- * Computes a cubic spline interpolation for the data set using the Akima
- * algorithm, as originally formulated by Hiroshi Akima in his 1970 paper
- * "A New Method of Interpolation and Smooth Curve Fitting Based on Local 
Procedures."
- * J. ACM 17, 4 (October 1970), 589-602. DOI=10.1145/321607.321609
- * http://doi.acm.org/10.1145/321607.321609
- * 
- * This implementation is based on the Akima implementation in the CubicSpline
- * class in the Math.NET Numerics library. The method referenced is
- * CubicSpline.InterpolateAkimaSorted
- * 
- * The {@link #interpolate(double[], double[])} method returns a
- * {@link PolynomialSplineFunction} consisting of n cubic polynomials, defined
- * over the subintervals determined by the x values, x[0] < x[i] ... < x[n]. 
The
- * Akima algorithm requires that n >= 5.
- * 
- * 
- */
-
-public class AkimaSplineInterpolator
-implements UnivariateInterpolator {
-
-
-/**
- * The minimum number of points that are needed to compute the function
- */
-public static final int MINIMUM_NUMBER_POINTS = 5;
-
-/**
- * Default constructor. Builds an AkimaSplineInterpolator object
- */
-public AkimaSplineInterpolator() {
-
-}
-
-/**
- * Computes an interpolating function for the data set.
- *
- * @param xvals the arguments for the interpolation points
- * @param yvals the values for the interpolation points
- * @return a function which interpolates the data set
- * @throws DimensionMismatchException if {@code x} and {@code y} have
- * different sizes.
- * @throws NonMonotonicSequenceException if {@code x} is not sorted in
- * strict increasing order.
- * @throws NumberIsTooSmallException if the size of {@code x} is smaller
- * than 5.
- */
-public PolynomialSplineFunction int

[2/8] git commit: MATH-1138 #comment Implemented new BiCubicSplineInterpolator, supporting Akima Spline Interpolator and updated tests

[luc]

MATH-1138 #comment Implemented new BiCubicSplineInterpolator,  supporting Akima 
Spline Interpolator and updated tests


Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/d8bfc8c8
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/d8bfc8c8
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/d8bfc8c8

Branch: refs/heads/master
Commit: d8bfc8c8f8864f9c22e0409780d5dd3fb30497ff
Parents: a3fdeb4
Author: Hank Grabowski 
Authored: Wed Oct 15 10:15:14 2014 -0400
Committer: Hank Grabowski 
Committed: Wed Oct 15 10:15:14 2014 -0400

--
 .../interpolation/AkimaSplineInterpolator.java  | 225 ++
 .../BicubicSplineInterpolatingFunction.java | 620 +++
 .../BicubicSplineInterpolator.java  | 140 +---
 .../TricubicSplineInterpolator.java |  35 +-
 .../AkimaSplineInterpolatorTest.java| 227 ++
 .../BicubicSplineInterpolatingFunctionTest.java | 746 +--
 .../BicubicSplineInterpolatorTest.java  | 217 --
 ...PolynomialBicubicSplineInterpolatorTest.java |  10 +-
 .../interpolation/SplineInterpolatorTest.java   |  42 +-
 .../TricubicSplineInterpolatorTest.java |   2 +-
 10 files changed, 923 insertions(+), 1341 deletions(-)
--


http://git-wip-us.apache.org/repos/asf/commons-math/blob/d8bfc8c8/src/main/java/org/apache/commons/math3/analysis/interpolation/AkimaSplineInterpolator.java
--
diff --git 
a/src/main/java/org/apache/commons/math3/analysis/interpolation/AkimaSplineInterpolator.java
 
b/src/main/java/org/apache/commons/math3/analysis/interpolation/AkimaSplineInterpolator.java
new file mode 100644
index 000..8fb896c
--- /dev/null
+++ 
b/src/main/java/org/apache/commons/math3/analysis/interpolation/AkimaSplineInterpolator.java
@@ -0,0 +1,225 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ *  http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.commons.math3.analysis.interpolation;
+
+import org.apache.commons.math3.analysis.polynomials.PolynomialFunction;
+import org.apache.commons.math3.analysis.polynomials.PolynomialSplineFunction;
+import org.apache.commons.math3.exception.DimensionMismatchException;
+import org.apache.commons.math3.exception.NonMonotonicSequenceException;
+import org.apache.commons.math3.exception.NullArgumentException;
+import org.apache.commons.math3.exception.NumberIsTooSmallException;
+import org.apache.commons.math3.exception.util.LocalizedFormats;
+import org.apache.commons.math3.util.FastMath;
+import org.apache.commons.math3.util.MathArrays;
+import org.apache.commons.math3.util.Precision;
+
+/**
+ * Computes a cubic spline interpolation for the data set using the Akima
+ * algorithm, as originally formulated by Hiroshi Akima in his 1970 paper
+ * "A New Method of Interpolation and Smooth Curve Fitting Based on Local 
Procedures."
+ * J. ACM 17, 4 (October 1970), 589-602. DOI=10.1145/321607.321609
+ * http://doi.acm.org/10.1145/321607.321609
+ * 
+ * This implementation is based on the Akima implementation in the CubicSpline
+ * class in the Math.NET Numerics library. The method referenced is
+ * CubicSpline.InterpolateAkimaSorted
+ * 
+ * The {@link #interpolate(double[], double[])} method returns a
+ * {@link PolynomialSplineFunction} consisting of n cubic polynomials, defined
+ * over the subintervals determined by the x values, x[0] < x[i] ... < x[n]. 
The
+ * Akima algorithm requires that n >= 5.
+ * 
+ * 
+ */
+
+public class AkimaSplineInterpolator
+implements UnivariateInterpolator {
+
+
+/**
+ * The minimum number of points that are needed to compute the function
+ */
+public static final int MINIMUM_NUMBER_POINTS = 5;
+
+/**
+ * Default constructor. Builds an AkimaSplineInterpolator object
+ */
+public AkimaSplineInterpolator() {
+
+}
+
+/**
+ * Computes an interpolating function for the data set.
+ *
+ * @param xvals the arguments for the interpolation points
+ * @param yvals the values for the interpola

[3/8] git commit: Merge remote-tracking branch 'upstream/master'

[luc]

Merge remote-tracking branch 'upstream/master'


Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/bd3a6eca
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/bd3a6eca
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/bd3a6eca

Branch: refs/heads/master
Commit: bd3a6ecaa777247aaa6175e5c4721bfbd1645451
Parents: d8bfc8c d26810c
Author: Hank Grabowski 
Authored: Wed Oct 15 10:20:34 2014 -0400
Committer: Hank Grabowski 
Committed: Wed Oct 15 10:20:34 2014 -0400

--
 pom.xml |  3 +++
 .../exception/MathIllegalStateException.java|  5 +++--
 .../AbstractIntegerDistributionTest.java| 21 +++-
 3 files changed, 26 insertions(+), 3 deletions(-)
--

[1/8] MATH-1138 #comment Implemented new BiCubicSplineInterpolator, supporting Akima Spline Interpolator and updated tests

[luc]

Repository: commons-math
Updated Branches:
  refs/heads/master a51908af1 -> b5e155e7d


http://git-wip-us.apache.org/repos/asf/commons-math/blob/d8bfc8c8/src/test/java/org/apache/commons/math3/analysis/interpolation/BicubicSplineInterpolatingFunctionTest.java
--
diff --git 
a/src/test/java/org/apache/commons/math3/analysis/interpolation/BicubicSplineInterpolatingFunctionTest.java
 
b/src/test/java/org/apache/commons/math3/analysis/interpolation/BicubicSplineInterpolatingFunctionTest.java
index 8c78aed..773a948 100644
--- 
a/src/test/java/org/apache/commons/math3/analysis/interpolation/BicubicSplineInterpolatingFunctionTest.java
+++ 
b/src/test/java/org/apache/commons/math3/analysis/interpolation/BicubicSplineInterpolatingFunctionTest.java
@@ -16,435 +16,147 @@
  */
 package org.apache.commons.math3.analysis.interpolation;
 
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
 import org.apache.commons.math3.exception.DimensionMismatchException;
-import org.apache.commons.math3.exception.MathIllegalArgumentException;
-import org.apache.commons.math3.exception.OutOfRangeException;
+import org.apache.commons.math3.exception.InsufficientDataException;
+import org.apache.commons.math3.exception.NonMonotonicSequenceException;
+import org.apache.commons.math3.exception.NullArgumentException;
 import org.apache.commons.math3.analysis.BivariateFunction;
 import org.apache.commons.math3.distribution.UniformRealDistribution;
 import org.apache.commons.math3.random.RandomGenerator;
 import org.apache.commons.math3.random.Well19937c;
+import org.apache.commons.math3.util.FastMath;
+import org.apache.commons.math3.util.Precision;
 import org.junit.Assert;
 import org.junit.Test;
-import org.junit.Ignore;
 
 /**
  * Test case for the bicubic function.
- * 
  */
-public final class BicubicSplineInterpolatingFunctionTest {
+public final class BicubicSplineInterpolatingFunctionTest
+{
 /**
  * Test preconditions.
  */
 @Test
-public void testPreconditions() {
-double[] xval = new double[] {3, 4, 5, 6.5};
-double[] yval = new double[] {-4, -3, -1, 2.5};
+public void testPreconditions()
+{
+double[] xval = new double[] { 3, 4, 5, 6.5, 7.5 };
+double[] yval = new double[] { -4, -3, -1, 2.5, 3.5 };
 double[][] zval = new double[xval.length][yval.length];
 
 @SuppressWarnings("unused")
-BivariateFunction bcf = new BicubicSplineInterpolatingFunction(xval, 
yval, zval,
-   
zval, zval, zval);
+BicubicSplineInterpolatingFunction bcf = new 
BicubicSplineInterpolatingFunction( xval, yval, zval );
 
-double[] wxval = new double[] {3, 2, 5, 6.5};
-try {
-bcf = new BicubicSplineInterpolatingFunction(wxval, yval, zval, 
zval, zval, zval);
-Assert.fail("an exception should have been thrown");
-} catch (MathIllegalArgumentException e) {
-// Expected
-}
-double[] wyval = new double[] {-4, -1, -1, 2.5};
-try {
-bcf = new BicubicSplineInterpolatingFunction(xval, wyval, zval, 
zval, zval, zval);
-Assert.fail("an exception should have been thrown");
-} catch (MathIllegalArgumentException e) {
-// Expected
-}
-double[][] wzval = new double[xval.length][yval.length - 1];
-try {
-bcf = new BicubicSplineInterpolatingFunction(xval, yval, wzval, 
zval, zval, zval);
-Assert.fail("an exception should have been thrown");
-} catch (DimensionMismatchException e) {
-// Expected
-}
-try {
-bcf = new BicubicSplineInterpolatingFunction(xval, yval, zval, 
wzval, zval, zval);
-Assert.fail("an exception should have been thrown");
-} catch (DimensionMismatchException e) {
-// Expected
-}
-try {
-bcf = new BicubicSplineInterpolatingFunction(xval, yval, zval, 
zval, wzval, zval);
-Assert.fail("an exception should have been thrown");
-} catch (DimensionMismatchException e) {
-// Expected
-}
-try {
-bcf = new BicubicSplineInterpolatingFunction(xval, yval, zval, 
zval, zval, wzval);
-Assert.fail("an exception should have been thrown");
-} catch (DimensionMismatchException e) {
-// Expected
-}
-
-wzval = new double[xval.length - 1][yval.length];
-try {
-bcf = new BicubicSplineInterpolatingFunction(xval, yval, wzval, 
zval, zval, zval);
-Assert.fail("an exception should have been thrown");
-} catch (DimensionMismatchException e) {
-// Expected
-}
-try {
-bcf = new BicubicSplineInterpolatingFunction(xval, yval, zval, 
wzval, zval, zv

[7/8] git commit: Notified fix for bicubic splines.

[luc]

Notified fix for bicubic splines.

Thanks to Hank Grabowski for the patch.

JIRA: MATH-1138

Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/4a339cda
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/4a339cda
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/4a339cda

Branch: refs/heads/master
Commit: 4a339cda2c3933a2adcb23ea0ea8470d68d1b010
Parents: 7df36c3
Author: Luc Maisonobe 
Authored: Fri Oct 17 10:29:20 2014 +0200
Committer: Luc Maisonobe 
Committed: Fri Oct 17 10:29:20 2014 +0200

--
 src/changes/changes.xml | 3 +++
 1 file changed, 3 insertions(+)
--


http://git-wip-us.apache.org/repos/asf/commons-math/blob/4a339cda/src/changes/changes.xml
--
diff --git a/src/changes/changes.xml b/src/changes/changes.xml
index 7762b80..bb5c525 100644
--- a/src/changes/changes.xml
+++ b/src/changes/changes.xml
@@ -73,6 +73,9 @@ Users are encouraged to upgrade to this version as this 
release not
   2. A few methods in the FastMath class are in fact slower that their
   counterpart in either Math or StrictMath (cf. MATH-740 and MATH-901).
 ">
+  
+Fixed bicubic spline interpolator, using Akima splines.
+  
   
 Changed classes in the inference package that instantiate 
distributions to
 pass null RandomGenerators to avoid initialization overhead for the 
default

[4/8] git commit: Removed unused import.

[luc]

Removed unused import.

Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/bf88cac1
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/bf88cac1
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/bf88cac1

Branch: refs/heads/master
Commit: bf88cac1ac03ce9378970e5a3d66ba77b1fe0dca
Parents: bd3a6ec
Author: Luc Maisonobe 
Authored: Fri Oct 17 10:22:52 2014 +0200
Committer: Luc Maisonobe 
Committed: Fri Oct 17 10:22:52 2014 +0200

--
 .../math3/analysis/interpolation/BicubicSplineInterpolator.java | 1 -
 1 file changed, 1 deletion(-)
--


http://git-wip-us.apache.org/repos/asf/commons-math/blob/bf88cac1/src/main/java/org/apache/commons/math3/analysis/interpolation/BicubicSplineInterpolator.java
--
diff --git 
a/src/main/java/org/apache/commons/math3/analysis/interpolation/BicubicSplineInterpolator.java
 
b/src/main/java/org/apache/commons/math3/analysis/interpolation/BicubicSplineInterpolator.java
index 36a9da2..a973f81 100644
--- 
a/src/main/java/org/apache/commons/math3/analysis/interpolation/BicubicSplineInterpolator.java
+++ 
b/src/main/java/org/apache/commons/math3/analysis/interpolation/BicubicSplineInterpolator.java
@@ -20,7 +20,6 @@ import 
org.apache.commons.math3.exception.DimensionMismatchException;
 import org.apache.commons.math3.exception.NoDataException;
 import org.apache.commons.math3.exception.NonMonotonicSequenceException;
 import org.apache.commons.math3.exception.NullArgumentException;
-import org.apache.commons.math3.exception.NumberIsTooSmallException;
 import org.apache.commons.math3.util.MathArrays;
 
 /**

[6/8] git commit: Added Hank Grabowski as contributor.

[luc]

Added Hank Grabowski as contributor.

Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/7df36c32
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/7df36c32
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/7df36c32

Branch: refs/heads/master
Commit: 7df36c32a50fe400afcbf2c258c6c15fdda500a4
Parents: f44d485
Author: Luc Maisonobe 
Authored: Fri Oct 17 10:25:46 2014 +0200
Committer: Luc Maisonobe 
Committed: Fri Oct 17 10:25:46 2014 +0200

--
 pom.xml | 3 +++
 1 file changed, 3 insertions(+)
--


http://git-wip-us.apache.org/repos/asf/commons-math/blob/7df36c32/pom.xml
--
diff --git a/pom.xml b/pom.xml
index 8430131..628ec6a 100644
--- a/pom.xml
+++ b/pom.xml
@@ -216,6 +216,9 @@
   Ken Geis
 
 
+  Hank Grabowski
+
+
   Bernhard Grünewaldt
 
 

git commit: Fixed link to source repository.

[luc]

Repository: commons-math
Updated Branches:
  refs/heads/master b5e155e7d -> 39387e75f


Fixed link to source repository.

Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/39387e75
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/39387e75
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/39387e75

Branch: refs/heads/master
Commit: 39387e75ff19d9ccfe59e1c6250e858382440b66
Parents: b5e155e
Author: Luc Maisonobe 
Authored: Sat Oct 18 17:09:06 2014 +0200
Committer: Luc Maisonobe 
Committed: Sat Oct 18 17:09:06 2014 +0200

--
 src/site/site.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)
--


http://git-wip-us.apache.org/repos/asf/commons-math/blob/39387e75/src/site/site.xml
--
diff --git a/src/site/site.xml b/src/site/site.xml
index 091f5d9..e8b78e0 100644
--- a/src/site/site.xml
+++ b/src/site/site.xml
@@ -41,7 +41,7 @@
  href="http://commons.apache.org/math/javadocs/api-2.2/index.html"/>
   
   http://svn.apache.org/viewvc/commons/proper/math/trunk"/>
+ href="http://git-wip-us.apache.org/repos/asf/commons-math.git"/>
   http://wiki.apache.org/commons/Math"/>
   

git commit: Fixed a forgotten reference to subversion.

[luc]

Repository: commons-math
Updated Branches:
  refs/heads/master 39387e75f -> 54e179b82


Fixed a forgotten reference to subversion.

Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/54e179b8
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/54e179b8
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/54e179b8

Branch: refs/heads/master
Commit: 54e179b82a8b0652bcb05f3fcb92d39133a1d7ff
Parents: 39387e7
Author: Luc Maisonobe 
Authored: Sat Oct 18 17:14:35 2014 +0200
Committer: Luc Maisonobe 
Committed: Sat Oct 18 17:14:35 2014 +0200

--
 src/site/xdoc/developers.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)
--


http://git-wip-us.apache.org/repos/asf/commons-math/blob/54e179b8/src/site/xdoc/developers.xml
--
diff --git a/src/site/xdoc/developers.xml b/src/site/xdoc/developers.xml
index c65340c..f280a6c 100644
--- a/src/site/xdoc/developers.xml
+++ b/src/site/xdoc/developers.xml
@@ -132,7 +132,7 @@

Submit code as attachments to the JIRA ticket.  Please use one
ticket for each feature, adding multiple patches to the ticket
-   as necessary.  Use the svn diff command to generate your patches as
+   as necessary.  Use the git diff command to generate your patches as
diffs.  Please do not submit modified copies of existing java files. Be
patient (but not too patient) with  committers 
reviewing
patches. Post a *nudge* message to commons-dev with a reference to the

git commit: There are no nightly builds anymore from subversion head.

[luc]

Repository: commons-math
Updated Branches:
  refs/heads/master 54e179b82 -> e89a80dd5


There are no nightly builds anymore from subversion head.

Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/e89a80dd
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/e89a80dd
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/e89a80dd

Branch: refs/heads/master
Commit: e89a80dd53ee51cad6597e9637ded1d55cd60f6d
Parents: 54e179b
Author: Luc Maisonobe 
Authored: Sat Oct 18 17:17:16 2014 +0200
Committer: Luc Maisonobe 
Committed: Sat Oct 18 17:17:16 2014 +0200

--
 src/site/xdoc/index.xml | 7 ++-
 1 file changed, 2 insertions(+), 5 deletions(-)
--


http://git-wip-us.apache.org/repos/asf/commons-math/blob/e89a80dd/src/site/xdoc/index.xml
--
diff --git a/src/site/xdoc/index.xml b/src/site/xdoc/index.xml
index dfd8304..11c1a2b 100644
--- a/src/site/xdoc/index.xml
+++ b/src/site/xdoc/index.xml
@@ -71,12 +71,9 @@
 

svn commit: r926165 [4/4] - in /websites/production/commons/content/proper/commons-math: ./ css/ js/ style/

[luc]

Modified: websites/production/commons/content/proper/commons-math/team-list.html
==
--- websites/production/commons/content/proper/commons-math/team-list.html 
(original)
+++ websites/production/commons/content/proper/commons-math/team-list.html Sat 
Oct 18 15:47:15 2014
@@ -1,13 +1,13 @@
 
 
 http://www.w3.org/1999/xhtml"; xml:lang="en" lang="en">
   
 
 
-
+
 
 Math - Team list
 
@@ -40,7 +40,7 @@
http://commons.apache.org/proper/commons-math/";>Apache Commons Math 
™
  
 
-Last Published: 07 October 2014
+Last Published: 18 October 2014
   | Version: 
3.4-SNAPSHOT
   

@@ -110,7 +110,7 @@
 Issue Tracking



- http://svn.apache.org/viewvc/commons/proper/math/trunk"; 
class="externalLink" title="Source Repository (current)">
+ http://git-wip-us.apache.org/repos/asf/commons-math.git"; 
class="externalLink" title="Source Repository (current)">
 Source Repository (current)



@@ -480,11 +480,15 @@
 
 Ted Dunning
 
-Ajo Fod
+Ole Ersoy
 
-John Gant
+Ajo Fod
 
+John Gant
+
 Ken Geis
+
+Hank Grabowski
 
 Bernhard Grünewaldt
 

svn commit: r926165 [1/4] - in /websites/production/commons/content/proper/commons-math: ./ css/ js/ style/

[luc]

Author: luc
Date: Sat Oct 18 15:47:15 2014
New Revision: 926165

Log:
updated site to current status (first files only)

Modified:
websites/production/commons/content/proper/commons-math/changes-report.html
websites/production/commons/content/proper/commons-math/checkstyle.html
websites/production/commons/content/proper/commons-math/checkstyle.rss
websites/production/commons/content/proper/commons-math/clirr-report.html

websites/production/commons/content/proper/commons-math/css/bootstrap-1.3.0.min.css

websites/production/commons/content/proper/commons-math/css/bootstrap.min.css

websites/production/commons/content/proper/commons-math/css/commons-maven.css

websites/production/commons/content/proper/commons-math/css/commons-trade.css
websites/production/commons/content/proper/commons-math/css/maven-base.css
websites/production/commons/content/proper/commons-math/css/maven-theme.css
websites/production/commons/content/proper/commons-math/css/print.css
websites/production/commons/content/proper/commons-math/css/site.css
websites/production/commons/content/proper/commons-math/dependencies.html
websites/production/commons/content/proper/commons-math/developers.html

websites/production/commons/content/proper/commons-math/distribution-management.html
websites/production/commons/content/proper/commons-math/download_math.html
websites/production/commons/content/proper/commons-math/findbugs.html
websites/production/commons/content/proper/commons-math/index.html
websites/production/commons/content/proper/commons-math/integration.html
websites/production/commons/content/proper/commons-math/issue-tracking.html
websites/production/commons/content/proper/commons-math/jdepend-report.html
websites/production/commons/content/proper/commons-math/jira-report.html
websites/production/commons/content/proper/commons-math/js/prettify.js
websites/production/commons/content/proper/commons-math/js/prettify.min.js
websites/production/commons/content/proper/commons-math/js/site.js
websites/production/commons/content/proper/commons-math/mail-lists.html
websites/production/commons/content/proper/commons-math/pmd.html
websites/production/commons/content/proper/commons-math/pmd.xml
websites/production/commons/content/proper/commons-math/project-info.html
websites/production/commons/content/proper/commons-math/project-reports.html
websites/production/commons/content/proper/commons-math/project-summary.html
websites/production/commons/content/proper/commons-math/proposal.html
websites/production/commons/content/proper/commons-math/rat-report.html

websites/production/commons/content/proper/commons-math/source-repository.html
websites/production/commons/content/proper/commons-math/style/project.css
websites/production/commons/content/proper/commons-math/surefire-report.html
websites/production/commons/content/proper/commons-math/team-list.html

Modified: 
websites/production/commons/content/proper/commons-math/changes-report.html
==
--- websites/production/commons/content/proper/commons-math/changes-report.html 
(original)
+++ websites/production/commons/content/proper/commons-math/changes-report.html 
Sat Oct 18 15:47:15 2014
@@ -1,13 +1,13 @@
 
 
 http://www.w3.org/1999/xhtml"; xml:lang="en" lang="en">
   
 
 
-
+
 
 Math - Commons Math Release Notes
 
@@ -40,7 +40,7 @@
http://commons.apache.org/proper/commons-math/";>Apache Commons Math 
™
  
 
-Last Published: 07 October 2014
+Last Published: 18 October 2014
   | Version: 
3.4-SNAPSHOT
   

@@ -110,7 +110,7 @@
 Issue Tracking



- http://svn.apache.org/viewvc/commons/proper/math/trunk"; 
class="externalLink" title="Source Repository (current)">
+ http://git-wip-us.apache.org/repos/asf/commons-math.git"; 
class="externalLink" title="Source Repository (current)">
 Source Repository (current)



@@ -419,6 +419,16 @@
 Changes
 By
 
+
+Fixed bicubic spline interpolator, using Akima splines. Fixes http://issues.apache.org/jira/browse/MATH-1138";>MATH-1138. Thanks to 
Hank Grabowski.
+luc
+
+
+Changed classes in the inference package that instantiate distributions to
+pass null RandomGenerators to avoid initialization overhead for the 
de

svn commit: r926165 [3/4] - in /websites/production/commons/content/proper/commons-math: ./ css/ js/ style/

[luc]

Modified: 
websites/production/commons/content/proper/commons-math/surefire-report.html
==
--- 
websites/production/commons/content/proper/commons-math/surefire-report.html 
(original)
+++ 
websites/production/commons/content/proper/commons-math/surefire-report.html 
Sat Oct 18 15:47:15 2014
@@ -1,13 +1,13 @@
 
 
 http://www.w3.org/1999/xhtml"; xml:lang="en" lang="en">
   
 
 
-
+
 
 Math - Surefire Report
 
@@ -40,7 +40,7 @@
http://commons.apache.org/proper/commons-math/";>Apache Commons Math 
™
  
 
-Last Published: 07 October 2014
+Last Published: 18 October 2014
   | Version: 
3.4-SNAPSHOT
   

@@ -110,7 +110,7 @@
 Issue Tracking



- http://svn.apache.org/viewvc/commons/proper/math/trunk"; 
class="externalLink" title="Source Repository (current)">
+ http://git-wip-us.apache.org/repos/asf/commons-math.git"; 
class="externalLink" title="Source Repository (current)">
 Source Repository (current)



@@ -385,12 +385,12 @@ function toggleDisplay(elementId) {
 Success Rate
 Time
 
-6164
+6165
 0
 0
-37
-99.4%
-298.72
+34
+99.449%
+285.134
 Note: failures are anticipated and checked for with assertions while errors 
are unanticipated.
 
 Package List
@@ -411,7 +411,7 @@ function toggleDisplay(elementId) {
 0
 0
 100%
-0
+0.008
 
 org.apache.commons.math3.transform
 54
@@ -419,7 +419,7 @@ function toggleDisplay(elementId) {
 0
 0
 100%
-0.492
+0.228
 
 org.apache.commons.math3.ml.neuralnet.twod
 14
@@ -427,7 +427,7 @@ function toggleDisplay(elementId) {
 0
 0
 100%
-0.017
+0.022
 
 org.apache.commons.math3.exception
 9
@@ -435,7 +435,7 @@ function toggleDisplay(elementId) {
 0
 0
 100%
-0.003
+0
 
 org.apache.commons.math3.analysis.polynomials
 41
@@ -443,7 +443,7 @@ function toggleDisplay(elementId) {
 0
 0
 100%
-1.345
+1.332
 
 org.apache.commons.math3.ml.clustering.evaluation
 2
@@ -459,7 +459,7 @@ function toggleDisplay(elementId) {
 0
 0
 100%
-0.209
+0.269
 
 org.apache.commons.math3.distribution.fitting
 9
@@ -475,7 +475,7 @@ function toggleDisplay(elementId) {
 0
 0
 100%
-0.372
+0.386
 
 org.apache.commons.math3.filter
 5
@@ -483,7 +483,7 @@ function toggleDisplay(elementId) {
 0
 0
 100%
-0.055
+0.047
 
 org.apache.commons.math3.optimization
 15
@@ -491,7 +491,7 @@ function toggleDisplay(elementId) {
 0
 0
 100%
-0.091
+0.092
 
 org.apache.commons.math3.optimization.direct
 73
@@ -499,7 +499,7 @@ function toggleDisplay(elementId) {
 0
 1
 98.63%
-25.338
+20.343
 
 org.apache.commons.math3.ml.neuralnet.oned
 4
@@ -507,7 +507,7 @@ function toggleDisplay(elementId) {
 0
 0
 100%
-0.004
+0.005
 
 org.apache.commons.math3.geometry.euclidean.twod.hull
 33
@@ -515,7 +515,7 @@ function toggleDisplay(elementId) {
 0
 0
 100%
-0.346
+0.341
 
 org.apache.commons.math3.geometry.spherical.oned
 40
@@ -523,7 +523,7 @@ function toggleDisplay(elementId) {
 0
 0
 100%
-0.08
+0.092
 
 org.apache.commons.math3.stat.inference
 65
@@ -531,7 +531,7 @@ function toggleDisplay(elementId) {
 0
 0
 100%
-1.107
+1.16
 
 org.apache.commons.math3.exception.util
 12
@@ -539,7 +539,7 @@ function toggleDisplay(elementId) {
 0
 0
 100%
-0.15
+0.161
 
 org.apache.commons.math3.random
 804
@@ -547,7 +547,7 @@ function toggleDisplay(elementId) {
 0
 0
 100%
-121.702
+114.428
 
 org.apache.commons.math3.primes
 3
@@ -555,7 +555,7 @@ function toggleDisplay(elementId) {
 0
 0
 100%
-0.085
+0.092
 
 org.apache.commons.math3.optim.nonlinear.vector.jacobian
 65
@@ -563,7 +563,7 @@ function toggleDisplay(elementId) {
 0
 0
 100%
-0.384
+0.543
 
 org.apache.commons.math3.analysis.solvers
 99
@@ -571,7 +571,7 @@ function toggleDisplay(elementId) {
 0
 0
 100%
-0.06
+0.072
 
 org.apache.commons.math3.optim
 11
@@ -579,15 +579,15 @@ function toggleDisplay(elementId) {
 0
 0
 100%
-0.003
+0.01
 
 org.apache.commons.math3.ode.nonstiff
-124
+125
 0
 0
 0
 100%
-2.689
+2.645
 
 org.apache.commons.math3.stat.clustering
 20
@@ -595,7 +595,7 @@ function toggleDisplay(elementId) {
 0
 0
 100%
-0.278
+0.282
 
 org.apache.commons.math3.genetics
 63
@@ -603,7 +603,7 @@ function toggleDisplay(elementId) {
 0
 0
 100%
-3.779
+3.819
 
 org.apache.commons.math3.optimization.linear
 30
@@ -611,7 +611,7 @@ function toggleDisplay(elementId) {
 0
 0
 100%
-0.219
+0.212
 
 org.apache.commons.math3.optim.nonlinear.scalar.gradient
 13
@@ -619,7 +619,7 @@ function toggleDisplay(elementId) {
 0
 0
 100%
-0.012
+0.019
 
 org.apache.commons.math3.complex
 227
@@ -627,7 +627,7

svn commit: r926165 [2/4] - in /websites/production/commons/content/proper/commons-math: ./ css/ js/ style/

[luc]

Modified: 
websites/production/commons/content/proper/commons-math/rat-report.html
==
--- websites/production/commons/content/proper/commons-math/rat-report.html 
(original)
+++ websites/production/commons/content/proper/commons-math/rat-report.html Sat 
Oct 18 15:47:15 2014
@@ -1,13 +1,13 @@
 
 
 http://www.w3.org/1999/xhtml"; xml:lang="en" lang="en">
   
 
 
-
+
 
 Math - Rat (Release Audit Tool) results
 
@@ -40,7 +40,7 @@
http://commons.apache.org/proper/commons-math/";>Apache Commons Math 
™
  
 
-Last Published: 07 October 2014
+Last Published: 18 October 2014
   | Version: 
3.4-SNAPSHOT
   

@@ -110,7 +110,7 @@
 Issue Tracking



- http://svn.apache.org/viewvc/commons/proper/math/trunk"; 
class="externalLink" title="Source Repository (current)">
+ http://git-wip-us.apache.org/repos/asf/commons-math.git"; 
class="externalLink" title="Source Repository (current)">
 Source Repository (current)



@@ -363,13 +363,13 @@
 *
 Summary
 ---
-Generated at: 2014-10-07T21:16:06+02:00
+Generated at: 2014-10-18T17:25:08+02:00
 Notes: 5
 Binaries: 22
 Archives: 0
-Standards: 1594
+Standards: 1596
 
-Apache Licensed: 1594
+Apache Licensed: 1596
 Generated Documents: 0
 
 JavaDocs are generated and so license header is optional
@@ -512,6 +512,7 @@ Archives:
   AL
src/test/java/org/apache/commons/math3/analysis/interpolation/LoessInterpolatorTest.java
   AL
src/test/java/org/apache/commons/math3/analysis/interpolation/BicubicSplineInterpolatingFunctionTest.java
   AL
src/test/java/org/apache/commons/math3/analysis/interpolation/SmoothingPolynomialBicubicSplineInterpolatorTest.java
+  AL
src/test/java/org/apache/commons/math3/analysis/interpolation/AkimaSplineInterpolatorTest.java
   AL
src/test/java/org/apache/commons/math3/analysis/interpolation/MicrosphereInterpolatorTest.java
   AL
src/test/java/org/apache/commons/math3/analysis/interpolation/UnivariatePeriodicInterpolatorTest.java
   AL
src/test/java/org/apache/commons/math3/analysis/interpolation/HermiteInterpolatorTest.java
@@ -1189,6 +1190,7 @@ Archives:
   AL
src/main/java/org/apache/commons/math3/analysis/interpolation/SplineInterpolator.java
   AL
src/main/java/org/apache/commons/math3/analysis/interpolation/TricubicSplineInterpolator.java
   AL
src/main/java/org/apache/commons/math3/analysis/interpolation/BicubicSplineInterpolatingFunction.java
+  AL
src/main/java/org/apache/commons/math3/analysis/interpolation/AkimaSplineInterpolator.java
   AL
src/main/java/org/apache/commons/math3/analysis/interpolation/FieldHermiteInterpolator.java
   AL
src/main/java/org/apache/commons/math3/analysis/interpolation/BivariateGridInterpolator.java
   AL
src/main/java/org/apache/commons/math3/analysis/interpolation/UnivariateInterpolator.java

Modified: 
websites/production/commons/content/proper/commons-math/source-repository.html
==
--- 
websites/production/commons/content/proper/commons-math/source-repository.html 
(original)
+++ 
websites/production/commons/content/proper/commons-math/source-repository.html 
Sat Oct 18 15:47:15 2014
@@ -1,13 +1,13 @@
 
 
 http://www.w3.org/1999/xhtml"; xml:lang="en" lang="en">
   
 
 
-
+
 
 Math - Source Repository
 
@@ -40,7 +40,7 @@
http://commons.apache.org/proper/commons-math/";>Apache Commons Math 
™
  
 
-Last Published: 07 October 2014
+Last Published: 18 October 2014
   | Version: 
3.4-SNAPSHOT
   

@@ -110,7 +110,7 @@
 Issue Tracking



- http://svn.apache.org/viewvc/commons/proper/math/trunk"; 
class="externalLink" title="Source Repository (current)">
+ http://git-wip-us.apache.org/repos/asf/commons-math.git"; 
class="externalLink" title="Source Repository (current)">
 Source Repository (current)




Modified: 
websites/p

svn commit: r926166 - /websites/production/commons/content/proper/commons-math/userguide/

[luc]

Author: luc
Date: Sat Oct 18 15:48:41 2014
New Revision: 926166

Log:
updated site to current status (userguide part)

Modified:

websites/production/commons/content/proper/commons-math/userguide/analysis.html

websites/production/commons/content/proper/commons-math/userguide/complex.html

websites/production/commons/content/proper/commons-math/userguide/distribution.html

websites/production/commons/content/proper/commons-math/userguide/exceptions.html

websites/production/commons/content/proper/commons-math/userguide/filter.html

websites/production/commons/content/proper/commons-math/userguide/fitting.html

websites/production/commons/content/proper/commons-math/userguide/fraction.html

websites/production/commons/content/proper/commons-math/userguide/genetics.html

websites/production/commons/content/proper/commons-math/userguide/geometry.html
websites/production/commons/content/proper/commons-math/userguide/index.html

websites/production/commons/content/proper/commons-math/userguide/linear.html
websites/production/commons/content/proper/commons-math/userguide/ml.html
websites/production/commons/content/proper/commons-math/userguide/ode.html

websites/production/commons/content/proper/commons-math/userguide/optimization.html

websites/production/commons/content/proper/commons-math/userguide/overview.html

websites/production/commons/content/proper/commons-math/userguide/random.html

websites/production/commons/content/proper/commons-math/userguide/special.html
websites/production/commons/content/proper/commons-math/userguide/stat.html

websites/production/commons/content/proper/commons-math/userguide/transform.html

websites/production/commons/content/proper/commons-math/userguide/utilities.html

Modified: 
websites/production/commons/content/proper/commons-math/userguide/analysis.html
==
--- 
websites/production/commons/content/proper/commons-math/userguide/analysis.html 
(original)
+++ 
websites/production/commons/content/proper/commons-math/userguide/analysis.html 
Sat Oct 18 15:48:41 2014
@@ -1,13 +1,13 @@
 
 
 http://www.w3.org/1999/xhtml"; xml:lang="en" lang="en">
   
 
 
-
+
 
 Math - 
 The Commons Math User Guide - Numerical Analysis
@@ -41,7 +41,7 @@
http://commons.apache.org/proper/commons-math/";>Apache Commons Math 
™
  
 
-Last Published: 07 October 2014
+Last Published: 18 October 2014
   | Version: 
3.4-SNAPSHOT
   

@@ -111,7 +111,7 @@
 Issue Tracking



- http://svn.apache.org/viewvc/commons/proper/math/trunk"; 
class="externalLink" title="Source Repository (current)">
+ http://git-wip-us.apache.org/repos/asf/commons-math.git"; 
class="externalLink" title="Source Repository (current)">
 Source Repository (current)




Modified: 
websites/production/commons/content/proper/commons-math/userguide/complex.html
==
--- 
websites/production/commons/content/proper/commons-math/userguide/complex.html 
(original)
+++ 
websites/production/commons/content/proper/commons-math/userguide/complex.html 
Sat Oct 18 15:48:41 2014
@@ -1,13 +1,13 @@
 
 
 http://www.w3.org/1999/xhtml"; xml:lang="en" lang="en">
   
 
 
-
+
 
 Math - 
 The Commons Math User Guide - Complex Numbers
@@ -41,7 +41,7 @@
http://commons.apache.org/proper/commons-math/";>Apache Commons Math 
™
  
 
-Last Published: 07 October 2014
+Last Published: 18 October 2014
   | Version: 
3.4-SNAPSHOT
   

@@ -111,7 +111,7 @@
 Issue Tracking



- http://svn.apache.org/viewvc/commons/proper/math/trunk"; 
class="externalLink" title="Source Repository (current)">
+ http://git-wip-us.apache.org/repos/asf/commons-math.git"; 
class="externalLink" title="Source Repository (current)">
 Source Repository (current)
 

svn commit: r926168 - in /websites/production/commons/content/proper/commons-math/apidocs: ./ org/apache/commons/math3/ org/apache/commons/math3/analysis/ org/apache/commons/math3/analysis/class-use/

[luc]

Author: luc
Date: Sat Oct 18 16:41:28 2014
New Revision: 926168

Log:
updated site to current status (apidocs part)


[This commit notification would consist of 659 parts, 
which exceeds the limit of 50 ones, so it was shortened to the summary.]

svn commit: r926171 - in /websites/production/commons/content/proper/commons-math/jacoco: ./ .resources/ org.apache.commons.math3.analysis.differentiation/ org.apache.commons.math3.analysis.function/

[luc]

Author: luc
Date: Sat Oct 18 17:20:09 2014
New Revision: 926171

Log:
updated site to current status (jacoco part)


[This commit notification would consist of 318 parts, 
which exceeds the limit of 50 ones, so it was shortened to the summary.]

svn commit: r926172 - in /websites/production/commons/content/proper/commons-math/testapidocs: ./ org/apache/commons/math3/ org/apache/commons/math3/analysis/ org/apache/commons/math3/analysis/class-u

[luc]

Author: luc
Date: Sat Oct 18 17:56:38 2014
New Revision: 926172

Log:
updated site to current status (testapidocs part)


[This commit notification would consist of 248 parts, 
which exceeds the limit of 50 ones, so it was shortened to the summary.]

svn commit: r926174 - in /websites/production/commons/content/proper/commons-math/xref: ./ org/apache/commons/math3/ org/apache/commons/math3/analysis/ org/apache/commons/math3/analysis/differentiatio

[luc]

Author: luc
Date: Sat Oct 18 18:50:33 2014
New Revision: 926174

Log:
updated site to current status (xref part)


[This commit notification would consist of 462 parts, 
which exceeds the limit of 50 ones, so it was shortened to the summary.]

svn commit: r926175 - in /websites/production/commons/content/proper/commons-math/xref-test: ./ org/apache/commons/math3/ org/apache/commons/math3/analysis/ org/apache/commons/math3/analysis/different

[luc]

Author: luc
Date: Sat Oct 18 19:47:07 2014
New Revision: 926175

Log:
updated site to current status (xref-test part)


[This commit notification would consist of 180 parts, 
which exceeds the limit of 50 ones, so it was shortened to the summary.]

svn commit: r926176 [3/31] - in /websites/production/commons/content/proper/commons-math: apidocs/org/apache/commons/math3/analysis/interpolation/ apidocs/org/apache/commons/math3/analysis/interpolati

[luc]

Added: 
websites/production/commons/content/proper/commons-math/apidocs/org/apache/commons/math3/distribution/LogisticDistribution.html
==
--- 
websites/production/commons/content/proper/commons-math/apidocs/org/apache/commons/math3/distribution/LogisticDistribution.html
 (added)
+++ 
websites/production/commons/content/proper/commons-math/apidocs/org/apache/commons/math3/distribution/LogisticDistribution.html
 Sat Oct 18 20:10:38 2014
@@ -0,0 +1,581 @@
+http://www.w3.org/TR/html4/loose.dtd";>
+
+
+
+
+LogisticDistribution (Apache Commons Math 3.4-SNAPSHOT API)
+
+
+
+
+
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+Overview
+Package
+Class
+Use
+Tree
+Deprecated
+Index
+Help
+
+http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";>
+
+
+
+Prev Class
+Next Class
+
+
+Frames
+No Frames
+
+
+All Classes
+
+
+
+
+
+
+
+Summary: 
+Nested | 
+Field | 
+Constr | 
+Method
+
+
+Detail: 
+Field | 
+Constr | 
+Method
+
+
+
+
+
+
+
+
+org.apache.commons.math3.distribution
+Class 
LogisticDistribution
+
+
+
+http://docs.oracle.com/javase/6/docs/api/java/lang/Object.html?is-external=true";
 title="class or interface in java.lang">java.lang.Object
+
+
+org.apache.commons.math3.distribution.AbstractRealDistribution
+
+
+org.apache.commons.math3.distribution.LogisticDistribution
+
+
+
+
+
+
+
+
+
+All Implemented Interfaces:
+http://docs.oracle.com/javase/6/docs/api/java/io/Serializable.html?is-external=true";
 title="class or interface in java.io">Serializable, RealDistribution
+
+
+
+public class LogisticDistribution
+extends AbstractRealDistribution
+This class implements the Logistic distribution.
+Since:
+  3.4
+See Also:http://en.wikipedia.org/wiki/Logistic_distribution";>Logistic Distribution 
(Wikipedia), 
+http://mathworld.wolfram.com/LogisticDistribution.html";>Logistic 
Distribution (Mathworld), 
+Serialized
 Form
+
+
+
+
+
+
+
+
+
+
+
+Field Summary
+
+
+
+
+Fields inherited from class org.apache.commons.math3.distribution.AbstractRealDistribution
+random,
 randomData,
 SOLVER_DEFAULT_ABSOLUTE_ACCURACY
+
+
+
+
+
+
+
+
+Constructor Summary
+
+Constructors 
+
+Constructor and Description
+
+
+LogisticDistribution(double mu,
+double s)
+Build a new instance.
+
+
+
+LogisticDistribution(RandomGenerator rng,
+double mu,
+double s)
+Build a new instance.
+
+
+
+
+
+
+
+
+
+
+Method Summary
+
+Methods 
+
+Modifier and Type
+Method and Description
+
+
+double
+cumulativeProbability(double x)
+For a random variable X whose values are 
distributed according
+ to this distribution, this method returns P(X <= x).
+
+
+
+double
+density(double x)
+Returns the probability density function (PDF) of this 
distribution
+ evaluated at the specified point x.
+
+
+
+double
+getLocation()
+Access the location parameter, mu.
+
+
+
+double
+getNumericalMean()
+Use this method to get the numerical value of the mean of 
this
+ distribution.
+
+
+
+double
+getNumericalVariance()
+Use this method to get the numerical value of the variance 
of this
+ distribution.
+
+
+
+double
+getScale()
+Access the scale parameter, s.
+
+
+
+double
+getSupportLowerBound()
+Access the lower bound of the support.
+
+
+
+double
+getSupportUpperBound()
+Access the upper bound of the support.
+
+
+
+double
+inverseCumulativeProbability(double p)
+Computes the quantile function of this distribution.
+
+
+
+boolean
+isSupportConnected()
+Use this method to get information about whether the 
support is connected,
+ i.e. whether all values between the lower and upper bound of the support
+ are included in the support.
+
+
+
+boolean
+isSupportLowerBoundInclusive()
+Whether or not the lower bound of support is in the domain 
of the density
+ function.
+
+
+
+boolean
+isSupportUpperBoundInclusive()
+Whether or not the upper bound of support is in the domain 
of the density
+ function.
+
+
+
+
+
+
+
+Methods inherited from class org.apache.commons.math3.distribution.AbstractRealDistribution
+cumulativeProbability,
 getSolverAbsoluteAccuracy,
 logDensity,
 probability,
 probability,
 reseedRandomGenerator,
 sample,
 sample
+
+
+
+
+
+Methods inherited from class java.lang.http://docs.oracle.com/javase/6/docs/api/java/lang/Object.html?is-external=true";
 title="class or interface in java.lang">Object
+http://docs.oracle.com/javase/6/docs/api/java/lang/Object.html?is-external=true#clone()"
 title="class or interface in java.lang">clone, http://docs.ora

svn commit: r926176 [2/31] - in /websites/production/commons/content/proper/commons-math: apidocs/org/apache/commons/math3/analysis/interpolation/ apidocs/org/apache/commons/math3/analysis/interpolati

[luc]

Added: 
websites/production/commons/content/proper/commons-math/apidocs/org/apache/commons/math3/distribution/GumbelDistribution.html
==
--- 
websites/production/commons/content/proper/commons-math/apidocs/org/apache/commons/math3/distribution/GumbelDistribution.html
 (added)
+++ 
websites/production/commons/content/proper/commons-math/apidocs/org/apache/commons/math3/distribution/GumbelDistribution.html
 Sat Oct 18 20:10:38 2014
@@ -0,0 +1,581 @@
+http://www.w3.org/TR/html4/loose.dtd";>
+
+
+
+
+GumbelDistribution (Apache Commons Math 3.4-SNAPSHOT API)
+
+
+
+
+
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+Overview
+Package
+Class
+Use
+Tree
+Deprecated
+Index
+Help
+
+http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";>
+
+
+
+Prev Class
+Next Class
+
+
+Frames
+No Frames
+
+
+All Classes
+
+
+
+
+
+
+
+Summary: 
+Nested | 
+Field | 
+Constr | 
+Method
+
+
+Detail: 
+Field | 
+Constr | 
+Method
+
+
+
+
+
+
+
+
+org.apache.commons.math3.distribution
+Class 
GumbelDistribution
+
+
+
+http://docs.oracle.com/javase/6/docs/api/java/lang/Object.html?is-external=true";
 title="class or interface in java.lang">java.lang.Object
+
+
+org.apache.commons.math3.distribution.AbstractRealDistribution
+
+
+org.apache.commons.math3.distribution.GumbelDistribution
+
+
+
+
+
+
+
+
+
+All Implemented Interfaces:
+http://docs.oracle.com/javase/6/docs/api/java/io/Serializable.html?is-external=true";
 title="class or interface in java.io">Serializable, RealDistribution
+
+
+
+public class GumbelDistribution
+extends AbstractRealDistribution
+This class implements the Gumbel distribution.
+Since:
+  3.4
+See Also:http://en.wikipedia.org/wiki/Gumbel_distribution";>Gumbel Distribution 
(Wikipedia), 
+http://mathworld.wolfram.com/GumbelDistribution.html";>Gumbel 
Distribution (Mathworld), 
+Serialized
 Form
+
+
+
+
+
+
+
+
+
+
+
+Field Summary
+
+
+
+
+Fields inherited from class org.apache.commons.math3.distribution.AbstractRealDistribution
+random,
 randomData,
 SOLVER_DEFAULT_ABSOLUTE_ACCURACY
+
+
+
+
+
+
+
+
+Constructor Summary
+
+Constructors 
+
+Constructor and Description
+
+
+GumbelDistribution(double mu,
+double beta)
+Build a new instance.
+
+
+
+GumbelDistribution(RandomGenerator rng,
+double mu,
+double beta)
+Build a new instance.
+
+
+
+
+
+
+
+
+
+
+Method Summary
+
+Methods 
+
+Modifier and Type
+Method and Description
+
+
+double
+cumulativeProbability(double x)
+For a random variable X whose values are 
distributed according
+ to this distribution, this method returns P(X <= x).
+
+
+
+double
+density(double x)
+Returns the probability density function (PDF) of this 
distribution
+ evaluated at the specified point x.
+
+
+
+double
+getLocation()
+Access the location parameter, mu.
+
+
+
+double
+getNumericalMean()
+Use this method to get the numerical value of the mean of 
this
+ distribution.
+
+
+
+double
+getNumericalVariance()
+Use this method to get the numerical value of the variance 
of this
+ distribution.
+
+
+
+double
+getScale()
+Access the scale parameter, beta.
+
+
+
+double
+getSupportLowerBound()
+Access the lower bound of the support.
+
+
+
+double
+getSupportUpperBound()
+Access the upper bound of the support.
+
+
+
+double
+inverseCumulativeProbability(double p)
+Computes the quantile function of this distribution.
+
+
+
+boolean
+isSupportConnected()
+Use this method to get information about whether the 
support is connected,
+ i.e. whether all values between the lower and upper bound of the support
+ are included in the support.
+
+
+
+boolean
+isSupportLowerBoundInclusive()
+Whether or not the lower bound of support is in the domain 
of the density
+ function.
+
+
+
+boolean
+isSupportUpperBoundInclusive()
+Whether or not the upper bound of support is in the domain 
of the density
+ function.
+
+
+
+
+
+
+
+Methods inherited from class org.apache.commons.math3.distribution.AbstractRealDistribution
+cumulativeProbability,
 getSolverAbsoluteAccuracy,
 logDensity,
 probability,
 probability,
 reseedRandomGenerator,
 sample,
 sample
+
+
+
+
+
+Methods inherited from class java.lang.http://docs.oracle.com/javase/6/docs/api/java/lang/Object.html?is-external=true";
 title="class or interface in java.lang">Object
+http://docs.oracle.com/javase/6/docs/api/java/lang/Object.html?is-external=true#clone()"
 title="class or interface in java.lang">clone, http://docs.oracle.com/javase/6/docs/api/java/la

svn commit: r926176 [4/31] - in /websites/production/commons/content/proper/commons-math: apidocs/org/apache/commons/math3/analysis/interpolation/ apidocs/org/apache/commons/math3/analysis/interpolati

[luc]

Added: 
websites/production/commons/content/proper/commons-math/apidocs/org/apache/commons/math3/distribution/class-use/LogisticDistribution.html
==
--- 
websites/production/commons/content/proper/commons-math/apidocs/org/apache/commons/math3/distribution/class-use/LogisticDistribution.html
 (added)
+++ 
websites/production/commons/content/proper/commons-math/apidocs/org/apache/commons/math3/distribution/class-use/LogisticDistribution.html
 Sat Oct 18 20:10:38 2014
@@ -0,0 +1,117 @@
+http://www.w3.org/TR/html4/loose.dtd";>
+
+
+
+
+Uses of Class 
org.apache.commons.math3.distribution.LogisticDistribution (Apache Commons Math 
3.4-SNAPSHOT API)
+
+
+
+
+
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+Overview
+Package
+Class
+Use
+Tree
+Deprecated
+Index
+Help
+
+http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";>
+
+
+
+Prev
+Next
+
+
+Frames
+No Frames
+
+
+All Classes
+
+
+
+
+
+
+
+
+
+
+Uses 
of Classorg.apache.commons.math3.distribution.LogisticDistribution
+
+No usage of 
org.apache.commons.math3.distribution.LogisticDistribution
+
+
+
+
+
+
+
+Overview
+Package
+Class
+Use
+Tree
+Deprecated
+Index
+Help
+
+http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";>
+
+
+
+Prev
+Next
+
+
+Frames
+No Frames
+
+
+All Classes
+
+
+
+
+
+
+
+
+
+Copyright © 2003–2014 http://www.apache.org/";>The Apache Software Foundation. All rights 
reserved.
+
+

Propchange: 
websites/production/commons/content/proper/commons-math/apidocs/org/apache/commons/math3/distribution/class-use/LogisticDistribution.html
--
svn:eol-style = native

Propchange: 
websites/production/commons/content/proper/commons-math/apidocs/org/apache/commons/math3/distribution/class-use/LogisticDistribution.html
--
svn:keywords = Author Date Id Revision

Added: 
websites/production/commons/content/proper/commons-math/apidocs/org/apache/commons/math3/distribution/class-use/NakagamiDistribution.html
==
--- 
websites/production/commons/content/proper/commons-math/apidocs/org/apache/commons/math3/distribution/class-use/NakagamiDistribution.html
 (added)
+++ 
websites/production/commons/content/proper/commons-math/apidocs/org/apache/commons/math3/distribution/class-use/NakagamiDistribution.html
 Sat Oct 18 20:10:38 2014
@@ -0,0 +1,117 @@
+http://www.w3.org/TR/html4/loose.dtd";>
+
+
+
+
+Uses of Class 
org.apache.commons.math3.distribution.NakagamiDistribution (Apache Commons Math 
3.4-SNAPSHOT API)
+
+
+
+
+
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+Overview
+Package
+Class
+Use
+Tree
+Deprecated
+Index
+Help
+
+http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";>
+
+
+
+Prev
+Next
+
+
+Frames
+No Frames
+
+
+All Classes
+
+
+
+
+
+
+
+
+
+
+Uses 
of Classorg.apache.commons.math3.distribution.NakagamiDistribution
+
+No usage of 
org.apache.commons.math3.distribution.NakagamiDistribution
+
+
+
+
+
+
+
+Overview
+Package
+Class
+Use
+Tree
+Deprecated
+Index
+Help
+
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reserved.
+
+

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websites/production/commons/content/proper/commons-math/apidocs/org/apache/commons/math3/distribution/

svn commit: r926176 [5/31] - in /websites/production/commons/content/proper/commons-math: apidocs/org/apache/commons/math3/analysis/interpolation/ apidocs/org/apache/commons/math3/analysis/interpolati

[luc]

Added: 
websites/production/commons/content/proper/commons-math/apidocs/org/apache/commons/math3/stat/descriptive/rank/PSquarePercentile.html
==
--- 
websites/production/commons/content/proper/commons-math/apidocs/org/apache/commons/math3/stat/descriptive/rank/PSquarePercentile.html
 (added)
+++ 
websites/production/commons/content/proper/commons-math/apidocs/org/apache/commons/math3/stat/descriptive/rank/PSquarePercentile.html
 Sat Oct 18 20:10:38 2014
@@ -0,0 +1,548 @@
+http://www.w3.org/TR/html4/loose.dtd";>
+
+
+
+
+PSquarePercentile (Apache Commons Math 3.4-SNAPSHOT API)
+
+
+
+
+
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+Overview
+Package
+Class
+Use
+Tree
+Deprecated
+Index
+Help
+
+http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";>
+
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+Prev Class
+Next Class
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+Summary: 
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+Field | 
+Constr | 
+Method
+
+
+
+
+
+
+
+
+org.apache.commons.math3.stat.descriptive.rank
+Class PSquarePercentile
+
+
+
+http://docs.oracle.com/javase/6/docs/api/java/lang/Object.html?is-external=true";
 title="class or interface in java.lang">java.lang.Object
+
+
+org.apache.commons.math3.stat.descriptive.AbstractUnivariateStatistic
+
+
+org.apache.commons.math3.stat.descriptive.AbstractStorelessUnivariateStatistic
+
+
+org.apache.commons.math3.stat.descriptive.rank.PSquarePercentile
+
+
+
+
+
+
+
+
+
+
+
+All Implemented Interfaces:
+http://docs.oracle.com/javase/6/docs/api/java/io/Serializable.html?is-external=true";
 title="class or interface in java.io">Serializable, StorelessUnivariateStatistic, UnivariateStatistic, MathArrays.Function
+
+
+
+public class PSquarePercentile
+extends AbstractStorelessUnivariateStatistic
+implements StorelessUnivariateStatistic, http://docs.oracle.com/javase/6/docs/api/java/io/Serializable.html?is-external=true";
 title="class or interface in java.io">Serializable
+A StorelessUnivariateStatistic
 estimating percentiles using the
+ http://www.cs.wustl.edu/~jain/papers/ftp/psqr.pdf>P2
+ Algorithm as explained by http://www.cse.wustl.edu/~jain/>Raj
+ Jain and Imrich Chlamtac in
+ http://www.cse.wustl.edu/~jain/papers/psqr.htm>P2 Algorithm
+ for Dynamic Calculation of Quantiles and Histogram Without Storing
+ Observations.
+ 
+ Note: This implementation is not synchronized and produces an approximate
+ result. For small samples, where data can be stored and processed in memory,
+ Percentile 
should be used.
+See Also:Serialized
 Form
+
+
+
+
+
+
+
+
+
+
+
+Nested Class Summary
+
+Nested Classes 
+
+Modifier and Type
+Class and Description
+
+
+protected static interface 
+PSquarePercentile.PSquareMarkers
+An interface that encapsulates abstractions of the
+ P-square algorithm markers as is explained in the original works.
+
+
+
+
+
+
+
+
+
+
+Constructor Summary
+
+Constructors 
+
+Constructor and Description
+
+
+PSquarePercentile(double p)
+Constructs a PSquarePercentile with the specific percentile 
value.
+
+
+
+
+
+
+
+
+
+
+Method Summary
+
+Methods 
+
+Modifier and Type
+Method and Description
+
+
+void
+clear()
+Clears the internal state of the Statistic
+
+
+
+StorelessUnivariateStatistic
+copy()
+Returns a copy of the statistic with the same internal 
state.
+
+
+
+boolean
+equals(http://docs.oracle.com/javase/6/docs/api/java/lang/Object.html?is-external=true";
 title="class or interface in java.lang">Object o)
+Returns true iff o is a 
PSquarePercentile returning the
+ same values as this for getResult() and getN() and 
also
+ having equal markers
+
+
+
+long
+getN()
+Returns the number of values that have been added.
+
+
+
+double
+getResult()
+Returns the current value of the Statistic.
+
+
+
+int
+hashCode()
+Returns hash code based on getResult() and getN()
+
+
+
+void
+increment(double observation)
+Updates the internal state of the statistic to reflect the 
addition of the new value.
+
+
+
+static PSquarePercentile.PSquareMarkers
+newMarkers(http://docs.oracle.com/javase/6/docs/api/java/util/List.html?is-external=true";
 title="class or interface in java.util">ListDouble> initialFive,
+double p)
+A creation method to build Markers
+
+
+
+double
+quantile()
+Returns the quantile estimated by this statistic in the 
range [0.0-1.0]
+
+
+
+http://docs.oracle.com/javase/6/docs/api/java/lang/String.html?is-external=true";
 title="class

svn commit: r926176 [1/31] - in /websites/production/commons/content/proper/commons-math: apidocs/org/apache/commons/math3/analysis/interpolation/ apidocs/org/apache/commons/math3/analysis/interpolati

[luc]

Author: luc
Date: Sat Oct 18 20:10:38 2014
New Revision: 926176

Log:
fixed deleted/added files

Added:

websites/production/commons/content/proper/commons-math/apidocs/org/apache/commons/math3/analysis/interpolation/AkimaSplineInterpolator.html
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websites/production/commons/content/proper/commons-math/apidocs/org/apache/commons/math3/analysis/interpolation/class-use/AkimaSplineInterpolator.html
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websites/production/commons/content/proper/commons-math/apidocs/org/apache/commons/math3/distribution/NakagamiDistribution.html
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websites/production/commons/content/proper/commons-math/apidocs/org/apache/commons/math3/distribution/class-use/ConstantRealDistribution.html
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websites/production/commons/content/proper/commons-math/apidocs/org/apache/commons/math3/distribution/class-use/GumbelDistribution.html
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websites/production/commons/content/proper/commons-math/apidocs/org/apache/commons/math3/distribution/class-use/NakagamiDistribution.html
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websites/production/commons/content/proper/commons-math/apidocs/org/apache/commons/math3/fitting/leastsquares/EvaluationRmsChecker.html
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websites/production/commons/content/proper/commons-math/apidocs/org/apache/commons/math3/stat/descriptive/rank/PSquarePercentile.html
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websites/production/commons/content/proper/commons-math/apidocs/org/apache/commons/math3/stat/descriptive/rank/Percentile.EstimationType.html
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websites/production/commons/content/proper/commons-math/apidocs/org/apache/commons/math3/util/KthSelector.html
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websites/production/commons/content/proper/commons-math/apidocs/org/apache/commons/math3/util/PivotingStrategyInterface.html
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websites/production/commons/content/proper/commons-math/apidocs/org/apache/commons/math3/util/RandomPivotingStrategy.html
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websites/production/commons/content/proper/commons-math/apidocs/org/apache/commons/math3/util/class-use/CentralPivotingStrategy.html
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websites/production/commons/content/proper/commons-math/apidocs/org/apache/commons/math3/util/class-use/KthSelector.html
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websites/production/commons/content/proper/commons-math/apidocs/org/apache/commons/math3/util/class-use/MedianOf3PivotingStrategy.html
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websites/production/commons/content/proper/commons-math/apidocs/org/apache/commons/math3/util/class-use/PivotingStrategyInterface.html
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websites/production/commons

svn commit: r926176 [8/31] - in /websites/production/commons/content/proper/commons-math: apidocs/org/apache/commons/math3/analysis/interpolation/ apidocs/org/apache/commons/math3/analysis/interpolati

[luc]

Added: 
websites/production/commons/content/proper/commons-math/apidocs/src-html/org/apache/commons/math3/analysis/interpolation/AkimaSplineInterpolator.html
==
--- 
websites/production/commons/content/proper/commons-math/apidocs/src-html/org/apache/commons/math3/analysis/interpolation/AkimaSplineInterpolator.html
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websites/production/commons/content/proper/commons-math/apidocs/src-html/org/apache/commons/math3/analysis/interpolation/AkimaSplineInterpolator.html
 Sat Oct 18 20:10:38 2014
@@ -0,0 +1,297 @@
+http://www.w3.org/TR/html4/loose.dtd";>
+
+
+Source code
+
+
+
+
+001/*
+002 * Licensed to the Apache Software 
Foundation (ASF) under one or more
+003 * contributor license agreements.  See 
the NOTICE file distributed with
+004 * this work for additional information 
regarding copyright ownership.
+005 * The ASF licenses this file to You 
under the Apache License, Version 2.0
+006 * (the "License"); you may not use this 
file except in compliance with
+007 * the License.  You may obtain a copy of 
the License at
+008 *
+009 *  
http://www.apache.org/licenses/LICENSE-2.0
+010 *
+011 * Unless required by applicable law or 
agreed to in writing, software
+012 * distributed under the License is 
distributed on an "AS IS" BASIS,
+013 * WITHOUT WARRANTIES OR CONDITIONS OF 
ANY KIND, either express or implied.
+014 * See the License for the specific 
language governing permissions and
+015 * limitations under the License.
+016 */
+017package 
org.apache.commons.math3.analysis.interpolation;
+018
+019import 
org.apache.commons.math3.analysis.polynomials.PolynomialFunction;
+020import 
org.apache.commons.math3.analysis.polynomials.PolynomialSplineFunction;
+021import 
org.apache.commons.math3.exception.DimensionMismatchException;
+022import 
org.apache.commons.math3.exception.NonMonotonicSequenceException;
+023import 
org.apache.commons.math3.exception.NullArgumentException;
+024import 
org.apache.commons.math3.exception.NumberIsTooSmallException;
+025import 
org.apache.commons.math3.exception.util.LocalizedFormats;
+026import 
org.apache.commons.math3.util.FastMath;
+027import 
org.apache.commons.math3.util.MathArrays;
+028import 
org.apache.commons.math3.util.Precision;
+029
+030/**
+031 * Computes a cubic spline interpolation 
for the data set using the Akima
+032 * algorithm, as originally formulated by 
Hiroshi Akima in his 1970 paper
+033 * "A New Method of Interpolation and 
Smooth Curve Fitting Based on Local Procedures."
+034 * J. ACM 17, 4 (October 1970), 589-602. 
DOI=10.1145/321607.321609
+035 * 
http://doi.acm.org/10.1145/321607.321609
+036 * 

+037 * This implementation is based on the 
Akima implementation in the CubicSpline
+038 * class in the Math.NET Numerics 
library. The method referenced is
+039 * CubicSpline.InterpolateAkimaSorted
+040 * 

+041 * The {@link #interpolate(double[], 
double[])} method returns a
+042 * {@link PolynomialSplineFunction} 
consisting of n cubic polynomials, defined
+043 * over the subintervals determined by 
the x values, x[0] < x[i] ... < x[n]. The
+044 * Akima algorithm requires that n >= 
5.
+045 * 
+046 * 

+047 */
+048
+049public class AkimaSplineInterpolator
+050implements UnivariateInterpolator {
+051
+052
+053/**
+054 * The minimum number of points that 
are needed to compute the function
+055 */
+056public static final int 
MINIMUM_NUMBER_POINTS = 5;
+057
+058/**
+059 * Default constructor. Builds an 
AkimaSplineInterpolator object
+060 */
+061public AkimaSplineInterpolator() {
+062
+063}
+064
+065/**
+066 * Computes an interpolating function 
for the data set.
+067 *
+068 * @param xvals the arguments for the 
interpolation points
+069 * @param yvals the values for the 
interpolation points
+070 * @return a function which 
interpolates the data set
+071 * @throws DimensionMismatchException 
if {@code x} and {@code y} have
+072 * different sizes.
+073 * @throws 
NonMonotonicSequenceException if {@code x} is not sorted in
+074 * strict increasing order.
+075 * @throws NumberIsTooSmallException 
if the size of {@code x} is smaller
+076 * than 5.
+077 */
+078public PolynomialSplineFunction 
interpolate(double[] xvals, double[] yvals)
+079throws 
DimensionMismatchException, NumberIsTooSmallException,
+080NonMonotonicSequenceException {
+081if (xvals == null || yvals == 
null) {
+082throw new 
NullArgumentException();
+083}
+084
+085if (xvals.length != yvals.length) 
{
+086throw new 
DimensionMismatchException(xvals.length, yvals.length);
+087}
+088
+089if (xvals.length < 
MINIMUM_NUMBER_POINTS) {
+090throw new 
NumberIsTooSmallException(
+091  
  LocalizedFormats.NUMBER_OF_POINTS,
+092   

svn commit: r926176 [9/31] - in /websites/production/commons/content/proper/commons-math: apidocs/org/apache/commons/math3/analysis/interpolation/ apidocs/org/apache/commons/math3/analysis/interpolati

[luc]

Added: 
websites/production/commons/content/proper/commons-math/apidocs/src-html/org/apache/commons/math3/distribution/NakagamiDistribution.html
==
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websites/production/commons/content/proper/commons-math/apidocs/src-html/org/apache/commons/math3/distribution/NakagamiDistribution.html
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websites/production/commons/content/proper/commons-math/apidocs/src-html/org/apache/commons/math3/distribution/NakagamiDistribution.html
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@@ -0,0 +1,246 @@
+http://www.w3.org/TR/html4/loose.dtd";>
+
+
+Source code
+
+
+
+
+001/*
+002 * Licensed to the Apache Software 
Foundation (ASF) under one or more
+003 * contributor license agreements.  See 
the NOTICE file distributed with
+004 * this work for additional information 
regarding copyright ownership.
+005 * The ASF licenses this file to You 
under the Apache License, Version 2.0
+006 * (the "License"); you may not use this 
file except in compliance with
+007 * the License.  You may obtain a copy of 
the License at
+008 *
+009 *  
http://www.apache.org/licenses/LICENSE-2.0
+010 *
+011 * Unless required by applicable law or 
agreed to in writing, software
+012 * distributed under the License is 
distributed on an "AS IS" BASIS,
+013 * WITHOUT WARRANTIES OR CONDITIONS OF 
ANY KIND, either express or implied.
+014 * See the License for the specific 
language governing permissions and
+015 * limitations under the License.
+016 */
+017package 
org.apache.commons.math3.distribution;
+018
+019import 
org.apache.commons.math3.exception.NotStrictlyPositiveException;
+020import 
org.apache.commons.math3.exception.NumberIsTooSmallException;
+021import 
org.apache.commons.math3.exception.util.LocalizedFormats;
+022import 
org.apache.commons.math3.random.RandomGenerator;
+023import 
org.apache.commons.math3.random.Well19937c;
+024import 
org.apache.commons.math3.special.Gamma;
+025import 
org.apache.commons.math3.util.FastMath;
+026
+027/**
+028 * This class implements the Nakagami 
distribution.
+029 *
+030 * @see Nakagami 
Distribution (Wikipedia)
+031 *
+032 * @since 3.4
+033 */
+034public class NakagamiDistribution extends 
AbstractRealDistribution {
+035
+036/** Default inverse cumulative 
probability accuracy. */
+037public static final double 
DEFAULT_INVERSE_ABSOLUTE_ACCURACY = 1e-9;
+038
+039/** Serializable version identifier. 
*/
+040private static final long 
serialVersionUID = 20141003;
+041
+042/** The shape parameter. */
+043private final double mu;
+044/** The scale parameter. */
+045private final double omega;
+046/** Inverse cumulative probability 
accuracy. */
+047private final double 
inverseAbsoluteAccuracy;
+048
+049/**
+050 * Build a new instance.
+051 *
+052 * @param mu shape parameter
+053 * @param omega scale parameter (must 
be positive)
+054 * @throws NumberIsTooSmallException 
if {@code mu < 0.5}
+055 * @throws 
NotStrictlyPositiveException if {@code omega <= 0}
+056 */
+057public NakagamiDistribution(double 
mu, double omega) {
+058this(mu, omega, 
DEFAULT_INVERSE_ABSOLUTE_ACCURACY);
+059}
+060
+061/**
+062 * Build a new instance.
+063 *
+064 * @param mu shape parameter
+065 * @param omega scale parameter (must 
be positive)
+066 * @param inverseAbsoluteAccuracy the 
maximum absolute error in inverse
+067 * cumulative probability estimates 
(defaults to {@link #DEFAULT_INVERSE_ABSOLUTE_ACCURACY}).
+068 * @throws NumberIsTooSmallException 
if {@code mu < 0.5}
+069 * @throws 
NotStrictlyPositiveException if {@code omega <= 0}
+070 */
+071public NakagamiDistribution(double 
mu, double omega, double inverseAbsoluteAccuracy) {
+072this(new Well19937c(), mu, omega, 
inverseAbsoluteAccuracy);
+073}
+074
+075/**
+076 * Build a new instance.
+077 *
+078 * @param rng Random number 
generator
+079 * @param mu shape parameter
+080 * @param omega scale parameter (must 
be positive)
+081 * @param inverseAbsoluteAccuracy the 
maximum absolute error in inverse
+082 * cumulative probability estimates 
(defaults to {@link #DEFAULT_INVERSE_ABSOLUTE_ACCURACY}).
+083 * @throws NumberIsTooSmallException 
if {@code mu < 0.5}
+084 * @throws 
NotStrictlyPositiveException if {@code omega <= 0}
+085 */
+086public 
NakagamiDistribution(RandomGenerator rng, double mu, double omega, double 
inverseAbsoluteAccuracy) {
+087super(rng);
+088
+089if (mu < 0.5) {
+090throw new 
NumberIsTooSmallException(mu, 0.5, true);
+091}
+092if (omega <= 0) {
+093throw new 
NotStrictlyPositiveException(LocalizedFormats.NOT_POSITIVE_SCALE, omega);
+094}
+095
+096this.mu = mu;
+097this.omega = omega;
+098this.inverseAbsoluteAccuracy = 
inverseAbs

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svn commit: r926176 [7/31] - in /websites/production/commons/content/proper/commons-math: apidocs/org/apache/commons/math3/analysis/interpolation/ apidocs/org/apache/commons/math3/analysis/interpolati

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websites/production/commons/content/proper/commons-math/apidocs/org/apache/commons/math3/util/PivotingStrategyInterface.html
==
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websites/production/commons/content/proper/commons-math/apidocs/org/apache/commons/math3/util/PivotingStrategyInterface.html
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@@ -0,0 +1,233 @@
+http://www.w3.org/TR/html4/loose.dtd";>
+
+
+
+
+PivotingStrategyInterface (Apache Commons Math 3.4-SNAPSHOT API)
+
+
+
+
+
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+Overview
+Package
+Class
+Use
+Tree
+Deprecated
+Index
+Help
+
+http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";>
+
+
+
+Prev 
Class
+Next 
Class
+
+
+Frames
+No Frames
+
+
+All Classes
+
+
+
+
+
+
+
+Summary: 
+Nested | 
+Field | 
+Constr | 
+Method
+
+
+Detail: 
+Field | 
+Constr | 
+Method
+
+
+
+
+
+
+
+
+org.apache.commons.math3.util
+Interface 
PivotingStrategyInterface
+
+
+
+
+
+
+All Known Implementing Classes:
+CentralPivotingStrategy, MedianOf3PivotingStrategy, 
RandomPivotingStrategy
+
+
+
+public interface PivotingStrategyInterface
+A strategy to pick a pivoting index of an array for doing 
partitioning.
+Since:
+  3.4
+See Also:MedianOf3PivotingStrategy, 
+RandomPivotingStrategy, 
+CentralPivotingStrategy
+
+
+
+
+
+
+
+
+
+
+
+Method Summary
+
+Methods 
+
+Modifier and Type
+Method and Description
+
+
+int
+pivotIndex(double[] work,
+int begin,
+int end)
+Find pivot index of the array so that partition and 
Kth
+ element selection can be made
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Method Detail
+
+
+
+
+
+pivotIndex
+int pivotIndex(double[] work,
+ int begin,
+ int end)
+   throws MathIllegalArgumentException
+Find pivot index of the array so that partition and 
Kth
+ element selection can be made
+Parameters:work - 
data arraybegin - index of the first element of the 
sliceend - index after the last element of the slice
+Returns:the index of the pivot 
element chosen between the
+ first and the last element of the array slice
+Throws:
+MathIllegalArgumentException - 
when indices exceeds range
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Overview
+Package
+Class
+Use
+Tree
+Deprecated
+Index
+Help
+
+http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";>
+
+
+
+Prev 
Class
+Next 
Class
+
+
+Frames
+No Frames
+
+
+All Classes
+
+
+
+
+
+
+
+Summary: 
+Nested | 
+Field | 
+Constr | 
+Method
+
+
+Detail: 
+Field | 
+Constr | 
+Method
+
+
+
+
+
+
+Copyright © 2003–2014 http://www.apache.org/";>The Apache Software Foundation. All rights 
reserved.
+
+

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+http://www.w3.org/TR/html4/loose.dtd";>
+
+
+
+
+RandomPivotingStrategy (Apache Commons Math 3.4-SNAPSHOT API)
+
+
+
+
+
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+Overview
+Package
+Class
+Use
+Tree
+Deprecated
+Index
+Help
+
+http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";>
+
+
+
+Prev 
Class
+Next 
Class
+

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+http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd";>http://www.w3.org/1999/xhtml"; lang="en">GumbelDistributionSessionsApache Commons Math > org.apache.commons.math3.distribution > GumbelDistributionGumbelDistributionElementMissed InstructionsCov.Missed BranchesCov.MissedCxtyMissedLinesMissedMethodsTotal27 of 13780%3 of 
1070%5195292class="ctr2">14href="GumbelDistribution.java.html#L126" 
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double)67%50%121601inverseCumulativeProbability(double)<
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 >alt="3"/>100%class="ctr2" id="e8">n/a010101getSupportLowerBound()100%n/a010101getSupportUpperBound()100%n/a010101isSupportLowerBoundInclusive()100%n/a010101isSupportUpperBoundInclusive()100%n/a01class="ctr1" id="h12">01id="j12">01href="GumbelDistribution.java.html#L156" 
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+http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd";>http://www.w3.org/1999/xhtml"; lang="en">GumbelDistribution.javaSessionsApache Commons Math > org.apache.commons.math3.distribution > GumbelDistributio
 n.javaGumbelDistribution.java/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance 
with
+ * the License.  You may obtain a copy of the License at
+ *
+ *  http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.commons.math3.distribution;
+
+import org.apache.commons.math3.exception.NotStrictlyPositiveException;
+import org.apache.commons.math3.exception.OutOfRangeException;
+import org.apache.commons.math3.exception.util.LocalizedFormats;
+import org.apache.commons.math3.random.RandomGenerator;
+import org.apache.commons.math3.random.Well19937c;
+import org.apache.commons.math3.util.FastMath;
+import org.apache.commons.math3.util.MathUtils;
+
+/**
+ * This class implements the Gumbel distr

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+http://www.w3.org/TR/html4/loose.dtd";>
+
+
+Source code
+
+
+
+
+001/*
+002 * Licensed to the Apache Software 
Foundation (ASF) under one or more
+003 * contributor license agreements.  See 
the NOTICE file distributed with
+004 * this work for additional information 
regarding copyright ownership.
+005 * The ASF licenses this file to You 
under the Apache License, Version 2.0
+006 * (the "License"); you may not use this 
file except in compliance with
+007 * the License.  You may obtain a copy of 
the License at
+008 *
+009 *  
http://www.apache.org/licenses/LICENSE-2.0
+010 *
+011 * Unless required by applicable law or 
agreed to in writing, software
+012 * distributed under the License is 
distributed on an "AS IS" BASIS,
+013 * WITHOUT WARRANTIES OR CONDITIONS OF 
ANY KIND, either express or implied.
+014 * See the License for the specific 
language governing permissions and
+015 * limitations under the License.
+016 */
+017package 
org.apache.commons.math3.stat.descriptive.rank;
+018
+019import java.io.IOException;
+020import java.io.ObjectInputStream;
+021import java.io.Serializable;
+022import java.text.DecimalFormat;
+023import java.util.ArrayList;
+024import java.util.Arrays;
+025import java.util.Collection;
+026import java.util.Collections;
+027import java.util.List;
+028
+029import 
org.apache.commons.math3.analysis.UnivariateFunction;
+030import 
org.apache.commons.math3.analysis.interpolation.LinearInterpolator;
+031import 
org.apache.commons.math3.analysis.interpolation.NevilleInterpolator;
+032import 
org.apache.commons.math3.analysis.interpolation.UnivariateInterpolator;
+033import 
org.apache.commons.math3.exception.InsufficientDataException;
+034import 
org.apache.commons.math3.exception.OutOfRangeException;
+035import 
org.apache.commons.math3.exception.util.LocalizedFormats;
+036import 
org.apache.commons.math3.stat.descriptive.AbstractStorelessUnivariateStatistic;
+037import 
org.apache.commons.math3.stat.descriptive.StorelessUnivariateStatistic;
+038import 
org.apache.commons.math3.util.MathArrays;
+039import 
org.apache.commons.math3.util.MathUtils;
+040import 
org.apache.commons.math3.util.Precision;
+041
+042/**
+043 * A {@link StorelessUnivariateStatistic} 
estimating percentiles using the
+044 * 
P2;
+045 * Algorithm as explained by Raj
+046 * Jain and Imrich Chlamtac 
in
+047 * P2;
 Algorithm
+048 * for Dynamic Calculation of Quantiles 
and Histogram Without Storing
+049 * Observations.
+050 * 

+051 * Note: This implementation is not 
synchronized and produces an approximate
+052 * result. For small samples, where data 
can be stored and processed in memory,
+053 * {@link Percentile} should be 
used.
+054 *
+055 */
+056public class PSquarePercentile extends 
AbstractStorelessUnivariateStatistic
+057implements 
StorelessUnivariateStatistic, Serializable {
+058
+059/**
+060 * The maximum array size used for 
psquare algorithm
+061 */
+062private static final int 
PSQUARE_CONSTANT = 5;
+063
+064/**
+065 * A Default quantile needed in case 
if user prefers to use default no
+066 * argument constructor.
+067 */
+068private static final double 
DEFAULT_QUANTILE_DESIRED = 50d;
+069
+070/**
+071 * Serial ID
+072 */
+073private static final long 
serialVersionUID = 2283912083175715479L;
+074
+075/**
+076 * A decimal formatter for print 
convenience
+077 */
+078private static final DecimalFormat 
DECIMAL_FORMAT = new DecimalFormat(
+079"00.00");
+080
+081/**
+082 * Initial list of 5 numbers 
corresponding to 5 markers. NOTE:watch
+083 * out for the add methods that are 
overloaded
+084 */
+085private final List 
initialFive = new FixedCapacityList(
+086PSQUARE_CONSTANT);
+087
+088/**
+089 * The quantile needed should be in 
range of 0-1. The constructor
+090 * {@link #PSquarePercentile(double)} 
ensures that passed in percentile is
+091 * divided by 100.
+092 */
+093private final double quantile;
+094
+095/**
+096 * lastObservation is the last 
observation value/input sample. No need to
+097 * serialize

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+http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd";>
+http://www.w3.org/1999/xhtml"; xml:lang="en" lang="en">
+
+CentralPivotingStrategy xref
+
+
+
+View
 Javadoc
+1   /*
+2* Licensed to the Apache Software Foundation (ASF) under 
one or more
+3* contributor license agreements.  See the NOTICE file 
distributed with
+4* this work for additional information regarding copyright 
ownership.
+5* The ASF licenses this file to You under the Apache 
License, Version 2.0
+6* (the "License"); you may not use this file except in 
compliance with
+7* the License.  You may obtain a copy of the License 
at
+8*
+9*  http://www.apache.org/licenses/LICENSE-2."; 
target="alexandria_uri">http://www.apache.org/licenses/LICENSE-2.0
+10   *
+11   * Unless required by applicable law or agreed to in 
writing, software
+12   * distributed under the License is distributed on an "AS 
IS" BASIS,
+13   * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either 
express or implied.
+14   * See the License for the specific language governing 
permissions and
+15   * limitations under the License.
+16   */
+17  package org.apache.commons.math3.util;
+18  
+19  import java.io.Serializable;
+20  
+21  import 
org.apache.commons.math3.exception.MathIllegalArgumentException;
+22  
+23  
+24  /**
+25   * A mid point strategy based on the average of 
begin and end indices.
+26   * @since 3.4
+27   */
+28  public class 
CentralPivotingStrategy
 implements PivotingStrategyInterface, 
Serializable {
+29  
+30  /** Serializable UID. */
+31  private static final 
long serialVersionUID = 20140713L;
+32  
+33  /**
+34   * {@inheritDoc}
+35   * This in particular picks a average of begin 
and end indices
+36   * @return The index corresponding to a simple 
average of
+37   * the first and the last element indices of the 
array slice
+38   * @throws MathIllegalArgumentException when 
indices exceeds range
+39   */
+40  public int 
pivotIndex(final double[] work, final int 
begin, final int end)
+41  throws MathIllegalArgumentException
 {
+42  
MathArrays.verifyValues(work, begin, end-begin);
+43  return begin + (end - begin)/2;
+44  }
+45  
+46  }
+
+
+Copyright © 2003–2014 http://www.apache.org/";>The Apache Software Foundation. All rights 
reserved.
+
+

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+http://www.w3.org/1999/xhtml"; xml:lang="en" lang="en">
+
+KthSelector xref
+
+
+
+View
 Javadoc
+1   /*
+2* Licensed to the Apache Software Foundation (ASF) under 
one or more
+3* contributor license agreements.  See the NOTICE file 
distributed with
+4* this work for additional information regarding copyright 
ownership.
+5* The ASF licenses this file to You under the Apache 
License, Version 2.0
+6* (the "License"); you may not use this file except in 
compliance with
+7* the License.  You may obtain a copy of the License 
at
+8*
+9*  htt

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+http://www.w3.org/1999/xhtml"; xml:lang="en" lang="en">
+
+LaplaceDistribution xref
+
+
+
+View
 Javadoc
+1   /*
+2* Licensed to the Apache Software Foundation (ASF) under 
one or more
+3* contributor license agreements.  See the NOTICE file 
distributed with
+4* this work for additional information regarding copyright 
ownership.
+5* The ASF licenses this file to You under the Apache 
License, Version 2.0
+6* (the "License"); you may not use this file except in 
compliance with
+7* the License.  You may obtain a copy of the License 
at
+8*
+9*  http://www.apache.org/licenses/LICENSE-2."; 
target="alexandria_uri">http://www.apache.org/licenses/LICENSE-2.0
+10   *
+11   * Unless required by applicable law or agreed to in 
writing, software
+12   * distributed under the License is distributed on an "AS 
IS" BASIS,
+13   * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either 
express or implied.
+14   * See the License for the specific language governing 
permissions and
+15   * limitations under the License.
+16   */
+17  package org.apache.commons.math3.distribution;
+18  
+19  import 
org.apache.commons.math3.exception.NotStrictlyPositiveException;
+20  import 
org.apache.commons.math3.exception.OutOfRangeException;
+21  import 
org.apache.commons.math3.exception.util.LocalizedFormats;
+22  import 
org.apache.commons.math3.random.RandomGenerator;
+23  import org.apache.commons.math3.random.Well19937c;
+24  import org.apache.commons.math3.util.FastMath;
+25  
+26  /**
+27   * This class implements the Laplace 
distribution.
+28   *
+29   * @see http://en.wikipedia.org/wiki/Laplace_distribution">Laplace
 distribution (Wikipedia)
+30   *
+31   * @since 3.4
+32   */
+33  public class 
LaplaceDistribution
 extends AbstractRealDistribution
 {
+34  
+35  /** Serializable version identifier. */
+36  private static final 
long serialVersionUID = 20141003;
+37  
+38  /** The location parameter. */
+39  private final 
double mu;
+40  /** The scale parameter. */
+41  private final 
double beta;
+42  
+43  /**
+44   * Build a new instance.
+45   *
+46   * @param mu location parameter
+47   * @param beta scale parameter (must be 
positive)
+48   * @throws NotStrictlyPositiveException if 
{@code beta <= 0}
+49   */
+50  public LaplaceDistribution(double mu, double beta) {
+51  this(new Well19937c(),
 mu, beta);
+52  }
+53  
+54  /**
+55   * Build a new instance.
+56   *
+57   * @param rng Random number generator
+58   * @param mu location parameter
+59   * @param beta scale parameter (must be 
positive)
+60   * @throws NotStrictlyPositiveException if 
{@code beta <= 0}
+61   */
+62  public LaplaceDistribution(RandomGenerator
 rng, double mu, double beta) {
+63  super(rng);
+64  
+65  if (beta <= 0.0) {
+66  throw new NotStrictlyPositiveException(LocalizedFormats.NOT_POSITIVE_SCALE,
 beta);
+67  }
+68  
+69  this.mu = mu;
+70  this.beta = beta;
+71  }
+72  
+73  /**
+74   * Access the location parameter, {@code 
mu}.
+75   *
+76   * @return the location parameter.
+77   */
+78  public double 
getLocation() {
+79  return mu;
+80  }
+81  
+82  /**
+83   * Access the scale parameter, {@code beta}.
+84   *
+85   * @return the scale parameter.
+86   */
+87  public double 
getScale() {
+88  return beta;
+89  }
+90  
+91  /** {@inheritDoc} */
+92  public double 
density(double x) {
+93  return FastMath.exp(-FastMath.abs(x - mu) / beta) 
/ (2.0 * beta);
+94  }
+95  
+96  /** {@inheritDoc} */
+97  public double 
cumulativeProbability(double x) {
+98  if (x <= mu) {
+99  return FastMath.exp((x - mu) / beta) / 2.0;
+100 } else {
+101 return 1.0 - FastMath.exp((mu - x) / beta) / 2.0;
+102 }
+103 }
+104 
+105 @Override
+106 public double 
inverseCumulativeProbability(double p) 
throws OutOfRangeException {
+107 if (p < 0.0 || p > 1.0) {
+108 throw new OutOfRangeException(p,
 0.0, 1.0);
+109 } else if (p == 
0) {
+110 return 0.0;
+111 } else if (p == 
1) {
+112 return

svn commit: r926176 [6/31] - in /websites/production/commons/content/proper/commons-math: apidocs/org/apache/commons/math3/analysis/interpolation/ apidocs/org/apache/commons/math3/analysis/interpolati

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+++ 
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 Sat Oct 18 20:10:38 2014
@@ -0,0 +1,162 @@
+http://www.w3.org/TR/html4/loose.dtd";>
+
+
+
+
+Uses of Interface 
org.apache.commons.math3.stat.descriptive.rank.PSquarePercentile.PSquareMarkers 
(Apache Commons Math 3.4-SNAPSHOT API)
+
+
+
+
+
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+Overview
+Package
+Class
+Use
+Tree
+Deprecated
+Index
+Help
+
+http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";>
+
+
+
+Prev
+Next
+
+
+Frames
+No 
Frames
+
+
+All 
Classes
+
+
+
+
+
+
+
+
+
+
+Uses of 
Interfaceorg.apache.commons.math3.stat.descriptive.rank.PSquarePercentile.PSquareMarkers
+
+
+
+
+
+Packages that use PSquarePercentile.PSquareMarkers 
+
+Package
+Description
+
+
+
+org.apache.commons.math3.stat.descriptive.rank
+
+Summary statistics based on ranks.
+
+
+
+
+
+
+
+
+
+
+Uses of PSquarePercentile.PSquareMarkers
 in org.apache.commons.math3.stat.descriptive.rank
+
+Methods in org.apache.commons.math3.stat.descriptive.rank
 that return PSquarePercentile.PSquareMarkers 
+
+Modifier and Type
+Method and Description
+
+
+
+static PSquarePercentile.PSquareMarkers
+PSquarePercentile.newMarkers(http://docs.oracle.com/javase/6/docs/api/java/util/List.html?is-external=true";
 title="class or interface in java.util">ListDouble> initialFive,
+double p)
+A creation method to build Markers
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Overview
+Package
+Class
+Use
+Tree
+Deprecated
+Index
+Help
+
+http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";>
+
+
+
+Prev
+Next
+
+
+Frames
+No 
Frames
+
+
+All 
Classes
+
+
+
+
+
+
+
+
+
+Copyright © 2003–2014 http://www.apache.org/";>The Apache Software Foundation. All rights 
reserved.
+
+

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 Sat Oct 18 20:10:38 2014
@@ -0,0 +1,117 @@
+http://www.w3.org/TR/html4/loose.dtd";>
+
+
+
+
+Uses of Class 
org.apache.commons.math3.stat.descriptive.rank.PSquarePercentile (Apache 
Commons Math 3.4-SNAPSHOT API)
+
+
+
+
+
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+Overview
+Package
+Class
+Use
+Tree
+Deprecated
+Index
+Help
+
+http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";>
+
+
+
+Prev
+Next
+
+
+Frames
+No Frames
+
+
+All 
Classes
+
+
+
+
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+Overview
+Package
+Class
+Use
+Tree
+Deprecated
+Index
+Help
+
+http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";>
+
+
+
+Prev Class
+Next Class
+
+
+Frames
+No 
Frames
+
+
+All Classes
+
+
+
+
+
+
+
+Summary: 
+Nested | 
+Field | 
+Constr | 
+Method
+
+
+Detail: 
+Field | 
+Constr | 
+Method
+
+
+
+
+
+
+
+
+org.apache.commons.math3.distribution
+Class 
ConstantRealDistributionTest
+
+
+
+http://docs.oracle.com/javase/6/docs/api/java/lang/Object.html?is-external=true";
 title="class or interface in java.lang">java.lang.Object
+
+
+org.apache.commons.math3.distribution.RealDistributionAbstractTest
+
+
+org.apache.commons.math3.distribution.ConstantRealDistributionTest
+
+
+
+
+
+
+
+
+
+
+public class ConstantRealDistributionTest
+extends RealDistributionAbstractTest
+Test cases for ConstantRealDistribution.
+
+
+
+
+
+
+
+
+
+
+
+Constructor Summary
+
+Constructors 
+
+Constructor and Description
+
+
+ConstantRealDistributionTest() 
+
+
+
+
+
+
+
+
+
+Method Summary
+
+Methods 
+
+Modifier and Type
+Method and Description
+
+
+double[]
+makeCumulativeTestPoints()
+Creates the default cumulative probability distribution 
test input values
+
+
+
+double[]
+makeCumulativeTestValues()
+Creates the default cumulative probability distribution 
test expected values
+
+
+
+double[]
+makeDensityTestValues()
+Creates the default probability density test expected 
values
+
+
+
+ConstantRealDistribution
+makeDistribution()
+Creates the default uniform real distribution instance to 
use in tests.
+
+
+
+void
+setUp()
+Setup sets all test instance data to default values
+
+
+
+void
+testInverseCumulativeProbabilities()
+Override default test, verifying that inverse cum is 
constant
+
+
+
+void
+testMeanVariance() 
+
+
+void
+testSampling()
+Test sampling
+
+
+
+
+
+
+
+Methods inherited from class org.apache.commons.math3.distribution.RealDistributionAbstractTest
+getCumulativeTestPoints,
 getCumulativeTestValues,
 getDensityTestValues,
 getDistribution,
 getInverseCumulativeTestPoints,
 getInverseCumulativeTestValues,
 getTolerance, makeInverseCumulativeTestPoints,
 makeInverseCumulativeTestValues,
 makeLogDensityTestValues,
 setCumulativeTestPoints,
 setCumulativeTestValues,
 se
 tDensityTestValues, setDistribution,
 setInverseCumulativeTestPoints,
 setInverseCumulativeTestValues,
 setTolerance,
 tearDown,
 testConsistency,
 testCumulativeProbabilities,
 testDensities,
 testDensityIntegrals,
 testDistributionClone,
 testIllegalArguments,
 testIsSupportLowerBoundInclusive,
 test
 IsSupportUpperBoundInclusive, testLogDensities,
 verifyCumulativeProbabilities,
 verifyDensities,
 verifyInverseCumulativeProbabilities,
 verifyLogDensities
+
+
+
+
+
+Methods inherited from class java.lang.http://docs.oracle.com/javase/6/docs/api/java/lang/Object.html?is-external=true";
 title="class or interface in java.lang">Object
+http://docs.oracle.com/javase/6/docs/api/java/lang/Object.html?is-external=true#clone()"
 title="class or interface in java.lang">clone, http://docs.oracle.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)"
 title="class or interface in java.lang">equals, http://docs.oracle.com/javase/6/docs/api/java/lang/Object.html?is-external=true#finalize()"
 title="class or interface in java.lang">finalize, http://docs.oracle.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()"
 title="class or interface in java.lang">getClass, http://docs.oracle.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()"
 title="class or interface in java.lang">hashCode, http://docs.oracle.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()"
 title="class or interface in java.lang">notify, http://docs.oracle.com/javase/6/docs/api/java/lang
 /Object.html?is-external=true#notifyAll

svn commit: r926176 [15/31] - in /websites/production/commons/content/proper/commons-math: apidocs/org/apache/commons/math3/analysis/interpolation/ apidocs/org/apache/commons/math3/analysis/interpolat

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Added: 
websites/production/commons/content/proper/commons-math/apidocs/src-html/org/apache/commons/math3/util/CentralPivotingStrategy.html
==
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 Sat Oct 18 20:10:38 2014
@@ -0,0 +1,118 @@
+http://www.w3.org/TR/html4/loose.dtd";>
+
+
+Source code
+
+
+
+
+001/*
+002 * Licensed to the Apache Software 
Foundation (ASF) under one or more
+003 * contributor license agreements.  See 
the NOTICE file distributed with
+004 * this work for additional information 
regarding copyright ownership.
+005 * The ASF licenses this file to You 
under the Apache License, Version 2.0
+006 * (the "License"); you may not use this 
file except in compliance with
+007 * the License.  You may obtain a copy of 
the License at
+008 *
+009 *  
http://www.apache.org/licenses/LICENSE-2.0
+010 *
+011 * Unless required by applicable law or 
agreed to in writing, software
+012 * distributed under the License is 
distributed on an "AS IS" BASIS,
+013 * WITHOUT WARRANTIES OR CONDITIONS OF 
ANY KIND, either express or implied.
+014 * See the License for the specific 
language governing permissions and
+015 * limitations under the License.
+016 */
+017package org.apache.commons.math3.util;
+018
+019import java.io.Serializable;
+020
+021import 
org.apache.commons.math3.exception.MathIllegalArgumentException;
+022
+023
+024/**
+025 * A mid point strategy based on the 
average of begin and end indices.
+026 * @since 3.4
+027 */
+028public class CentralPivotingStrategy 
implements PivotingStrategyInterface, Serializable {
+029
+030/** Serializable UID. */
+031private static final long 
serialVersionUID = 20140713L;
+032
+033/**
+034 * {@inheritDoc}
+035 * This in particular picks a average 
of begin and end indices
+036 * @return The index corresponding to 
a simple average of
+037 * the first and the last element 
indices of the array slice
+038 * @throws 
MathIllegalArgumentException when indices exceeds range
+039 */
+040public int pivotIndex(final double[] 
work, final int begin, final int end)
+041throws 
MathIllegalArgumentException {
+042MathArrays.verifyValues(work, 
begin, end-begin);
+043return begin + (end - begin)/2;
+044}
+045
+046}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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+
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+
+
+
+
+
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+
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+
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+
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+
+
+
+
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+
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+

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==
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 Sat Oct 18 20:10:38 2014
@@ -0,0 +1,229 @@
+http://www.w3.org/TR/html4/loose.dtd";>
+
+
+Source code
+
+
+
+
+001/*
+002 * Licensed to the Apache Software 
Foundation (ASF) under one or more
+003 * contributor license agreements.  See 
the NOTICE file distributed with
+004 * this work for additional information 
regarding copyright ownership.
+005 * The ASF licenses this file to You 
under the Apache License, Version 2.0
+006 * (the "License"); you may not use this 
file except in compliance with
+007 * the License.  You may obtain a copy of 
the License at
+008 *
+009 *  
http://www.apache.org/licenses/LICENSE-2.0
+010 *
+011 * Unless required by applicable law or 
agreed to in writing, software
+012 * distributed under the License is 
di

svn commit: r926176 [26/31] - in /websites/production/commons/content/proper/commons-math: apidocs/org/apache/commons/math3/analysis/interpolation/ apidocs/org/apache/commons/math3/analysis/interpolat

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websites/production/commons/content/proper/commons-math/xref-test/org/apache/commons/math3/fitting/leastsquares/EvaluationRmsCheckerTest.html
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+http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd";>
+http://www.w3.org/1999/xhtml"; xml:lang="en" lang="en">
+
+EvaluationRmsCheckerTest xref
+
+
+
+View
 Javadoc
+1   /*
+2* Licensed to the Apache Software Foundation (ASF) under 
one or more
+3* contributor license agreements.  See the NOTICE file 
distributed with
+4* this work for additional information regarding copyright 
ownership.
+5* The ASF licenses this file to You under the Apache 
License, Version 2.0
+6* (the "License"); you may not use this file except in 
compliance with
+7* the License.  You may obtain a copy of the License 
at
+8*
+9*  http://www.apache.org/licenses/LICENSE-2."; 
target="alexandria_uri">http://www.apache.org/licenses/LICENSE-2.0
+10   *
+11   * Unless required by applicable law or agreed to in 
writing, software
+12   * distributed under the License is distributed on an "AS 
IS" BASIS,
+13   * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either 
express or implied.
+14   * See the License for the specific language governing 
permissions and
+15   * limitations under the License.
+16   */
+17  package 
org.apache.commons.math3.fitting.leastsquares;
+18  
+19  import 
org.apache.commons.math3.fitting.leastsquares.LeastSquaresProblem.Evaluation;
+20  import org.apache.commons.math3.linear.RealMatrix;
+21  import org.apache.commons.math3.linear.RealVector;
+22  import 
org.apache.commons.math3.optim.ConvergenceChecker;
+23  import org.junit.Assert;
+24  import org.junit.Test;
+25  
+26  /** Unit tests for {@link EvaluationRmsChecker}. 
*/
+27  public class 
EvaluationRmsCheckerTest
 {
+28  
+29  /** check {@link ConvergenceChecker#converged(int, 
Object, Object)}. */
+30  @Test
+31  public void 
testConverged() {
+32  //setup
+33  
ConvergenceChecker checker = new EvaluationRmsChecker(0.1, 1);
+34  Evaluation 
e200 = mockEvaluation(200);
+35  Evaluation e1 
= mockEvaluation(1);
+36  
+37  //action + verify
+38  //just matches rel tol
+39  
Assert.assertEquals(true, 
checker.converged(0, e200, mockEvaluation(210)));
+40  //just matches abs tol
+41  
Assert.assertEquals(true, 
checker.converged(0, e1, mockEvaluation(1.9)));
+42  //matches both
+43  
Assert.assertEquals(true, 
checker.converged(0, e1, mockEvaluation(1.01)));
+44  //matches neither
+45  
Assert.assertEquals(false, checker.converged(0, e200, mockEvaluation(300)));
+46  }
+47  
+48  /**
+49   * Create a mock {@link Evaluation}.
+50   *
+51   * @param rms the evaluation's rms.
+52   * @return a new mock evaluation.
+53   */
+54  private static Evaluation mockEvaluation(final double 
rms) {
+55  return new 
Evaluation() {
+56  public RealMatrix getCovariances(double threshold) {
+57  
return null;
+58  }
+59  
+60  public RealVector getSigma(double covarianceSingularityThreshold) {
+61  
return null;
+62  }
+63  
+64  public double 
getRMS() {
+65  
return rms;
+66  }
+67  
+68  public RealMatrix getJacobian() {
+69  
return null;
+70  }
+71  
+72  public double 
getCost() {
+73  
return 0;
+74  }
+75  
+76  public RealVector getResiduals() {
+77  
return null;
+78  }
+79  
+80  public RealVector getPoint() {
+81  
return null;
+82  }
+83  };
+84  }
+85  
+86  }
+
+
+Copyright © 2003–2014 http://www.apache.org/";>The Apache Software Foundation. All rights 
reserved.
+
+

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 Sat Oct 18 20:10:38 2014
@@ -0,0 +1,1144 @@
+http://www.w3.org/TR/html4/loose.dtd";>
+
+
+Source code
+
+
+
+
+001/*
+002 * Licensed to the Apache Software 
Foundation (ASF) under one or more
+003 * contributor license agreements.  See 
the NOTICE file distributed with
+004 * this work for additional information 
regarding copyright ownership.
+005 * The ASF licenses this file to You 
under the Apache License, Version 2.0
+006 * (the "License"); you may not use this 
file except in compliance with
+007 * the License.  You may obtain a copy of 
the License at
+008 *
+009 *  
http://www.apache.org/licenses/LICENSE-2.0
+010 *
+011 * Unless required by applicable law or 
agreed to in writing, software
+012 * distributed under the License is 
distributed on an "AS IS" BASIS,
+013 * WITHOUT WARRANTIES OR CONDITIONS OF 
ANY KIND, either express or implied.
+014 * See the License for the specific 
language governing permissions and
+015 * limitations under the License.
+016 */
+017package 
org.apache.commons.math3.stat.descriptive.rank;
+018
+019import java.io.Serializable;
+020import java.util.Arrays;
+021import java.util.BitSet;
+022
+023import 
org.apache.commons.math3.exception.MathIllegalArgumentException;
+024import 
org.apache.commons.math3.exception.MathUnsupportedOperationException;
+025import 
org.apache.commons.math3.exception.NullArgumentException;
+026import 
org.apache.commons.math3.exception.OutOfRangeException;
+027import 
org.apache.commons.math3.exception.util.LocalizedFormats;
+028import 
org.apache.commons.math3.stat.descriptive.AbstractUnivariateStatistic;
+029import 
org.apache.commons.math3.stat.ranking.NaNStrategy;
+030import 
org.apache.commons.math3.util.FastMath;
+031import 
org.apache.commons.math3.util.KthSelector;
+032import 
org.apache.commons.math3.util.MathArrays;
+033import 
org.apache.commons.math3.util.MathUtils;
+034import 
org.apache.commons.math3.util.MedianOf3PivotingStrategy;
+035import 
org.apache.commons.math3.util.PivotingStrategyInterface;
+036import 
org.apache.commons.math3.util.Precision;
+037
+038/**
+039 * Provides percentile computation.
+040 * 

+041 * There are several commonly used 
methods for estimating percentiles (a.k.a.
+042 * quantiles) based on sample data.  For 
large samples, the different methods
+043 * agree closely, but when sample sizes 
are small, different methods will give
+044 * significantly different results.  The 
algorithm implemented here works as follows:
+045 * 

+046 * 
Let 
n be the length of the (sorted) array and
+047 * 0 < p <= 
100 be the desired percentile.
+048 * 
If  n = 1 
 return the unique array element (regardless of
+049 * the value of 
p); otherwise 
+050 * 
Compute the estimated 
percentile position
+051 *  pos = p * (n + 1) / 
100 and the difference, d
+052 * between pos 
and floor(pos) (i.e. the fractional
+053 * part of 
pos).
+054 * 
 If pos < 
1 return the smallest element in the array.
+055 * 
 Else if pos 
>= n return the largest element in the array.
+056 * 
 Else let 
lower be the element in position
+057 * floor(pos) in 
the array and let upper be the
+058 * next element in the array.  Return 
lower + d * (upper - lower)
+059 * 
+060 * 

+061 * 

+062 * To compute percentiles, the data must 
be at least partially ordered.  Input
+063 * arrays are copied and recursively 
partitioned using an ordering definition.
+064 * The ordering used by 
Arrays.sort(double[]) is the one determined
+065 * by {@link 
java.lang.Double#compareTo(Double)}.  This ordering makes
+066 * Double.NaN 
larger than any other value (including
+067 * 
Double.POSITIVE_INFINITY).  Therefore, for example, 
the median
+068 * (50th percentile) of
+069 * {0, 1, 2, 3, 4, 
Double.NaN} evaluates to 2.5.
+070 * 

+071 * Since percentile estimation usually 
involves interpolation between array
+072 * elements, arrays containing  
NaN or infinite values will often
+073 * result in NaN 
or infinite values returned.
+074 * 

+075 * Further, to include different 
estimation types such as R1, R2 as mentioned in
+076 * svn commit: r926176 [21/31] - in /websites/production/commons/content/proper/commons-math: apidocs/org/apache/commons/math3/analysis/interpolation/ apidocs/org/apache/commons/math3/analysis/interpolat


2014-10-18

Thread
luc

Added: 
websites/production/commons/content/proper/commons-math/testapidocs/org/apache/commons/math3/distribution/LogisticsDistributionTest.html
==
--- 
websites/production/commons/content/proper/commons-math/testapidocs/org/apache/commons/math3/distribution/LogisticsDistributionTest.html
 (added)
+++ 
websites/production/commons/content/proper/commons-math/testapidocs/org/apache/commons/math3/distribution/LogisticsDistributionTest.html
 Sat Oct 18 20:10:38 2014
@@ -0,0 +1,368 @@
+http://www.w3.org/TR/html4/loose.dtd";>
+
+
+
+
+LogisticsDistributionTest (Apache Commons Math 3.4-SNAPSHOT Test 
API)
+
+
+
+
+
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+Overview
+Package
+Class
+Use
+Tree
+Deprecated
+Index
+Help
+
+http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";>
+
+
+
+Prev Class
+Next Class
+
+
+Frames
+No Frames
+
+
+All Classes
+
+
+
+
+
+
+
+Summary: 
+Nested | 
+Field | 
+Constr | 
+Method
+
+
+Detail: 
+Field | 
+Constr | 
+Method
+
+
+
+
+
+
+
+
+org.apache.commons.math3.distribution
+Class 
LogisticsDistributionTest
+
+
+
+http://docs.oracle.com/javase/6/docs/api/java/lang/Object.html?is-external=true";
 title="class or interface in java.lang">java.lang.Object
+
+
+org.apache.commons.math3.distribution.RealDistributionAbstractTest
+
+
+org.apache.commons.math3.distribution.LogisticsDistributionTest
+
+
+
+
+
+
+
+
+
+
+public class LogisticsDistributionTest
+extends RealDistributionAbstractTest
+Test cases for LogisticsDistribution.
+
+
+
+
+
+
+
+
+
+
+
+Constructor Summary
+
+Constructors 
+
+Constructor and Description
+
+
+LogisticsDistributionTest() 
+
+
+
+
+
+
+
+
+
+Method Summary
+
+Methods 
+
+Modifier and Type
+Method and Description
+
+
+double[]
+makeCumulativeTestPoints()
+Creates the default cumulative probability test input 
values
+
+
+
+double[]
+makeCumulativeTestValues()
+Creates the default cumulative probability test expected 
values
+
+
+
+double[]
+makeDensityTestValues()
+Creates the default density test expected values
+
+
+
+LogisticDistribution
+makeDistribution()
+Creates the default continuous distribution instance to use 
in tests.
+
+
+
+void
+testParameters() 
+
+
+void
+testSupport() 
+
+
+
+
+
+
+Methods inherited from class org.apache.commons.math3.distribution.RealDistributionAbstractTest
+getCumulativeTestPoints,
 getCumulativeTestValues,
 getDensityTestValues,
 getDistribution,
 getInverseCumulativeTestPoints,
 getInverseCumulativeTestValues,
 getTolerance, makeInverseCumulativeTestPoints,
 makeInverseCumulativeTestValues,
 makeLogDensityTestValues,
 setCumulativeTestPoints,
 setCumulativeTestValues,
 se
 tDensityTestValues, setDistribution,
 setInverseCumulativeTestPoints,
 setInverseCumulativeTestValues,
 setTolerance,
 setUp,
 tearDown,
 testConsistency, testCumulativeProbabilities,
 testDensities,
 testDensityIntegrals,
 testDistributionClone,
 testIllegalArguments,
 testInverseCumulativeProbabilities,
 testIsSupportLowerBoundInclusive,
 testIsSupportUpperBoundInclusive,
 testLogDensities,
 testSampling,
 verifyCumulativeProbabilities,
 verifyDensities,
 verifyInverseCumulativeProbabilities, verifyLogDensities
+
+
+
+
+
+Methods inherited from class java.lang.http://docs.oracle.com/javase/6/docs/api/java/lang/Object.html?is-external=true";
 title="class or interface in java.lang">Object
+http://docs.oracle.com/javase/6/docs/api/java/lang/Object.html?is-external=true#clone()"
 title="class or interface in java.lang">clone, http://docs.oracle.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)"
 title="class or interface in java.lang">equals, http://docs.oracle.com/javase/6/docs/api/java/lang/Object.html?is-external=true#finalize()"
 title="class or interface in java.lang">finalize, http://docs.oracle.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()"
 title="class or interface in java.lang">getClass, http://docs.oracle.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()"
 title="class or interface in java.lang">hashCode, http://docs.oracle.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()"
 title="class or interface in java.lang">notify, http://docs.oracle.com/javase/6/docs/api/java/lang
 /Object.html?is-external=true#notifyAll()" title="class or interface in 
java.lang">notifyAll, http://docs.oracle.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()"
 title="class or interface in java.lang">toString, http://docs.oracle.com/java



svn commit: r926176 [19/31] - in /websites/production/commons/content/proper/commons-math: apidocs/org/apache/commons/math3/analysis/interpolation/ apidocs/org/apache/commons/math3/analysis/interpolat


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+http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd";>http://www.w3.org/1999/xhtml"; lang="en">Percentile.EstimationType.new 
Percentile.EstimationType() {...}SessionsApache Commons Math > org.apache.commons.math3.stat.descriptive.rank > 
Percentile.EstimationType.new 
Percentile.EstimationType() {...}Percentile.EstimationType.new Percentile.EstimationType() 
{...}ElementMissed InstructionsCov.Missed BranchesCov.MissedCxtyMissedLinesMissedMethodsTotal0 of 33100%0 of 4100%040402index(double, 
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0.7.0.201403182114
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+http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd";>http://www.w3.org/1999/xhtml"; lang="en">Percentile.EstimationType.new 
Percentile.EstimationType() {...}SessionsApache Commons Math > org.apache.commons.math3.stat.descriptive.rank > 
Percentile.EstimationType.new 
Percentile.EstimationType() {...}Percentile.EstimationType.new Percentile.EstimationType() 
{...}ElementMissed InstructionsCov.Missed BranchesCov.MissedCxtyMissedLinesMissedMethodsTotal0 of 46100%0 of 4100%040402index(double, 
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+http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd";>http://www.w3.org/1999/xhtml"; lang="en">Percentile.EstimationTypeSessionsApache Commons Math > org.apache.commons.math3.stat.descriptive.rank > 
Percentile.EstimationTypePercentile.EstimationTypeElementMissed InstructionsCov.Missed BranchesCov.MissedCxtyMissedLinesMissedMethodsTotal5 of 23298%0 of 
8100%
 11203018valueOf(String)0%n/a11static {...}100%n/a0101101estimate(double[], int[], 
double, int, KthSelector)100%100%0301001evaluate(double[], int[], double, KthSelector)100%100%030401Percentile.EstimationType(String, int, String)100%n/a010301evaluate(double[], double, KthSelector)<
 img src="../.resources/greenbar.gif" width="7" height="10" title="7" 
alt="7"/>100%n/a010101values()100%n/a010101getName()100%n/a010101Created with http://www.eclemma.org/jacoco";>JaCoCo 
0.7.0.201403182114
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svn commit: r926176 [28/31] - in /websites/production/commons/content/proper/commons-math: apidocs/org/apache/commons/math3/analysis/interpolation/ apidocs/org/apache/commons/math3/analysis/interpolat


2014-10-18

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Added: 
websites/production/commons/content/proper/commons-math/xref/org/apache/commons/math3/analysis/interpolation/AkimaSplineInterpolator.html
==
--- 
websites/production/commons/content/proper/commons-math/xref/org/apache/commons/math3/analysis/interpolation/AkimaSplineInterpolator.html
 (added)
+++ 
websites/production/commons/content/proper/commons-math/xref/org/apache/commons/math3/analysis/interpolation/AkimaSplineInterpolator.html
 Sat Oct 18 20:10:38 2014
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+http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd";>
+http://www.w3.org/1999/xhtml"; xml:lang="en" lang="en">
+
+AkimaSplineInterpolator xref
+
+
+
+View
 Javadoc
+1   /*
+2* Licensed to the Apache Software Foundation (ASF) under 
one or more
+3* contributor license agreements.  See the NOTICE file 
distributed with
+4* this work for additional information regarding copyright 
ownership.
+5* The ASF licenses this file to You under the Apache 
License, Version 2.0
+6* (the "License"); you may not use this file except in 
compliance with
+7* the License.  You may obtain a copy of the License 
at
+8*
+9*  http://www.apache.org/licenses/LICENSE-2."; 
target="alexandria_uri">http://www.apache.org/licenses/LICENSE-2.0
+10   *
+11   * Unless required by applicable law or agreed to in 
writing, software
+12   * distributed under the License is distributed on an "AS 
IS" BASIS,
+13   * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either 
express or implied.
+14   * See the License for the specific language governing 
permissions and
+15   * limitations under the License.
+16   */
+17  package 
org.apache.commons.math3.analysis.interpolation;
+18  
+19  import 
org.apache.commons.math3.analysis.polynomials.PolynomialFunction;
+20  import 
org.apache.commons.math3.analysis.polynomials.PolynomialSplineFunction;
+21  import 
org.apache.commons.math3.exception.DimensionMismatchException;
+22  import 
org.apache.commons.math3.exception.NonMonotonicSequenceException;
+23  import 
org.apache.commons.math3.exception.NullArgumentException;
+24  import 
org.apache.commons.math3.exception.NumberIsTooSmallException;
+25  import 
org.apache.commons.math3.exception.util.LocalizedFormats;
+26  import org.apache.commons.math3.util.FastMath;
+27  import org.apache.commons.math3.util.MathArrays;
+28  import org.apache.commons.math3.util.Precision;
+29  
+30  /**
+31   * Computes a cubic spline interpolation for the 
data set using the Akima
+32   * algorithm, as originally formulated by Hiroshi 
Akima in his 1970 paper
+33   * "A New Method of Interpolation and Smooth Curve 
Fitting Based on Local Procedures."
+34   * J. ACM 17, 4 (October 1970), 589-602. 
DOI=10.1145/321607.321609
+35   * http://doi.acm.org/10.1145/321607.32160"; 
target="alexandria_uri">http://doi.acm.org/10.1145/321607.321609
+36   * 

+37   * This implementation is based on the Akima 
implementation in the CubicSpline
+38   * class in the Math.NET Numerics library. The 
method referenced is
+39   * CubicSpline.InterpolateAkimaSorted
+40   * 

+41   * The {@link #interpolate(double[], double[])} 
method returns a
+42   * {@link PolynomialSplineFunction} consisting of n 
cubic polynomials, defined
+43   * over the subintervals determined by the x values, 
x[0] < x[i] ... < x[n]. The
+44   * Akima algorithm requires that n >= 5.
+45   * 
+46   * 

+47   */
+48  
+49  public class 
AkimaSplineInterpolator
+50  implements UnivariateInterpolator
 {
+51  
+52  
+53  /**
+54   * The minimum number of points that are needed 
to compute the function
+55   */
+56  public static 
final int MINIMUM_NUMBER_POINTS = 5;
+57  
+58  /**
+59   * Default constructor. Builds an 
AkimaSplineInterpolator object
+60   */
+61  public AkimaSplineInterpolator()
 {
+62  
+63  }
+64  
+65  /**
+66   * Computes an interpolating function for the 
data set.
+67   *
+68   * @param xvals the arguments for the 
interpolation points
+69   * @param yvals the values for the interpolation 
points
+70   * @return a function which interpolates the 
data set
+71   * @throws DimensionMismatchException if {@code 
x} and {@code y} have
+72   * different sizes.
+73   * @throws NonMonotonicSequenceException if 
{@code x} is not sorted in
+74   * strict increasing order.
+75   * @



svn commit: r926176 [18/31] - in /websites/production/commons/content/proper/commons-math: apidocs/org/apache/commons/math3/analysis/interpolation/ apidocs/org/apache/commons/math3/analysis/interpolat


2014-10-18

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Added: 
websites/production/commons/content/proper/commons-math/jacoco/org.apache.commons.math3.stat.descriptive.rank/PSquarePercentile.java.html
==
--- 
websites/production/commons/content/proper/commons-math/jacoco/org.apache.commons.math3.stat.descriptive.rank/PSquarePercentile.java.html
 (added)
+++ 
websites/production/commons/content/proper/commons-math/jacoco/org.apache.commons.math3.stat.descriptive.rank/PSquarePercentile.java.html
 Sat Oct 18 20:10:38 2014
@@ -0,0 +1,997 @@
+http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd";>http://www.w3.org/1999/xhtml"; lang="en">PSquarePercentile.javaSessionsApache Commons Math > org.apache.commons.math3.stat.descriptive.rank > 
PSquarePe
 rcentile.javaPSquarePercentile.java/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance 
with
+ * the License.  You may obtain a copy of the License at
+ *
+ *  http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.commons.math3.stat.descriptive.rank;
+
+import java.io.IOException;
+import java.io.ObjectInputStream;
+import java.io.Serializable;
+import java.text.DecimalFormat;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.List;
+
+import org.apache.commons.math3.analysis.UnivariateFunction;
+import org.apache.commons.math3.analysis.interpolation.LinearInterpolator;
+import org.apache.commons.math3.analysis.interpolation.NevilleInterpolator;
+import org.apache.commons.math3.analysis.interpolation.UnivariateInterpolator;
+import org.apache.commons.math3.exception.InsufficientDataException;
+import org.apache.commons.math3.exception.OutOfRangeException;
+import org.apache.commons.math3.exception.util.LocalizedFormats;
+import 
org.apache.commons.math3.stat.descriptive.AbstractStorelessUnivariateStatistic;
+import org.apache.commons.math3.stat.descriptive.StorelessUnivariateStatistic;
+import org.apache.commons.math3.util.MathArrays;
+import org.apache.commons.math3.util.MathUtils;
+import org.apache.commons.math3.util.Precision;
+
+/**
+ * A {@link StorelessUnivariateStatistic} estimating percentiles using the
+ * 
P2;
+ * Algorithm as explained by Raj
+ * Jain and Imrich Chlamtac in
+ * P2;
 Algorithm
+ * for Dynamic Calculation of Quantiles and Histogram Without Storing
+ * Observations.
+ * 

+ * Note: This implementation is not synchronized and produces an approximate
+ * result. For small samples, where data can be stored and processed in memory,
+ * {@link Percentile} should be used.
+ *
+ */
+public class PSquarePercentile extends AbstractStorelessUnivariateStatistic
+implements StorelessUnivariateStatistic, Serializable {
+
+/**
+ * The maximum array size used for psquare algorithm
+ */
+private static final int PSQUARE_CONSTANT = 5;
+
+/**
+ * A Default quantile needed in case if user prefers to use default no
+ * argument constructor.
+ */
+private static final double DEFAULT_QUANTILE_DESIRED = 50d;
+
+/**
+ * Serial ID
+ */
+private static final long serialVersionUID = 2283912083175715479L;
+
+/**
+ * A decimal formatter for print convenience
+ */
+private static final DecimalFormat 
DECIMAL_FORMAT = new DecimalFormat(
+"00.00");
+
+/**
+ * Initial list of 5 numbers corresponding to 5 markers. 
NOTE:watch
+ * out for the add methods that are overloaded
+ */
+private final List initialFive = 
new FixedCapacityList(
+PSQUARE_CONSTANT);
+
+/**
+ * The quantile needed should be in range of 0-1. The constructor
+ * {@link #PSquarePercentile(double)} ensures that passed in percentile is
+ * divided by 100.
+ */
+private final double quantile;
+
+/**
+ * lastObservation is the last observation value/input sample. No need to
+ * serialize
+ */
+private transient double lastObservation;
+
+/**
+ * Markers is the marker collection object which comes to effect
+ * only after 5 values are inserted
+ */
+private PSquareMarkers ma



svn commit: r926176 [24/31] - in /websites/production/commons/content/proper/commons-math: apidocs/org/apache/commons/math3/analysis/interpolation/ apidocs/org/apache/commons/math3/analysis/interpolat


2014-10-18

Thread
luc

Added: 
websites/production/commons/content/proper/commons-math/testapidocs/src-html/org/apache/commons/math3/stat/descriptive/rank/PSquarePercentileTest.html
==
--- 
websites/production/commons/content/proper/commons-math/testapidocs/src-html/org/apache/commons/math3/stat/descriptive/rank/PSquarePercentileTest.html
 (added)
+++ 
websites/production/commons/content/proper/commons-math/testapidocs/src-html/org/apache/commons/math3/stat/descriptive/rank/PSquarePercentileTest.html
 Sat Oct 18 20:10:38 2014
@@ -0,0 +1,832 @@
+http://www.w3.org/TR/html4/loose.dtd";>
+
+
+Source code
+
+
+
+
+001/*
+002 * Licensed to the Apache Software 
Foundation (ASF) under one or more
+003 * contributor license agreements.  See 
the NOTICE file distributed with
+004 * this work for additional information 
regarding copyright ownership.
+005 * The ASF licenses this file to You 
under the Apache License, Version 2.0
+006 * (the "License"); you may not use this 
file except in compliance with
+007 * the License.  You may obtain a copy of 
the License at
+008 *
+009 *  
http://www.apache.org/licenses/LICENSE-2.0
+010 *
+011 * Unless required by applicable law or 
agreed to in writing, software
+012 * distributed under the License is 
distributed on an "AS IS" BASIS,
+013 * WITHOUT WARRANTIES OR CONDITIONS OF 
ANY KIND, either express or implied.
+014 * See the License for the specific 
language governing permissions and
+015 * limitations under the License.
+016 */
+017package 
org.apache.commons.math3.stat.descriptive.rank;
+018
+019import java.io.IOException;
+020import java.util.ArrayList;
+021import java.util.Arrays;
+022import java.util.HashSet;
+023import java.util.Iterator;
+024import java.util.LinkedHashSet;
+025import java.util.Set;
+026
+027import 
org.apache.commons.math3.distribution.LogNormalDistribution;
+028import 
org.apache.commons.math3.distribution.NormalDistribution;
+029import 
org.apache.commons.math3.distribution.RealDistribution;
+030import 
org.apache.commons.math3.exception.MathIllegalArgumentException;
+031import 
org.apache.commons.math3.exception.OutOfRangeException;
+032import 
org.apache.commons.math3.random.RandomGenerator;
+033import 
org.apache.commons.math3.random.Well19937c;
+034import 
org.apache.commons.math3.stat.descriptive.StorelessUnivariateStatistic;
+035import 
org.apache.commons.math3.stat.descriptive.StorelessUnivariateStatisticAbstractTest;
+036import 
org.apache.commons.math3.stat.descriptive.UnivariateStatistic;
+037import 
org.apache.commons.math3.stat.descriptive.rank.PSquarePercentile.PSquareMarkers;
+038import 
org.apache.commons.math3.util.FastMath;
+039import org.junit.Assert;
+040import org.junit.Test;
+041
+042/**
+043 * Test cases for the {@link 
PSquarePercentile} class which naturally extends
+044 * {@link 
StorelessUnivariateStatisticAbstractTest}. 
+045 */
+046public class PSquarePercentileTest 
extends
+047
StorelessUnivariateStatisticAbstractTest {
+048
+049protected double percentile5 = 
8.2299d;
+050protected double percentile95 = 
16.72195;// 20.82d; this is approximation
+051protected double tolerance = 
10E-12;
+052
+053private final RandomGenerator 
randomGenerator = new Well19937c(1000);
+054
+055@Override
+056public double getTolerance() {
+057return 1.0e-2;// tolerance limit 
changed as this is an approximation
+058// algorithm and also gets 
accurate after few tens of
+059// samples
+060}
+061
+062/**
+063 * Verifies that copied statistics 
remain equal to originals when
+064 * incremented the same way by making 
the copy after a majority of elements
+065 * are incremented
+066 */
+067@Test
+068public void 
testCopyConsistencyWithInitialMostElements() {
+069
+070StorelessUnivariateStatistic 
master =
+071
(StorelessUnivariateStatistic) getUnivariateStatistic();
+072
+073StorelessUnivariateStatistic 
replica = null;
+074
+075// select a portion of testArray 
till 75 % of the length to load first
+076long index = FastMath.round(0.75 
* testArray.length);
+077
+078// Put first half in master and 
copy master to replica
+079master.incrementAll(testArray, 0, 
(int) index);
+080replica = master.copy();
+081
+082// Check same
+083
Assert.assertTrue(replica.equals(master));
+084
Assert.assertTrue(master.equals(replica));
+085
+086// Now add second part to both 
and check again
+087master.incrementAll(testArray, 
(int) index,
+088(int) (testArray.length - 
index));
+089replica.incrementAll(testArray, 
(int) index,
+090(int) (testArray.length - 
index));
+091
Assert.assertTrue(replica.equals(master));
+092
Assert.assertTrue(master.equals(replica));
+093}
+094
+095/**
+096 * Verifies that copied statistics 
remain equal t



svn commit: r926176 [25/31] - in /websites/production/commons/content/proper/commons-math: apidocs/org/apache/commons/math3/analysis/interpolation/ apidocs/org/apache/commons/math3/analysis/interpolat


2014-10-18

Thread
luc

Added: 
websites/production/commons/content/proper/commons-math/xref-test/org/apache/commons/math3/analysis/interpolation/AkimaSplineInterpolatorTest.html
==
--- 
websites/production/commons/content/proper/commons-math/xref-test/org/apache/commons/math3/analysis/interpolation/AkimaSplineInterpolatorTest.html
 (added)
+++ 
websites/production/commons/content/proper/commons-math/xref-test/org/apache/commons/math3/analysis/interpolation/AkimaSplineInterpolatorTest.html
 Sat Oct 18 20:10:38 2014
@@ -0,0 +1,240 @@
+http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd";>
+http://www.w3.org/1999/xhtml"; xml:lang="en" lang="en">
+
+AkimaSplineInterpolatorTest xref
+
+
+
+View
 Javadoc
+1   /*
+2* Licensed to the Apache Software Foundation (ASF) under 
one or more
+3* contributor license agreements.  See the NOTICE file 
distributed with
+4* this work for additional information regarding copyright 
ownership.
+5* The ASF licenses this file to You under the Apache 
License, Version 2.0
+6* (the "License"); you may not use this file except in 
compliance with
+7* the License.  You may obtain a copy of the License 
at
+8*
+9*  http://www.apache.org/licenses/LICENSE-2."; 
target="alexandria_uri">http://www.apache.org/licenses/LICENSE-2.0
+10   *
+11   * Unless required by applicable law or agreed to in 
writing, software
+12   * distributed under the License is distributed on an "AS 
IS" BASIS,
+13   * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either 
express or implied.
+14   * See the License for the specific language governing 
permissions and
+15   * limitations under the License.
+16   */
+17  package 
org.apache.commons.math3.analysis.interpolation;
+18  
+19  import 
org.apache.commons.math3.analysis.UnivariateFunction;
+20  import 
org.apache.commons.math3.distribution.UniformRealDistribution;
+21  import 
org.apache.commons.math3.exception.DimensionMismatchException;
+22  import 
org.apache.commons.math3.exception.NonMonotonicSequenceException;
+23  import 
org.apache.commons.math3.exception.NullArgumentException;
+24  import 
org.apache.commons.math3.exception.NumberIsTooSmallException;
+25  import 
org.apache.commons.math3.random.RandomGenerator;
+26  import org.apache.commons.math3.random.Well19937c;
+27  import org.apache.commons.math3.util.FastMath;
+28  import org.apache.commons.math3.util.Precision;
+29  import org.junit.Assert;
+30  import org.junit.Test;
+31  
+32  import static 
org.junit.Assert.*;
+33  
+34  public class 
AkimaSplineInterpolatorTest
+35  {
+36  
+37  @Test
+38  public void 
testIllegalArguments()
+39  {
+40  // Data set arrays of different size.
+41  
UnivariateInterpolator i = new 
AkimaSplineInterpolator();
+42  
+43  try
+44  {
+45  double yval[] = { 0.0, 1.0, 2.0, 3.0, 4.0 };
+46  
i.interpolate( null, yval );
+47  
Assert.fail( "Failed to detect x null pointer" 
);
+48  }
+49  catch ( NullArgumentException iae )
+50  {
+51  // Expected.
+52  }
+53  
+54  try
+55  {
+56  double xval[] = { 0.0, 1.0, 2.0, 3.0, 4.0 };
+57  
i.interpolate( xval, null );
+58  
Assert.fail( "Failed to detect y null pointer" 
);
+59  }
+60  catch ( NullArgumentException iae )
+61  {
+62  // Expected.
+63  }
+64  
+65  try
+66  {
+67  double xval[] = { 0.0, 1.0, 2.0, 3.0 };
+68  double yval[] = { 0.0, 1.0, 2.0, 3.0 };
+69  
i.interpolate( xval, yval );
+70  
Assert.fail( "Failed to detect insufficient 
data" );
+71  }
+72  catch ( NumberIsTooSmallException iae )
+73  {
+74  // Expected.
+75  }
+76  
+77  try
+78  {
+79  double xval[] = { 0.0, 1.0, 2.0, 3.0, 4.0 };
+80  double yval[] = { 0.0, 1.0, 2.0, 3.0, 4.0, 5.0 };
+81  
i.interpolate( xval, yval );
+82  
Assert.fail( "Failed to detect data set array with 
different sizes." );
+83  }
+84  catch ( DimensionMismatchException iae )
+85  {
+86  // Expected.
+87  }
+88  
+89  // X values not sorted.
+90  try
+91  {
+92  double xval[] = { 0.0, 1.0, 0.5, 7.0, 3.5, 2.2, 
8.0 };
+93  double yval[] = { 0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 
6.0 };
+94  
i.interpolate( xval, yval );
+95  
Assert.fail( "Failed to detect unsorted 
arguments." );
+96  }
+97  catch ( NonMonotonicSequenceException iae )
+98  {
+99  // Expected.
+100 }
+101 }
+102 
+103 /*
+104  * Interpolate a straight line. 
 y = 2 x - 5 
 Tolerances determined by performing same calculation using
+105  * Math.NET over ten runs



svn commit: r926176 [23/31] - in /websites/production/commons/content/proper/commons-math: apidocs/org/apache/commons/math3/analysis/interpolation/ apidocs/org/apache/commons/math3/analysis/interpolat


2014-10-18

Thread
luc

Added: 
websites/production/commons/content/proper/commons-math/testapidocs/src-html/org/apache/commons/math3/analysis/interpolation/AkimaSplineInterpolatorTest.html
==
--- 
websites/production/commons/content/proper/commons-math/testapidocs/src-html/org/apache/commons/math3/analysis/interpolation/AkimaSplineInterpolatorTest.html
 (added)
+++ 
websites/production/commons/content/proper/commons-math/testapidocs/src-html/org/apache/commons/math3/analysis/interpolation/AkimaSplineInterpolatorTest.html
 Sat Oct 18 20:10:38 2014
@@ -0,0 +1,299 @@
+http://www.w3.org/TR/html4/loose.dtd";>
+
+
+Source code
+
+
+
+
+001/*
+002 * Licensed to the Apache Software 
Foundation (ASF) under one or more
+003 * contributor license agreements.  See 
the NOTICE file distributed with
+004 * this work for additional information 
regarding copyright ownership.
+005 * The ASF licenses this file to You 
under the Apache License, Version 2.0
+006 * (the "License"); you may not use this 
file except in compliance with
+007 * the License.  You may obtain a copy of 
the License at
+008 *
+009 *  
http://www.apache.org/licenses/LICENSE-2.0
+010 *
+011 * Unless required by applicable law or 
agreed to in writing, software
+012 * distributed under the License is 
distributed on an "AS IS" BASIS,
+013 * WITHOUT WARRANTIES OR CONDITIONS OF 
ANY KIND, either express or implied.
+014 * See the License for the specific 
language governing permissions and
+015 * limitations under the License.
+016 */
+017package 
org.apache.commons.math3.analysis.interpolation;
+018
+019import 
org.apache.commons.math3.analysis.UnivariateFunction;
+020import 
org.apache.commons.math3.distribution.UniformRealDistribution;
+021import 
org.apache.commons.math3.exception.DimensionMismatchException;
+022import 
org.apache.commons.math3.exception.NonMonotonicSequenceException;
+023import 
org.apache.commons.math3.exception.NullArgumentException;
+024import 
org.apache.commons.math3.exception.NumberIsTooSmallException;
+025import 
org.apache.commons.math3.random.RandomGenerator;
+026import 
org.apache.commons.math3.random.Well19937c;
+027import 
org.apache.commons.math3.util.FastMath;
+028import 
org.apache.commons.math3.util.Precision;
+029import org.junit.Assert;
+030import org.junit.Test;
+031
+032import static org.junit.Assert.*;
+033
+034public class 
AkimaSplineInterpolatorTest
+035{
+036
+037@Test
+038public void testIllegalArguments()
+039{
+040// Data set arrays of different 
size.
+041UnivariateInterpolator i = new 
AkimaSplineInterpolator();
+042
+043try
+044{
+045double yval[] = { 0.0, 1.0, 
2.0, 3.0, 4.0 };
+046i.interpolate( null, yval 
);
+047Assert.fail( "Failed to 
detect x null pointer" );
+048}
+049catch ( NullArgumentException iae 
)
+050{
+051// Expected.
+052}
+053
+054try
+055{
+056double xval[] = { 0.0, 1.0, 
2.0, 3.0, 4.0 };
+057i.interpolate( xval, null 
);
+058Assert.fail( "Failed to 
detect y null pointer" );
+059}
+060catch ( NullArgumentException iae 
)
+061{
+062// Expected.
+063}
+064
+065try
+066{
+067double xval[] = { 0.0, 1.0, 
2.0, 3.0 };
+068double yval[] = { 0.0, 1.0, 
2.0, 3.0 };
+069i.interpolate( xval, yval 
);
+070Assert.fail( "Failed to 
detect insufficient data" );
+071}
+072catch ( NumberIsTooSmallException 
iae )
+073{
+074// Expected.
+075}
+076
+077try
+078{
+079double xval[] = { 0.0, 1.0, 
2.0, 3.0, 4.0 };
+080double yval[] = { 0.0, 1.0, 
2.0, 3.0, 4.0, 5.0 };
+081i.interpolate( xval, yval 
);
+082Assert.fail( "Failed to 
detect data set array with different sizes." );
+083}
+084catch ( 
DimensionMismatchException iae )
+085{
+086// Expected.
+087}
+088
+089// X values not sorted.
+090try
+091{
+092double xval[] = { 0.0, 1.0, 
0.5, 7.0, 3.5, 2.2, 8.0 };
+093double yval[] = { 0.0, 1.0, 
2.0, 3.0, 4.0, 5.0, 6.0 };
+094i.interpolate( xval, yval 
);
+095Assert.fail( "Failed to 
detect unsorted arguments." );
+096}
+097catch ( 
NonMonotonicSequenceException iae )
+098{
+099// Expected.
+100}
+101}
+102
+103/*
+104 * Interpolate a straight line. 
 y = 2 x - 5 
 Tolerances determined by performing same 
calculation using
+105 * Math.NET over ten runs of 100 
random number draws for the same function over the same span with the same 
number
+106 * of elements
+107 */
+108@Test
+109public void testInterpolateLine()
+110{
+111final int numberOfElements = 
10;
+



svn commit: r926176 [22/31] - in /websites/production/commons/content/proper/commons-math: apidocs/org/apache/commons/math3/analysis/interpolation/ apidocs/org/apache/commons/math3/analysis/interpolat


2014-10-18

Thread
luc

Added: 
websites/production/commons/content/proper/commons-math/testapidocs/org/apache/commons/math3/fitting/leastsquares/EvaluationRmsCheckerTest.html
==
--- 
websites/production/commons/content/proper/commons-math/testapidocs/org/apache/commons/math3/fitting/leastsquares/EvaluationRmsCheckerTest.html
 (added)
+++ 
websites/production/commons/content/proper/commons-math/testapidocs/org/apache/commons/math3/fitting/leastsquares/EvaluationRmsCheckerTest.html
 Sat Oct 18 20:10:38 2014
@@ -0,0 +1,262 @@
+http://www.w3.org/TR/html4/loose.dtd";>
+
+
+
+
+EvaluationRmsCheckerTest (Apache Commons Math 3.4-SNAPSHOT Test 
API)
+
+
+
+
+
+
+JavaScript is disabled on your browser.
+
+
+
+
+
+
+
+
+Overview
+Package
+Class
+Use
+Tree
+Deprecated
+Index
+Help
+
+http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";>
+
+
+
+Prev Class
+Next Class
+
+
+Frames
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+
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+All Classes
+
+
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+Summary: 
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+Constr | 
+Method
+
+
+Detail: 
+Field | 
+Constr | 
+Method
+
+
+
+
+
+
+
+
+org.apache.commons.math3.fitting.leastsquares
+Class 
EvaluationRmsCheckerTest
+
+
+
+http://docs.oracle.com/javase/6/docs/api/java/lang/Object.html?is-external=true";
 title="class or interface in java.lang">java.lang.Object
+
+
+org.apache.commons.math3.fitting.leastsquares.EvaluationRmsCheckerTest
+
+
+
+
+
+
+
+
+public class EvaluationRmsCheckerTest
+extends http://docs.oracle.com/javase/6/docs/api/java/lang/Object.html?is-external=true";
 title="class or interface in java.lang">Object
+Unit tests for EvaluationRmsChecker.
+
+
+
+
+
+
+
+
+
+
+
+Constructor Summary
+
+Constructors 
+
+Constructor and Description
+
+
+EvaluationRmsCheckerTest() 
+
+
+
+
+
+
+
+
+
+Method Summary
+
+Methods 
+
+Modifier and Type
+Method and Description
+
+
+void
+testConverged()
+check ConvergenceChecker.converged(int, Object, 
Object).
+
+
+
+
+
+
+
+Methods inherited from class java.lang.http://docs.oracle.com/javase/6/docs/api/java/lang/Object.html?is-external=true";
 title="class or interface in java.lang">Object
+http://docs.oracle.com/javase/6/docs/api/java/lang/Object.html?is-external=true#clone()"
 title="class or interface in java.lang">clone, http://docs.oracle.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)"
 title="class or interface in java.lang">equals, http://docs.oracle.com/javase/6/docs/api/java/lang/Object.html?is-external=true#finalize()"
 title="class or interface in java.lang">finalize, http://docs.oracle.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()"
 title="class or interface in java.lang">getClass, http://docs.oracle.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()"
 title="class or interface in java.lang">hashCode, http://docs.oracle.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()"
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 /Object.html?is-external=true#notifyAll()" title="class or interface in 
java.lang">notifyAll, http://docs.oracle.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()"
 title="class or interface in java.lang">toString, http://docs.oracle.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()"
 title="class or interface in java.lang">wait, http://docs.oracle.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)"
 title="class or interface in java.lang">wait, http://docs.oracle.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long,%20int)"
 title="class or interface in java.lang">wait
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Constructor Detail
+
+
+
+
+
+EvaluationRmsCheckerTest
+public EvaluationRmsCheckerTest()
+
+
+
+
+
+
+
+
+
+Method Detail
+
+
+
+
+
+testConverged
+public void testConverged()
+check ConvergenceChecker.converged(int, Object, 
Object).
+
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+
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+Next Class
+
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+
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+Summary: 
+Nested | 
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+Constr | 
+Method
+
+
+Detail: 
+Field | 
+Constr | 
+Method
+
+
+
+
+
+
+Copyright © 2003–2014 http://www.apache.org/"



svn commit: r926176 [27/31] - in /websites/production/commons/content/proper/commons-math: apidocs/org/apache/commons/math3/analysis/interpolation/ apidocs/org/apache/commons/math3/analysis/interpolat


2014-10-18

Thread
luc

Added: 
websites/production/commons/content/proper/commons-math/xref-test/org/apache/commons/math3/stat/descriptive/rank/PSquarePercentileTest.html
==
--- 
websites/production/commons/content/proper/commons-math/xref-test/org/apache/commons/math3/stat/descriptive/rank/PSquarePercentileTest.html
 (added)
+++ 
websites/production/commons/content/proper/commons-math/xref-test/org/apache/commons/math3/stat/descriptive/rank/PSquarePercentileTest.html
 Sat Oct 18 20:10:38 2014
@@ -0,0 +1,773 @@
+http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd";>
+http://www.w3.org/1999/xhtml"; xml:lang="en" lang="en">
+
+PSquarePercentileTest xref
+
+
+
+View
 Javadoc
+1   /*
+2* Licensed to the Apache Software Foundation (ASF) under 
one or more
+3* contributor license agreements.  See the NOTICE file 
distributed with
+4* this work for additional information regarding copyright 
ownership.
+5* The ASF licenses this file to You under the Apache 
License, Version 2.0
+6* (the "License"); you may not use this file except in 
compliance with
+7* the License.  You may obtain a copy of the License 
at
+8*
+9*  http://www.apache.org/licenses/LICENSE-2."; 
target="alexandria_uri">http://www.apache.org/licenses/LICENSE-2.0
+10   *
+11   * Unless required by applicable law or agreed to in 
writing, software
+12   * distributed under the License is distributed on an "AS 
IS" BASIS,
+13   * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either 
express or implied.
+14   * See the License for the specific language governing 
permissions and
+15   * limitations under the License.
+16   */
+17  package 
org.apache.commons.math3.stat.descriptive.rank;
+18  
+19  import java.io.IOException;
+20  import java.util.ArrayList;
+21  import java.util.Arrays;
+22  import java.util.HashSet;
+23  import java.util.Iterator;
+24  import java.util.LinkedHashSet;
+25  import java.util.Set;
+26  
+27  import 
org.apache.commons.math3.distribution.LogNormalDistribution;
+28  import 
org.apache.commons.math3.distribution.NormalDistribution;
+29  import 
org.apache.commons.math3.distribution.RealDistribution;
+30  import 
org.apache.commons.math3.exception.MathIllegalArgumentException;
+31  import 
org.apache.commons.math3.exception.OutOfRangeException;
+32  import 
org.apache.commons.math3.random.RandomGenerator;
+33  import org.apache.commons.math3.random.Well19937c;
+34  import 
org.apache.commons.math3.stat.descriptive.StorelessUnivariateStatistic;
+35  import 
org.apache.commons.math3.stat.descriptive.StorelessUnivariateStatisticAbstractTest;
+36  import 
org.apache.commons.math3.stat.descriptive.UnivariateStatistic;
+37  import 
org.apache.commons.math3.stat.descriptive.rank.PSquarePercentile.PSquareMarkers;
+38  import org.apache.commons.math3.util.FastMath;
+39  import org.junit.Assert;
+40  import org.junit.Test;
+41  
+42  /**
+43   * Test cases for the {@link PSquarePercentile} 
class which naturally extends
+44   * {@link StorelessUnivariateStatisticAbstractTest}. 

+45   */
+46  public class 
PSquarePercentileTest
 extends
+47  StorelessUnivariateStatisticAbstractTest
 {
+48  
+49  protected double percentile5 = 8.2299d;
+50  protected double percentile95 = 16.72195;// 20.82d; this is approximation
+51  protected double tolerance = 10E-12;
+52  
+53  private final 
RandomGenerator randomGenerator = new 
Well19937c(1000);
+54  
+55  @Override
+56  public double 
getTolerance() {
+57  return 1.0e-2;// tolerance 
limit changed as this is an approximation
+58  // algorithm and also gets accurate after few tens of
+59  // samples
+60  }
+61  
+62  /**
+63   * Verifies that copied statistics remain equal 
to originals when
+64   * incremented the same way by making the copy 
after a majority of elements
+65   * are incremented
+66   */
+67  @Test
+68  public void 
testCopyConsistencyWithInitialMostElements() {
+69  
+70  
StorelessUnivariateStatistic master =
+71  
(StorelessUnivariateStatistic) getUnivariateStatistic();
+72  
+73  
StorelessUnivariateStatistic replica = null;
+74  
+75  // select a portion of testArray till 75 % of the length to 
load first
+76  long index = FastMath.round(0.75 * 
testArray.length);
+77  
+78  // Put first half in master and copy master to replica
+79  
master.incrementAll(testArray, 0, (int) 
index);
+80  replica = 
master.copy();
+81  
+82  // Check same
+83  
Assert.assertTrue(replica.equals(master));
+84  
Assert.assertTrue(master.equals(replica));
+85  
+86  // Now add second part to both and check again
+87  
master.incrementAll(testArray, (int) index,
+88  
(int) (testArray.length - index));
+89  
replica.incrementAll(testArray, (int) 
index,
+90  
(int) (



svn commit: r926176 [30/31] - in /websites/production/commons/content/proper/commons-math: apidocs/org/apache/commons/math3/analysis/interpolation/ apidocs/org/apache/commons/math3/analysis/interpolat


2014-10-18

Thread
luc

Added: 
websites/production/commons/content/proper/commons-math/xref/org/apache/commons/math3/stat/descriptive/rank/PSquarePercentile.html
==
--- 
websites/production/commons/content/proper/commons-math/xref/org/apache/commons/math3/stat/descriptive/rank/PSquarePercentile.html
 (added)
+++ 
websites/production/commons/content/proper/commons-math/xref/org/apache/commons/math3/stat/descriptive/rank/PSquarePercentile.html
 Sat Oct 18 20:10:38 2014
@@ -0,0 +1,1009 @@
+http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd";>
+http://www.w3.org/1999/xhtml"; xml:lang="en" lang="en">
+
+PSquarePercentile xref
+
+
+
+View
 Javadoc
+1   /*
+2* Licensed to the Apache Software Foundation (ASF) under 
one or more
+3* contributor license agreements.  See the NOTICE file 
distributed with
+4* this work for additional information regarding copyright 
ownership.
+5* The ASF licenses this file to You under the Apache 
License, Version 2.0
+6* (the "License"); you may not use this file except in 
compliance with
+7* the License.  You may obtain a copy of the License 
at
+8*
+9*  http://www.apache.org/licenses/LICENSE-2."; 
target="alexandria_uri">http://www.apache.org/licenses/LICENSE-2.0
+10   *
+11   * Unless required by applicable law or agreed to in 
writing, software
+12   * distributed under the License is distributed on an "AS 
IS" BASIS,
+13   * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either 
express or implied.
+14   * See the License for the specific language governing 
permissions and
+15   * limitations under the License.
+16   */
+17  package 
org.apache.commons.math3.stat.descriptive.rank;
+18  
+19  import java.io.IOException;
+20  import java.io.ObjectInputStream;
+21  import java.io.Serializable;
+22  import java.text.DecimalFormat;
+23  import java.util.ArrayList;
+24  import java.util.Arrays;
+25  import java.util.Collection;
+26  import java.util.Collections;
+27  import java.util.List;
+28  
+29  import 
org.apache.commons.math3.analysis.UnivariateFunction;
+30  import 
org.apache.commons.math3.analysis.interpolation.LinearInterpolator;
+31  import 
org.apache.commons.math3.analysis.interpolation.NevilleInterpolator;
+32  import 
org.apache.commons.math3.analysis.interpolation.UnivariateInterpolator;
+33  import 
org.apache.commons.math3.exception.InsufficientDataException;
+34  import 
org.apache.commons.math3.exception.OutOfRangeException;
+35  import 
org.apache.commons.math3.exception.util.LocalizedFormats;
+36  import 
org.apache.commons.math3.stat.descriptive.AbstractStorelessUnivariateStatistic;
+37  import 
org.apache.commons.math3.stat.descriptive.StorelessUnivariateStatistic;
+38  import org.apache.commons.math3.util.MathArrays;
+39  import org.apache.commons.math3.util.MathUtils;
+40  import org.apache.commons.math3.util.Precision;
+41  
+42  /**
+43   * A {@link StorelessUnivariateStatistic} estimating 
percentiles using the
+44   * P2";
 
target="alexandria_uri">http://www.cs.wustl.edu/~jain/papers/ftp/psqr.pdf>P2;
+45   * Algorithm as explained by Ra"; 
target="alexandria_uri">http://www.cse.wustl.edu/~jain/>Raj
+46   * Jain and Imrich Chlamtac in
+47   * P2";
 
target="alexandria_uri">http://www.cse.wustl.edu/~jain/papers/psqr.htm>P2;
 Algorithm
+48   * for Dynamic Calculation of Quantiles and 
Histogram Without Storing
+49   * Observations.
+50   * 

+51   * Note: This implementation is not synchronized and 
produces an approximate
+52   * result. For small samples, where data can be 
stored and processed in memory,
+53   * {@link Percentile} should be used.
+54   *
+55   */
+56  public class 
PSquarePercentile
 extends AbstractStorelessUnivariateStatistic
+57  implements StorelessUnivariateStatistic, 
Serializable {
+58  
+59  /**
+60   * The maximum array size used for psquare 
algorithm
+61   */
+62  private static final 
int PSQUARE_CONSTANT = 5;
+63  
+64  /**
+65   * A Default quantile needed in case if user 
prefers to use default no
+66   * argument constructor.
+67   */
+68  private static final 
double DEFAULT_QUANTILE_DESIRED = 50d;
+69  
+70  /**
+71   * Serial ID
+72   */
+73  private static final 
long serialVersionUID = 
2283912083175715479L;
+74  
+75  /**
+76   * A decimal formatter for print convenience
+77   */
+78  private static final 
DecimalFormat DECIMAL_FORMAT = new 
DecimalFormat(
+79  "00.00");
+80  
+81  /**
+82   * Initial list of 5 numbers corresponding to 5 
markers. NOTE:watch
+83   * out for the add methods that are 
overloaded
+84   */
+85  private final 
List initialFive = new 
FixedCapacityList



svn commit: r926176 [12/31] - in /websites/production/commons/content/proper/commons-math: apidocs/org/apache/commons/math3/analysis/interpolation/ apidocs/org/apache/commons/math3/analysis/interpolat


2014-10-18

Thread
luc

Added: 
websites/production/commons/content/proper/commons-math/apidocs/src-html/org/apache/commons/math3/stat/descriptive/rank/PSquarePercentile.html
==
--- 
websites/production/commons/content/proper/commons-math/apidocs/src-html/org/apache/commons/math3/stat/descriptive/rank/PSquarePercentile.html
 (added)
+++ 
websites/production/commons/content/proper/commons-math/apidocs/src-html/org/apache/commons/math3/stat/descriptive/rank/PSquarePercentile.html
 Sat Oct 18 20:10:38 2014
@@ -0,0 +1,1068 @@
+http://www.w3.org/TR/html4/loose.dtd";>
+
+
+Source code
+
+
+
+
+001/*
+002 * Licensed to the Apache Software 
Foundation (ASF) under one or more
+003 * contributor license agreements.  See 
the NOTICE file distributed with
+004 * this work for additional information 
regarding copyright ownership.
+005 * The ASF licenses this file to You 
under the Apache License, Version 2.0
+006 * (the "License"); you may not use this 
file except in compliance with
+007 * the License.  You may obtain a copy of 
the License at
+008 *
+009 *  
http://www.apache.org/licenses/LICENSE-2.0
+010 *
+011 * Unless required by applicable law or 
agreed to in writing, software
+012 * distributed under the License is 
distributed on an "AS IS" BASIS,
+013 * WITHOUT WARRANTIES OR CONDITIONS OF 
ANY KIND, either express or implied.
+014 * See the License for the specific 
language governing permissions and
+015 * limitations under the License.
+016 */
+017package 
org.apache.commons.math3.stat.descriptive.rank;
+018
+019import java.io.IOException;
+020import java.io.ObjectInputStream;
+021import java.io.Serializable;
+022import java.text.DecimalFormat;
+023import java.util.ArrayList;
+024import java.util.Arrays;
+025import java.util.Collection;
+026import java.util.Collections;
+027import java.util.List;
+028
+029import 
org.apache.commons.math3.analysis.UnivariateFunction;
+030import 
org.apache.commons.math3.analysis.interpolation.LinearInterpolator;
+031import 
org.apache.commons.math3.analysis.interpolation.NevilleInterpolator;
+032import 
org.apache.commons.math3.analysis.interpolation.UnivariateInterpolator;
+033import 
org.apache.commons.math3.exception.InsufficientDataException;
+034import 
org.apache.commons.math3.exception.OutOfRangeException;
+035import 
org.apache.commons.math3.exception.util.LocalizedFormats;
+036import 
org.apache.commons.math3.stat.descriptive.AbstractStorelessUnivariateStatistic;
+037import 
org.apache.commons.math3.stat.descriptive.StorelessUnivariateStatistic;
+038import 
org.apache.commons.math3.util.MathArrays;
+039import 
org.apache.commons.math3.util.MathUtils;
+040import 
org.apache.commons.math3.util.Precision;
+041
+042/**
+043 * A {@link StorelessUnivariateStatistic} 
estimating percentiles using the
+044 * 
P2;
+045 * Algorithm as explained by Raj
+046 * Jain and Imrich Chlamtac 
in
+047 * P2;
 Algorithm
+048 * for Dynamic Calculation of Quantiles 
and Histogram Without Storing
+049 * Observations.
+050 * 

+051 * Note: This implementation is not 
synchronized and produces an approximate
+052 * result. For small samples, where data 
can be stored and processed in memory,
+053 * {@link Percentile} should be 
used.
+054 *
+055 */
+056public class PSquarePercentile extends 
AbstractStorelessUnivariateStatistic
+057implements 
StorelessUnivariateStatistic, Serializable {
+058
+059/**
+060 * The maximum array size used for 
psquare algorithm
+061 */
+062private static final int 
PSQUARE_CONSTANT = 5;
+063
+064/**
+065 * A Default quantile needed in case 
if user prefers to use default no
+066 * argument constructor.
+067 */
+068private static final double 
DEFAULT_QUANTILE_DESIRED = 50d;
+069
+070/**
+071 * Serial ID
+072 */
+073private static final long 
serialVersionUID = 2283912083175715479L;
+074
+075/**
+076 * A decimal formatter for print 
convenience
+077 */
+078private static final DecimalFormat 
DECIMAL_FORMAT = new DecimalFormat(
+079"00.00");
+080
+081/**
+082 * Initial list of 5 numbers 
corresponding to 5 markers. NOTE:watch
+083 * out for the add methods that are 
overloaded
+084 */
+085private final List 
initialFive = new FixedCapacityList(
+086PSQUARE_CONSTANT);
+087
+088/**
+089 * The quantile needed should be in 
range of 0-1. The constructor
+090 * {@link #PSquarePercentile(double)} 
ensures that passed in percentile is
+091 * divided by 100.
+092 */
+093private final double quantile;
+094
+095/**
+096 * lastObservation is the last 
observation value/input sample. No need to
+097 * serialize
+098 */
+099private transient double



[2/4] git commit: MATH-1138 #comment BicubicSplineInterpolator Maintenance


2014-10-21

Thread
luc

MATH-1138 #comment BicubicSplineInterpolator Maintenance

Moved the new bi-cubic interpolator functions to new Piecewise* version
of the same files.  Restored the original bi-cubic functions and
restored the tricubic function to use the original functions as well


Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/31fae643
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/31fae643
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/31fae643

Branch: refs/heads/master
Commit: 31fae6431438e26d6b47b988164847048ceab314
Parents: e89a80d
Author: Hank Grabowski 
Authored: Mon Oct 20 21:31:39 2014 -0400
Committer: Luc Maisonobe 
Committed: Tue Oct 21 09:49:21 2014 +0200

--
 .../BicubicSplineInterpolatingFunction.java | 620 ---
 .../BicubicSplineInterpolator.java  | 141 +++-
 ...ewiseBicubicSplineInterpolatingFunction.java | 195 +
 .../PiecewiseBicubicSplineInterpolator.java |  64 ++
 ...hingPolynomialBicubicSplineInterpolator.java |   4 +-
 .../TricubicSplineInterpolator.java |  35 +-
 .../BicubicSplineInterpolatingFunctionTest.java | 746 ++-
 .../BicubicSplineInterpolatorTest.java  | 217 ++
 ...eBicubicSplineInterpolatingFunctionTest.java | 280 +++
 .../PiecewiseBicubicSplineInterpolatorTest.java | 277 +++
 .../TricubicSplineInterpolatorTest.java |   2 +-
 11 files changed, 2136 insertions(+), 445 deletions(-)
--


http://git-wip-us.apache.org/repos/asf/commons-math/blob/31fae643/src/main/java/org/apache/commons/math3/analysis/interpolation/BicubicSplineInterpolatingFunction.java
--
diff --git 
a/src/main/java/org/apache/commons/math3/analysis/interpolation/BicubicSplineInterpolatingFunction.java
 
b/src/main/java/org/apache/commons/math3/analysis/interpolation/BicubicSplineInterpolatingFunction.java
index c0ce3c5..079e9fc 100644
--- 
a/src/main/java/org/apache/commons/math3/analysis/interpolation/BicubicSplineInterpolatingFunction.java
+++ 
b/src/main/java/org/apache/commons/math3/analysis/interpolation/BicubicSplineInterpolatingFunction.java
@@ -18,76 +18,143 @@ package org.apache.commons.math3.analysis.interpolation;
 
 import java.util.Arrays;
 import org.apache.commons.math3.analysis.BivariateFunction;
-import org.apache.commons.math3.analysis.polynomials.PolynomialSplineFunction;
 import org.apache.commons.math3.exception.DimensionMismatchException;
-import org.apache.commons.math3.exception.InsufficientDataException;
 import org.apache.commons.math3.exception.NoDataException;
-import org.apache.commons.math3.exception.NullArgumentException;
 import org.apache.commons.math3.exception.OutOfRangeException;
 import org.apache.commons.math3.exception.NonMonotonicSequenceException;
 import org.apache.commons.math3.util.MathArrays;
 
 /**
- * Function that implements the http://www.paulinternet.nl/?page=bicubic";> bicubic spline
- * interpolation.
+ * Function that implements the
+ * http://en.wikipedia.org/wiki/Bicubic_interpolation";>
+ * bicubic spline interpolation.
  *
  * @since 2.1
  */
 public class BicubicSplineInterpolatingFunction
 implements BivariateFunction {
+/** Number of coefficients. */
+private static final int NUM_COEFF = 16;
+/**
+ * Matrix to compute the spline coefficients from the function values
+ * and function derivatives values
+ */
+private static final double[][] AINV = {
+{ 1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 },
+{ 0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0 },
+{ -3,3,0,0,-2,-1,0,0,0,0,0,0,0,0,0,0 },
+{ 2,-2,0,0,1,1,0,0,0,0,0,0,0,0,0,0 },
+{ 0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0 },
+{ 0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0 },
+{ 0,0,0,0,0,0,0,0,-3,3,0,0,-2,-1,0,0 },
+{ 0,0,0,0,0,0,0,0,2,-2,0,0,1,1,0,0 },
+{ -3,0,3,0,0,0,0,0,-2,0,-1,0,0,0,0,0 },
+{ 0,0,0,0,-3,0,3,0,0,0,0,0,-2,0,-1,0 },
+{ 9,-9,-9,9,6,3,-6,-3,6,-6,3,-3,4,2,2,1 },
+{ -6,6,6,-6,-3,-3,3,3,-4,4,-2,2,-2,-2,-1,-1 },
+{ 2,0,-2,0,0,0,0,0,1,0,1,0,0,0,0,0 },
+{ 0,0,0,0,2,0,-2,0,0,0,0,0,1,0,1,0 },
+{ -6,6,6,-6,-4,-2,4,2,-3,3,-3,3,-2,-1,-2,-1 },
+{ 4,-4,-4,4,2,2,-2,-2,2,-2,2,-2,1,1,1,1 }
+};
 
 /** Samples x-coordinates */
 private final double[] xval;
-
 /** Samples y-coordinates */
 private final double[] yval;
-
 /** Set of cubic splines patching the whole data grid */
-private final double[][] fval;
+private final BicubicSplineFunction[][] splines;
+/**
+ * Partial derivatives.
+ * The value of the first index determines the kind of derivatives:
+ * 0 = first partial derivatives wrt x
+ * 1 = first partial derivatives wrt y
+ 



[4/4] git commit: MATH-1138 #comment added deprecation and accuracy warnings


2014-10-21

Thread
luc

MATH-1138 #comment added deprecation and accuracy warnings


Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/79ae77fd
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/79ae77fd
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/79ae77fd

Branch: refs/heads/master
Commit: 79ae77fda8b987b01b2e49dd0ae84819778634dc
Parents: 7200c43
Author: Hank Grabowski 
Authored: Mon Oct 20 22:13:59 2014 -0400
Committer: Luc Maisonobe 
Committed: Tue Oct 21 09:50:05 2014 +0200

--
 .../math3/analysis/interpolation/BicubicSplineInterpolator.java   | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)
--


http://git-wip-us.apache.org/repos/asf/commons-math/blob/79ae77fd/src/main/java/org/apache/commons/math3/analysis/interpolation/BicubicSplineInterpolator.java
--
diff --git 
a/src/main/java/org/apache/commons/math3/analysis/interpolation/BicubicSplineInterpolator.java
 
b/src/main/java/org/apache/commons/math3/analysis/interpolation/BicubicSplineInterpolator.java
index bf48d0f..09acd07 100644
--- 
a/src/main/java/org/apache/commons/math3/analysis/interpolation/BicubicSplineInterpolator.java
+++ 
b/src/main/java/org/apache/commons/math3/analysis/interpolation/BicubicSplineInterpolator.java
@@ -25,7 +25,8 @@ import 
org.apache.commons.math3.exception.NumberIsTooSmallException;
 import org.apache.commons.math3.util.MathArrays;
 
 /**
- * Generates a bicubic interpolating function.
+ * Generates a bicubic interpolating function. Due to numerical accuracy 
issues this should not
+ * be used.
  *
  * @since 2.2
  * @deprecated as of 3.4 replaced by {@link 
org.apache.commons.math3.analysis.interpolation.PiecewiseBicubicSplineInterpolator}






[1/4] MATH-1138 #comment BicubicSplineInterpolator Maintenance


2014-10-21

Thread
luc

Repository: commons-math
Updated Branches:
  refs/heads/master e89a80dd5 -> 79ae77fda


http://git-wip-us.apache.org/repos/asf/commons-math/blob/31fae643/src/test/java/org/apache/commons/math3/analysis/interpolation/BicubicSplineInterpolatorTest.java
--
diff --git 
a/src/test/java/org/apache/commons/math3/analysis/interpolation/BicubicSplineInterpolatorTest.java
 
b/src/test/java/org/apache/commons/math3/analysis/interpolation/BicubicSplineInterpolatorTest.java
index 69d52a1..c4a56bb 100644
--- 
a/src/test/java/org/apache/commons/math3/analysis/interpolation/BicubicSplineInterpolatorTest.java
+++ 
b/src/test/java/org/apache/commons/math3/analysis/interpolation/BicubicSplineInterpolatorTest.java
@@ -17,10 +17,7 @@
 package org.apache.commons.math3.analysis.interpolation;
 
 import org.apache.commons.math3.exception.DimensionMismatchException;
-import org.apache.commons.math3.exception.InsufficientDataException;
 import org.apache.commons.math3.exception.MathIllegalArgumentException;
-import org.apache.commons.math3.exception.NonMonotonicSequenceException;
-import org.apache.commons.math3.exception.NullArgumentException;
 import org.apache.commons.math3.analysis.BivariateFunction;
 import org.apache.commons.math3.distribution.UniformRealDistribution;
 import org.apache.commons.math3.random.RandomGenerator;
@@ -30,131 +27,53 @@ import org.junit.Test;
 
 /**
  * Test case for the bicubic interpolator.
+ * 
  */
-public final class BicubicSplineInterpolatorTest
-{
+public final class BicubicSplineInterpolatorTest {
 /**
  * Test preconditions.
  */
 @Test
-public void testPreconditions()
-{
-double[] xval = new double[] { 3, 4, 5, 6.5, 7.5 };
-double[] yval = new double[] { -4, -3, -1, 2.5, 3.5 };
+public void testPreconditions() {
+double[] xval = new double[] {3, 4, 5, 6.5};
+double[] yval = new double[] {-4, -3, -1, 2.5};
 double[][] zval = new double[xval.length][yval.length];
 
-@SuppressWarnings( "unused" )
 BivariateGridInterpolator interpolator = new 
BicubicSplineInterpolator();
 
-try
-{
-interpolator.interpolate( null, yval, zval );
-Assert.fail( "Failed to detect x null pointer" );
-}
-catch ( NullArgumentException iae )
-{
-// Expected.
-}
-
-try
-{
-interpolator.interpolate( xval, null, zval );
-Assert.fail( "Failed to detect y null pointer" );
-}
-catch ( NullArgumentException iae )
-{
-// Expected.
-}
-
-try
-{
-interpolator.interpolate( xval, yval, null );
-Assert.fail( "Failed to detect z null pointer" );
-}
-catch ( NullArgumentException iae )
-{
-// Expected.
-}
-
-try
-{
-double xval1[] = { 0.0, 1.0, 2.0, 3.0 };
-interpolator.interpolate( xval1, yval, zval );
-Assert.fail( "Failed to detect insufficient x data" );
-}
-catch ( InsufficientDataException iae )
-{
-// Expected.
-}
-
-try
-{
-double yval1[] = { 0.0, 1.0, 2.0, 3.0 };
-interpolator.interpolate( xval, yval1, zval );
-Assert.fail( "Failed to detect insufficient y data" );
-}
-catch ( InsufficientDataException iae )
-{
-// Expected.
-}
-
-try
-{
-double zval1[][] = new double[4][4];
-interpolator.interpolate( xval, yval, zval1 );
-Assert.fail( "Failed to detect insufficient z data" );
-}
-catch ( InsufficientDataException iae )
-{
-// Expected.
-}
-
-try
-{
-double xval1[] = { 0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0 };
-interpolator.interpolate( xval1, yval, zval );
-Assert.fail( "Failed to detect data set array with different 
sizes." );
-}
-catch ( DimensionMismatchException iae )
-{
-// Expected.
-}
+@SuppressWarnings("unused")
+BivariateFunction p = interpolator.interpolate(xval, yval, zval);
 
-try
-{
-double yval1[] = { 0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0 };
-interpolator.interpolate( xval, yval1, zval );
-Assert.fail( "Failed to detect data set array with different 
sizes." );
-}
-catch ( DimensionMismatchException iae )
-{
-// Expected.
+double[] wxval = new double[] {3, 2, 5, 6.5};
+try {
+p = interpolator.interpolate(wxval, yval, zval);
+Assert.fail("an exception should have been thrown");
+} catch (MathIllegalArgumentException e) {
+// Expected
+}
+
+double[] wyval 



[3/4] git commit: MATH-1138 #comment added deprecation and accuracy warnings


2014-10-21

Thread
luc

MATH-1138 #comment added deprecation and accuracy warnings


Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/7200c43d
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/7200c43d
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/7200c43d

Branch: refs/heads/master
Commit: 7200c43dea3dbfbd9d38b937c44b6e71744b05c5
Parents: 31fae64
Author: Hank Grabowski 
Authored: Mon Oct 20 21:40:02 2014 -0400
Committer: Luc Maisonobe 
Committed: Tue Oct 21 09:49:59 2014 +0200

--
 .../interpolation/BicubicSplineInterpolatingFunction.java  | 6 +-
 .../analysis/interpolation/BicubicSplineInterpolator.java  | 2 ++
 2 files changed, 7 insertions(+), 1 deletion(-)
--


http://git-wip-us.apache.org/repos/asf/commons-math/blob/7200c43d/src/main/java/org/apache/commons/math3/analysis/interpolation/BicubicSplineInterpolatingFunction.java
--
diff --git 
a/src/main/java/org/apache/commons/math3/analysis/interpolation/BicubicSplineInterpolatingFunction.java
 
b/src/main/java/org/apache/commons/math3/analysis/interpolation/BicubicSplineInterpolatingFunction.java
index 079e9fc..522c2a5 100644
--- 
a/src/main/java/org/apache/commons/math3/analysis/interpolation/BicubicSplineInterpolatingFunction.java
+++ 
b/src/main/java/org/apache/commons/math3/analysis/interpolation/BicubicSplineInterpolatingFunction.java
@@ -27,10 +27,14 @@ import org.apache.commons.math3.util.MathArrays;
 /**
  * Function that implements the
  * http://en.wikipedia.org/wiki/Bicubic_interpolation";>
- * bicubic spline interpolation.
+ * bicubic spline interpolation. Due to numerical accuracy issues this 
should not
+ * be used.
  *
  * @since 2.1
+ * @deprecated as of 3.4 replaced by
+ * {@link 
org.apache.commons.math3.analysis.interpolation.PiecewiseBicubicSplineInterpolatingFunction}
  */
+@Deprecated
 public class BicubicSplineInterpolatingFunction
 implements BivariateFunction {
 /** Number of coefficients. */

http://git-wip-us.apache.org/repos/asf/commons-math/blob/7200c43d/src/main/java/org/apache/commons/math3/analysis/interpolation/BicubicSplineInterpolator.java
--
diff --git 
a/src/main/java/org/apache/commons/math3/analysis/interpolation/BicubicSplineInterpolator.java
 
b/src/main/java/org/apache/commons/math3/analysis/interpolation/BicubicSplineInterpolator.java
index 5e2c92f..bf48d0f 100644
--- 
a/src/main/java/org/apache/commons/math3/analysis/interpolation/BicubicSplineInterpolator.java
+++ 
b/src/main/java/org/apache/commons/math3/analysis/interpolation/BicubicSplineInterpolator.java
@@ -28,7 +28,9 @@ import org.apache.commons.math3.util.MathArrays;
  * Generates a bicubic interpolating function.
  *
  * @since 2.2
+ * @deprecated as of 3.4 replaced by {@link 
org.apache.commons.math3.analysis.interpolation.PiecewiseBicubicSplineInterpolator}
  */
+@Deprecated
 public class BicubicSplineInterpolator
 implements BivariateGridInterpolator {
 /** Whether to initialize internal data used to compute the analytical






git commit: Provide access to state derivatives in ContinuousOutputModel.


2014-10-22

Thread
luc

Repository: commons-math
Updated Branches:
  refs/heads/master 79ae77fda -> 25aa4bd36


Provide access to state derivatives in ContinuousOutputModel.

JIRA: MATH-1160

Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/25aa4bd3
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/25aa4bd3
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/25aa4bd3

Branch: refs/heads/master
Commit: 25aa4bd3665d8b265f03fa2b3e7ab6ee68256367
Parents: 79ae77f
Author: Luc Maisonobe 
Authored: Wed Oct 22 17:34:29 2014 +0200
Committer: Luc Maisonobe 
Committed: Wed Oct 22 17:34:29 2014 +0200

--
 src/changes/changes.xml |  3 +++
 .../math3/ode/ContinuousOutputModel.java| 14 +
 .../math3/ode/ContinuousOutputModelTest.java| 21 +---
 3 files changed, 31 insertions(+), 7 deletions(-)
--


http://git-wip-us.apache.org/repos/asf/commons-math/blob/25aa4bd3/src/changes/changes.xml
--
diff --git a/src/changes/changes.xml b/src/changes/changes.xml
index bb5c525..9350d6b 100644
--- a/src/changes/changes.xml
+++ b/src/changes/changes.xml
@@ -73,6 +73,9 @@ Users are encouraged to upgrade to this version as this 
release not
   2. A few methods in the FastMath class are in fact slower that their
   counterpart in either Math or StrictMath (cf. MATH-740 and MATH-901).
 ">
+  
+Provide access to state derivatives in ContinuousOutputModel.
+  
   
 Fixed bicubic spline interpolator, using Akima splines.
   

http://git-wip-us.apache.org/repos/asf/commons-math/blob/25aa4bd3/src/main/java/org/apache/commons/math3/ode/ContinuousOutputModel.java
--
diff --git 
a/src/main/java/org/apache/commons/math3/ode/ContinuousOutputModel.java 
b/src/main/java/org/apache/commons/math3/ode/ContinuousOutputModel.java
index 599eab9..d9f6192 100644
--- a/src/main/java/org/apache/commons/math3/ode/ContinuousOutputModel.java
+++ b/src/main/java/org/apache/commons/math3/ode/ContinuousOutputModel.java
@@ -332,12 +332,25 @@ public class ContinuousOutputModel
* Get the state vector of the interpolated point.
* @return state vector at time {@link #getInterpolatedTime}
* @exception MaxCountExceededException if the number of functions 
evaluations is exceeded
+   * @see #getInterpolatedDerivatives()
* @see #getInterpolatedSecondaryState(int)
*/
   public double[] getInterpolatedState() throws MaxCountExceededException {
 return steps.get(index).getInterpolatedState();
   }
 
+  /**
+   * Get the derivatives of the state vector of the interpolated point.
+   * @return derivatives of the state vector at time {@link 
#getInterpolatedTime}
+   * @exception MaxCountExceededException if the number of functions 
evaluations is exceeded
+   * @see #getInterpolatedState()
+   * @see #getInterpolatedSecondaryState(int)
+   * @since 3.4
+   */
+  public double[] getInterpolatedDerivatives() throws 
MaxCountExceededException {
+return steps.get(index).getInterpolatedDerivatives();
+  }
+
   /** Get the interpolated secondary state corresponding to the secondary 
equations.
* @param secondaryStateIndex index of the secondary set, as returned by 
{@link
* org.apache.commons.math3.ode.ExpandableStatefulODE#addSecondaryEquations(
@@ -345,6 +358,7 @@ public class ContinuousOutputModel
* ExpandableStatefulODE.addSecondaryEquations(SecondaryEquations)}
* @return interpolated secondary state at the current interpolation date
* @see #getInterpolatedState()
+   * @see #getInterpolatedDerivatives()
* @since 3.2
* @exception MaxCountExceededException if the number of functions 
evaluations is exceeded
*/

http://git-wip-us.apache.org/repos/asf/commons-math/blob/25aa4bd3/src/test/java/org/apache/commons/math3/ode/ContinuousOutputModelTest.java
--
diff --git 
a/src/test/java/org/apache/commons/math3/ode/ContinuousOutputModelTest.java 
b/src/test/java/org/apache/commons/math3/ode/ContinuousOutputModelTest.java
index 2f4053d..3a098ba 100644
--- a/src/test/java/org/apache/commons/math3/ode/ContinuousOutputModelTest.java
+++ b/src/test/java/org/apache/commons/math3/ode/ContinuousOutputModelTest.java
@@ -63,22 +63,29 @@ public class ContinuousOutputModelTest {
 pb.getFinalTime(), new double[pb.getDimension()]);
 
 Random random = new Random(347588535632l);
-double maxError = 0.0;
+double maxError= 0.0;
+double maxErrorDot = 0.0;
 for (int i = 0; i < 1000; ++i) {
   double r = random.nextDouble();
   double time = r * pb.getInitialTime() + (1.0 - r) * p



git commit: Improved javadoc for ContinuousOutputModel and StepInterpolator.


2014-10-22

Thread
luc

Repository: commons-math
Updated Branches:
  refs/heads/master 25aa4bd36 -> f8e6bc8ec


Improved javadoc for ContinuousOutputModel and StepInterpolator.

The fact the arrays are reused is stated more clearly, as weel as the
fact changing the time changes the array content.

Yes, it is a bad design, we should change it in the next major version
to allocate fresh new arrays :-(

Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/f8e6bc8e
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/f8e6bc8e
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/f8e6bc8e

Branch: refs/heads/master
Commit: f8e6bc8ec72fd02cde8c705ca17609c76a07d3b8
Parents: 25aa4bd
Author: Luc Maisonobe 
Authored: Wed Oct 22 21:36:40 2014 +0200
Committer: Luc Maisonobe 
Committed: Wed Oct 22 21:36:40 2014 +0200

--
 .../math3/ode/ContinuousOutputModel.java| 32 +---
 .../math3/ode/sampling/StepInterpolator.java| 28 +
 2 files changed, 49 insertions(+), 11 deletions(-)
--


http://git-wip-us.apache.org/repos/asf/commons-math/blob/f8e6bc8e/src/main/java/org/apache/commons/math3/ode/ContinuousOutputModel.java
--
diff --git 
a/src/main/java/org/apache/commons/math3/ode/ContinuousOutputModel.java 
b/src/main/java/org/apache/commons/math3/ode/ContinuousOutputModel.java
index d9f6192..6d324d1 100644
--- a/src/main/java/org/apache/commons/math3/ode/ContinuousOutputModel.java
+++ b/src/main/java/org/apache/commons/math3/ode/ContinuousOutputModel.java
@@ -233,12 +233,19 @@ public class ContinuousOutputModel
* integration is over because some internal variables are set only
* once the last step has been handled.
* Setting the time outside of the integration interval is now
-   * allowed (it was not allowed up to version 5.9 of Mantissa), but
-   * should be used with care since the accuracy of the interpolator
-   * will probably be very poor far from this interval. This allowance
-   * has been added to simplify implementation of search algorithms
-   * near the interval endpoints.
+   * allowed, but should be used with care since the accuracy of the
+   * interpolator will probably be very poor far from this interval.
+   * This allowance has been added to simplify implementation of search
+   * algorithms near the interval endpoints.
+   * Note that each time this method is called, the internal arrays
+   * returned in {@link #getInterpolatedState()}, {@link
+   * #getInterpolatedDerivatives()} and {@link 
#getInterpolatedSecondaryState(int)}
+   * will be overwritten. So if their content must be preserved
+   * across several calls, user must copy them.
* @param time time of the interpolated point
+   * @see #getInterpolatedState()
+   * @see #getInterpolatedDerivatives()
+   * @see #getInterpolatedSecondaryState(int)
*/
   public void setInterpolatedTime(final double time) {
 
@@ -330,8 +337,13 @@ public class ContinuousOutputModel
 
   /**
* Get the state vector of the interpolated point.
+   * The returned vector is a reference to a reused array, so
+   * it should not be modified and it should be copied if it needs
+   * to be preserved across several calls to the associated
+   * {@link #setInterpolatedTime(double)} method.
* @return state vector at time {@link #getInterpolatedTime}
* @exception MaxCountExceededException if the number of functions 
evaluations is exceeded
+   * @see #setInterpolatedTime(double)
* @see #getInterpolatedDerivatives()
* @see #getInterpolatedSecondaryState(int)
*/
@@ -341,8 +353,13 @@ public class ContinuousOutputModel
 
   /**
* Get the derivatives of the state vector of the interpolated point.
+   * The returned vector is a reference to a reused array, so
+   * it should not be modified and it should be copied if it needs
+   * to be preserved across several calls to the associated
+   * {@link #setInterpolatedTime(double)} method.
* @return derivatives of the state vector at time {@link 
#getInterpolatedTime}
* @exception MaxCountExceededException if the number of functions 
evaluations is exceeded
+   * @see #setInterpolatedTime(double)
* @see #getInterpolatedState()
* @see #getInterpolatedSecondaryState(int)
* @since 3.4
@@ -352,11 +369,16 @@ public class ContinuousOutputModel
   }
 
   /** Get the interpolated secondary state corresponding to the secondary 
equations.
+   * The returned vector is a reference to a reused array, so
+   * it should not be modified and it should be copied if it needs
+   * to be preserved across several calls to the associated
+   * {@link #setInterpolatedTime(double)} method.
* @param secondaryStateIndex index of the secondary set, as returned by 
{@l



git commit: Added getInterpolatedSecondaryDerivatives to ContinuousOutputModel.


2014-10-22

Thread
luc

Repository: commons-math
Updated Branches:
  refs/heads/master f8e6bc8ec -> 45ae5c7e4


Added getInterpolatedSecondaryDerivatives to ContinuousOutputModel.

This method is a close relative to getInterpolatedDerivatives, but is
associated with the secondary state.

JIRA: MATH-1160

Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/45ae5c7e
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/45ae5c7e
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/45ae5c7e

Branch: refs/heads/master
Commit: 45ae5c7e42b07ff24e2385de57f70e9484a46ae3
Parents: f8e6bc8
Author: Luc Maisonobe 
Authored: Wed Oct 22 21:40:32 2014 +0200
Committer: Luc Maisonobe 
Committed: Wed Oct 22 21:40:32 2014 +0200

--
 .../math3/ode/ContinuousOutputModel.java| 25 
 1 file changed, 25 insertions(+)
--


http://git-wip-us.apache.org/repos/asf/commons-math/blob/45ae5c7e/src/main/java/org/apache/commons/math3/ode/ContinuousOutputModel.java
--
diff --git 
a/src/main/java/org/apache/commons/math3/ode/ContinuousOutputModel.java 
b/src/main/java/org/apache/commons/math3/ode/ContinuousOutputModel.java
index 6d324d1..75e4979 100644
--- a/src/main/java/org/apache/commons/math3/ode/ContinuousOutputModel.java
+++ b/src/main/java/org/apache/commons/math3/ode/ContinuousOutputModel.java
@@ -346,6 +346,7 @@ public class ContinuousOutputModel
* @see #setInterpolatedTime(double)
* @see #getInterpolatedDerivatives()
* @see #getInterpolatedSecondaryState(int)
+   * @see #getInterpolatedSecondaryDerivatives(int)
*/
   public double[] getInterpolatedState() throws MaxCountExceededException {
 return steps.get(index).getInterpolatedState();
@@ -362,6 +363,7 @@ public class ContinuousOutputModel
* @see #setInterpolatedTime(double)
* @see #getInterpolatedState()
* @see #getInterpolatedSecondaryState(int)
+   * @see #getInterpolatedSecondaryDerivatives(int)
* @since 3.4
*/
   public double[] getInterpolatedDerivatives() throws 
MaxCountExceededException {
@@ -381,6 +383,7 @@ public class ContinuousOutputModel
* @see #setInterpolatedTime(double)
* @see #getInterpolatedState()
* @see #getInterpolatedDerivatives()
+   * @see #getInterpolatedSecondaryDerivatives(int)
* @since 3.2
* @exception MaxCountExceededException if the number of functions 
evaluations is exceeded
*/
@@ -389,6 +392,28 @@ public class ContinuousOutputModel
 return steps.get(index).getInterpolatedSecondaryState(secondaryStateIndex);
   }
 
+  /** Get the interpolated secondary derivatives corresponding to the 
secondary equations.
+   * The returned vector is a reference to a reused array, so
+   * it should not be modified and it should be copied if it needs
+   * to be preserved across several calls to the associated
+   * {@link #setInterpolatedTime(double)} method.
+   * @param secondaryStateIndex index of the secondary set, as returned by 
{@link
+   * org.apache.commons.math3.ode.ExpandableStatefulODE#addSecondaryEquations(
+   * org.apache.commons.math3.ode.SecondaryEquations)
+   * ExpandableStatefulODE.addSecondaryEquations(SecondaryEquations)}
+   * @return interpolated secondary derivatives at the current interpolation 
date
+   * @see #setInterpolatedTime(double)
+   * @see #getInterpolatedState()
+   * @see #getInterpolatedDerivatives()
+   * @see #getInterpolatedSecondaryState(int)
+   * @since 3.4
+   * @exception MaxCountExceededException if the number of functions 
evaluations is exceeded
+   */
+  public double[] getInterpolatedSecondaryDerivatives(final int 
secondaryStateIndex)
+throws MaxCountExceededException {
+return 
steps.get(index).getInterpolatedSecondaryDerivatives(secondaryStateIndex);
+  }
+
   /** Compare a step interval and a double.
* @param time point to locate
* @param interval step interval






git commit: Fixed checkstyle warnings.


2014-11-03

Thread
luc

Repository: commons-math
Updated Branches:
  refs/heads/master ed565027c -> cd28a018f


Fixed checkstyle warnings.

Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/cd28a018
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/cd28a018
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/cd28a018

Branch: refs/heads/master
Commit: cd28a018fb327d38a30c502bedca66cffb26f271
Parents: ed56502
Author: Luc Maisonobe 
Authored: Mon Nov 3 21:16:08 2014 +0100
Committer: Luc Maisonobe 
Committed: Mon Nov 3 21:16:08 2014 +0100

--
 .../commons/math3/fitting/leastsquares/LeastSquaresFactory.java   | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)
--


http://git-wip-us.apache.org/repos/asf/commons-math/blob/cd28a018/src/main/java/org/apache/commons/math3/fitting/leastsquares/LeastSquaresFactory.java
--
diff --git 
a/src/main/java/org/apache/commons/math3/fitting/leastsquares/LeastSquaresFactory.java
 
b/src/main/java/org/apache/commons/math3/fitting/leastsquares/LeastSquaresFactory.java
index 1a92ac9..aa3be8e 100644
--- 
a/src/main/java/org/apache/commons/math3/fitting/leastsquares/LeastSquaresFactory.java
+++ 
b/src/main/java/org/apache/commons/math3/fitting/leastsquares/LeastSquaresFactory.java
@@ -51,6 +51,7 @@ public class LeastSquaresFactory {
  * @param model  the model function. Produces the computed values.
  * @param observed   the observed (target) values
  * @param start  the initial guess.
+ * @param weight the weight matrix
  * @param checkerconvergence checker
  * @param maxEvaluations the maximum number of times to evaluate the model
  * @param maxIterations  the maximum number to times to iterate in the 
algorithm
@@ -74,7 +75,7 @@ public class LeastSquaresFactory {
observed,
start,
checker,
-   
maxEvaluations, 
+   
maxEvaluations,

maxIterations,

lazyEvaluation,

paramValidator);






[math] Fixed a problem with vanishing sub-hyperplanes during BSP tree merging.


2014-11-23

Thread
luc

Repository: commons-math
Updated Branches:
  refs/heads/master 8aec465b4 -> 046e3a2f5


Fixed a problem with vanishing sub-hyperplanes during BSP tree merging.

Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/046e3a2f
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/046e3a2f
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/046e3a2f

Branch: refs/heads/master
Commit: 046e3a2f58decdc3eb9f69e14fc0f5c3a9e6b4c3
Parents: 8aec465
Author: Luc Maisonobe 
Authored: Sun Nov 23 21:32:06 2014 +0100
Committer: Luc Maisonobe 
Committed: Sun Nov 23 21:46:22 2014 +0100

--
 src/changes/changes.xml |   3 +
 .../geometry/euclidean/twod/PolygonsSet.java|   3 +-
 .../math3/geometry/partitioning/BSPTree.java| 109 ---
 .../geometry/partitioning/RegionFactory.java|  47 ++--
 .../euclidean/twod/PolygonsSetTest.java |  19 
 5 files changed, 155 insertions(+), 26 deletions(-)
--


http://git-wip-us.apache.org/repos/asf/commons-math/blob/046e3a2f/src/changes/changes.xml
--
diff --git a/src/changes/changes.xml b/src/changes/changes.xml
index 5377621..c8f0afd 100644
--- a/src/changes/changes.xml
+++ b/src/changes/changes.xml
@@ -73,6 +73,9 @@ Users are encouraged to upgrade to this version as this 
release not
   2. A few methods in the FastMath class are in fact slower that their
   counterpart in either Math or StrictMath (cf. MATH-740 and MATH-901).
 ">
+  
+Fixed a problem with vanishing cut sub-hyperplanes during BSP tree 
merging.
+  
   
 "o.a.c.m.stat.regression.OLSMultipleLinearRegression": Use threshold
 when performing "QRDecomposition".

http://git-wip-us.apache.org/repos/asf/commons-math/blob/046e3a2f/src/main/java/org/apache/commons/math3/geometry/euclidean/twod/PolygonsSet.java
--
diff --git 
a/src/main/java/org/apache/commons/math3/geometry/euclidean/twod/PolygonsSet.java
 
b/src/main/java/org/apache/commons/math3/geometry/euclidean/twod/PolygonsSet.java
index 99ab841..fe7c463 100644
--- 
a/src/main/java/org/apache/commons/math3/geometry/euclidean/twod/PolygonsSet.java
+++ 
b/src/main/java/org/apache/commons/math3/geometry/euclidean/twod/PolygonsSet.java
@@ -710,7 +710,8 @@ public class PolygonsSet extends 
AbstractRegion {
 int i = 0;
 
 for (final List loop : loops) {
-if (loop.size() < 2) {
+if (loop.size() < 2 ||
+(loop.size() == 2 && loop.get(0).getStart() == null && 
loop.get(1).getEnd() == null)) {
 // single infinite line
 final Line line = loop.get(0).getLine();
 vertices[i++] = new Vector2D[] {

http://git-wip-us.apache.org/repos/asf/commons-math/blob/046e3a2f/src/main/java/org/apache/commons/math3/geometry/partitioning/BSPTree.java
--
diff --git 
a/src/main/java/org/apache/commons/math3/geometry/partitioning/BSPTree.java 
b/src/main/java/org/apache/commons/math3/geometry/partitioning/BSPTree.java
index 8f32783..b059904 100644
--- a/src/main/java/org/apache/commons/math3/geometry/partitioning/BSPTree.java
+++ b/src/main/java/org/apache/commons/math3/geometry/partitioning/BSPTree.java
@@ -465,8 +465,7 @@ public class BSPTree {
 minus.merge(merged.minus, leafMerger, merged, false);
 merged.condense();
 if (merged.cut != null) {
-merged.cut =
-
merged.fitToCell(merged.cut.getHyperplane().wholeHyperplane());
+merged.cut = 
merged.fitToCell(merged.cut.getHyperplane().wholeHyperplane());
 }
 
 return merged;
@@ -526,6 +525,27 @@ public class BSPTree {
 
 }
 
+/** This interface handles the corner cases when an internal node cut 
sub-hyperplane vanishes.
+ * 
+ * Such cases happens for example when a cut sub-hyperplane is inserted 
into
+ * another tree (during a merge operation), and is split in several parts,
+ * some of which becomes smaller than the tolerance. The corresponding node
+ * as then no cut sub-hyperplane anymore, but does have children. This 
interface
+ * specifies how to handle this situation.
+ * setting
+ * 
+ * @since 3.4
+ */
+public interface VanishingCutHandler {
+
+/** Fix a node with both vanished cut and children.
+ * @param node node to fix
+ * @return fixed node
+ */
+BSPTree fixNode(BSPTree node);
+
+}
+
  



[math] Reactivated method commented out during development.


2014-11-23

Thread
luc

Repository: commons-math
Updated Branches:
  refs/heads/master 046e3a2f5 -> 0802df0f7


Reactivated method commented out during development.

The method has been deprecated and replaced by a new method. It is not
used at all in the library, but is public so should be preserved.

Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/0802df0f
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/0802df0f
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/0802df0f

Branch: refs/heads/master
Commit: 0802df0f7376ca7aaffa7a23b2cc1f2c4c0c8aa9
Parents: 046e3a2
Author: Luc Maisonobe 
Authored: Sun Nov 23 21:51:10 2014 +0100
Committer: Luc Maisonobe 
Committed: Sun Nov 23 21:51:10 2014 +0100

--
 .../math3/geometry/partitioning/BSPTree.java| 42 ++--
 1 file changed, 22 insertions(+), 20 deletions(-)
--


http://git-wip-us.apache.org/repos/asf/commons-math/blob/0802df0f/src/main/java/org/apache/commons/math3/geometry/partitioning/BSPTree.java
--
diff --git 
a/src/main/java/org/apache/commons/math3/geometry/partitioning/BSPTree.java 
b/src/main/java/org/apache/commons/math3/geometry/partitioning/BSPTree.java
index b059904..26ae45f 100644
--- a/src/main/java/org/apache/commons/math3/geometry/partitioning/BSPTree.java
+++ b/src/main/java/org/apache/commons/math3/geometry/partitioning/BSPTree.java
@@ -19,7 +19,9 @@ package org.apache.commons.math3.geometry.partitioning;
 import java.util.ArrayList;
 import java.util.List;
 
+import org.apache.commons.math3.exception.MathIllegalStateException;
 import org.apache.commons.math3.exception.MathInternalError;
+import org.apache.commons.math3.exception.util.LocalizedFormats;
 import org.apache.commons.math3.geometry.Point;
 import org.apache.commons.math3.geometry.Space;
 import org.apache.commons.math3.geometry.Vector;
@@ -631,26 +633,26 @@ public class BSPTree {
 
 }
 
-///** Insert the instance into another tree.
-// * The instance itself is modified so its former parent should
-// * not be used anymore.
-// * @param parentTree parent tree to connect to (may be null)
-// * @param isPlusChild if true and if parentTree is not null, the
-// * resulting tree should be the plus child of its parent, ignored if
-// * parentTree is null
-// * @see LeafMerger
-// * @deprecated as of 3.4, replaced with {@link #insertInTree(BSPTree, 
boolean, VanishingCutHandler)}
-// */
-//@Deprecated
-//public void insertInTree(final BSPTree parentTree, final boolean 
isPlusChild) {
-//insertInTree(parentTree, isPlusChild, new VanishingCutHandler() {
-///** {@inheritDoc} */
-//public BSPTree fixNode(BSPTree node) {
-//// the cut should not be null
-//throw new 
MathIllegalStateException(LocalizedFormats.NULL_NOT_ALLOWED);
-//}
-//});
-//}
+/** Insert the instance into another tree.
+ * The instance itself is modified so its former parent should
+ * not be used anymore.
+ * @param parentTree parent tree to connect to (may be null)
+ * @param isPlusChild if true and if parentTree is not null, the
+ * resulting tree should be the plus child of its parent, ignored if
+ * parentTree is null
+ * @see LeafMerger
+ * @deprecated as of 3.4, replaced with {@link #insertInTree(BSPTree, 
boolean, VanishingCutHandler)}
+ */
+@Deprecated
+public void insertInTree(final BSPTree parentTree, final boolean 
isPlusChild) {
+insertInTree(parentTree, isPlusChild, new VanishingCutHandler() {
+/** {@inheritDoc} */
+public BSPTree fixNode(BSPTree node) {
+// the cut should not be null
+throw new 
MathIllegalStateException(LocalizedFormats.NULL_NOT_ALLOWED);
+}
+});
+}
 
 /** Insert the instance into another tree.
  * The instance itself is modified so its former parent should






[7/8] [math] Fixed a problem with too thin polygons considered to have infinite size.


2014-12-02

Thread
luc

Fixed a problem with too thin polygons considered to have infinite size.


Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/e6aae3a8
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/e6aae3a8
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/e6aae3a8

Branch: refs/heads/master
Commit: e6aae3a8bffb981b8dce19642cc1ab831a428cae
Parents: 893ef53
Author: Luc Maisonobe 
Authored: Tue Dec 2 22:09:06 2014 +0100
Committer: Luc Maisonobe 
Committed: Tue Dec 2 22:09:06 2014 +0100

--
 src/changes/changes.xml |   3 +
 .../geometry/euclidean/twod/PolygonsSet.java| 414 +--
 .../euclidean/twod/PolygonsSetTest.java |  60 +--
 3 files changed, 330 insertions(+), 147 deletions(-)
--


http://git-wip-us.apache.org/repos/asf/commons-math/blob/e6aae3a8/src/changes/changes.xml
--
diff --git a/src/changes/changes.xml b/src/changes/changes.xml
index 46ad704..a4b462c 100644
--- a/src/changes/changes.xml
+++ b/src/changes/changes.xml
@@ -73,6 +73,9 @@ Users are encouraged to upgrade to this version as this 
release not
   2. A few methods in the FastMath class are in fact slower that their
   counterpart in either Math or StrictMath (cf. MATH-740 and MATH-901).
 ">
+  
+Fixed a problem with too thin polygons considered to have infinite 
size.
+  
   
 Boundary attributes in regions now provides the BSP tree nodes that
 were used to split the sub-hyperplane froming the boundary part of the 
facet. 

http://git-wip-us.apache.org/repos/asf/commons-math/blob/e6aae3a8/src/main/java/org/apache/commons/math3/geometry/euclidean/twod/PolygonsSet.java
--
diff --git 
a/src/main/java/org/apache/commons/math3/geometry/euclidean/twod/PolygonsSet.java
 
b/src/main/java/org/apache/commons/math3/geometry/euclidean/twod/PolygonsSet.java
index 532d6a0..8361831 100644
--- 
a/src/main/java/org/apache/commons/math3/geometry/euclidean/twod/PolygonsSet.java
+++ 
b/src/main/java/org/apache/commons/math3/geometry/euclidean/twod/PolygonsSet.java
@@ -20,7 +20,6 @@ import java.util.ArrayList;
 import java.util.Collection;
 import java.util.List;
 
-import org.apache.commons.math3.exception.MathInternalError;
 import org.apache.commons.math3.geometry.Point;
 import org.apache.commons.math3.geometry.euclidean.oned.Euclidean1D;
 import org.apache.commons.math3.geometry.euclidean.oned.Interval;
@@ -31,10 +30,9 @@ import 
org.apache.commons.math3.geometry.partitioning.AbstractSubHyperplane;
 import org.apache.commons.math3.geometry.partitioning.BSPTree;
 import org.apache.commons.math3.geometry.partitioning.BSPTreeVisitor;
 import org.apache.commons.math3.geometry.partitioning.BoundaryAttribute;
+import org.apache.commons.math3.geometry.partitioning.Hyperplane;
 import org.apache.commons.math3.geometry.partitioning.Side;
 import org.apache.commons.math3.geometry.partitioning.SubHyperplane;
-import org.apache.commons.math3.geometry.partitioning.utilities.AVLTree;
-import org.apache.commons.math3.geometry.partitioning.utilities.OrderedTuple;
 import org.apache.commons.math3.util.FastMath;
 
 /** This class represents a 2D region: a set of polygons.
@@ -689,19 +687,34 @@ public class PolygonsSet extends 
AbstractRegion {
 vertices = new Vector2D[0][];
 } else {
 
-// sort the segments according to their start point
-final SegmentsBuilder visitor = new SegmentsBuilder();
+// build the unconnected segments
+final SegmentsBuilder visitor = new 
SegmentsBuilder(getTolerance());
 getTree(true).visit(visitor);
-final AVLTree sorted = visitor.getSorted();
-
-// identify the loops, starting from the open ones
-// (their start segments are naturally at the sorted set 
beginning)
-final ArrayList> loops = new 
ArrayList>();
-while (!sorted.isEmpty()) {
-final AVLTree.Node node = 
sorted.getSmallest();
-final List loop = followLoop(node, 
sorted);
+final List segments = 
visitor.getSegments();
+
+// connect all segments, using topological criteria first
+// and using Euclidean distance only as a last resort
+int pending = segments.size();
+pending -= naturalFollowerConnections(segments);
+if (pending > 0) {
+pending -= splitEdgeConnections(segments);
+}
+if (pending > 0) {
+pending -= closeVertices



[8/8] [math] Deprecated AVLTree and OrderedTuple.


2014-12-02

Thread
luc

Deprecated AVLTree and OrderedTuple.

These two classes were dirty hacks used only for the extraction of
boundary from 2D Euclidean BSP trees. They were not really efficient and
produces some problems as topology was not preserved.

A completely new implementation of boundary extraction has been set up
as of 3.4, that preserves more topological information and therefore
should be more robust. This new implementation does not use these
classes anymore.

As AVLTree is not really a math concept, this class is not considered to
belong to [math] scope. OrderedTuple is more a grey zone, but it is
really something inefficient and no need for it is foreseen.

Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/d21d3a94
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/d21d3a94
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/d21d3a94

Branch: refs/heads/master
Commit: d21d3a94abdbcf5a890fb1b5de28f1060e9e584d
Parents: e6aae3a
Author: Luc Maisonobe 
Authored: Tue Dec 2 22:18:57 2014 +0100
Committer: Luc Maisonobe 
Committed: Tue Dec 2 22:18:57 2014 +0100

--
 .../commons/math3/geometry/partitioning/utilities/AVLTree.java| 3 +++
 .../math3/geometry/partitioning/utilities/OrderedTuple.java   | 3 +++
 .../math3/geometry/partitioning/utilities/AVLTreeTest.java| 1 +
 3 files changed, 7 insertions(+)
--


http://git-wip-us.apache.org/repos/asf/commons-math/blob/d21d3a94/src/main/java/org/apache/commons/math3/geometry/partitioning/utilities/AVLTree.java
--
diff --git 
a/src/main/java/org/apache/commons/math3/geometry/partitioning/utilities/AVLTree.java
 
b/src/main/java/org/apache/commons/math3/geometry/partitioning/utilities/AVLTree.java
index 36826c6..9412421 100644
--- 
a/src/main/java/org/apache/commons/math3/geometry/partitioning/utilities/AVLTree.java
+++ 
b/src/main/java/org/apache/commons/math3/geometry/partitioning/utilities/AVLTree.java
@@ -42,7 +42,10 @@ package 
org.apache.commons.math3.geometry.partitioning.utilities;
  * @param  the type of the elements
  *
  * @since 3.0
+ * @deprecated as of 3.4, this class is not used anymore and considered
+ * to be out of scope of Apache Commons Math
  */
+@Deprecated
 public class AVLTree> {
 
 /** Top level node. */

http://git-wip-us.apache.org/repos/asf/commons-math/blob/d21d3a94/src/main/java/org/apache/commons/math3/geometry/partitioning/utilities/OrderedTuple.java
--
diff --git 
a/src/main/java/org/apache/commons/math3/geometry/partitioning/utilities/OrderedTuple.java
 
b/src/main/java/org/apache/commons/math3/geometry/partitioning/utilities/OrderedTuple.java
index 6c46be7..2dad2d7 100644
--- 
a/src/main/java/org/apache/commons/math3/geometry/partitioning/utilities/OrderedTuple.java
+++ 
b/src/main/java/org/apache/commons/math3/geometry/partitioning/utilities/OrderedTuple.java
@@ -89,7 +89,10 @@ import org.apache.commons.math3.util.FastMath;
  * 
  *
  * @since 3.0
+ * @deprecated as of 3.4, this class is not used anymore and considered
+ * to be out of scope of Apache Commons Math
  */
+@Deprecated
 public class OrderedTuple implements Comparable {
 
 /** Sign bit mask. */

http://git-wip-us.apache.org/repos/asf/commons-math/blob/d21d3a94/src/test/java/org/apache/commons/math3/geometry/partitioning/utilities/AVLTreeTest.java
--
diff --git 
a/src/test/java/org/apache/commons/math3/geometry/partitioning/utilities/AVLTreeTest.java
 
b/src/test/java/org/apache/commons/math3/geometry/partitioning/utilities/AVLTreeTest.java
index 9d7f424..49cfef6 100644
--- 
a/src/test/java/org/apache/commons/math3/geometry/partitioning/utilities/AVLTreeTest.java
+++ 
b/src/test/java/org/apache/commons/math3/geometry/partitioning/utilities/AVLTreeTest.java
@@ -20,6 +20,7 @@ import 
org.apache.commons.math3.geometry.partitioning.utilities.AVLTree;
 import org.junit.Assert;
 import org.junit.Test;
 
+@Deprecated
 public class AVLTreeTest {
 
 @Test






[4/8] [math] Identified a new failure mode for polygons.


2014-12-02

Thread
luc

Identified a new failure mode for polygons.

Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/c29e3d68
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/c29e3d68
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/c29e3d68

Branch: refs/heads/master
Commit: c29e3d681f2a46cc3288dc4f38925efbcf30c233
Parents: e11c000
Author: Luc Maisonobe 
Authored: Sun Nov 30 11:40:27 2014 +0100
Committer: Luc Maisonobe 
Committed: Tue Dec 2 15:24:31 2014 +0100

--
 .../euclidean/twod/PolygonsSetTest.java | 37 
 1 file changed, 37 insertions(+)
--


http://git-wip-us.apache.org/repos/asf/commons-math/blob/c29e3d68/src/test/java/org/apache/commons/math3/geometry/euclidean/twod/PolygonsSetTest.java
--
diff --git 
a/src/test/java/org/apache/commons/math3/geometry/euclidean/twod/PolygonsSetTest.java
 
b/src/test/java/org/apache/commons/math3/geometry/euclidean/twod/PolygonsSetTest.java
index 348ace8..c6c68a0 100644
--- 
a/src/test/java/org/apache/commons/math3/geometry/euclidean/twod/PolygonsSetTest.java
+++ 
b/src/test/java/org/apache/commons/math3/geometry/euclidean/twod/PolygonsSetTest.java
@@ -24,6 +24,7 @@ import 
org.apache.commons.math3.geometry.euclidean.oned.IntervalsSet;
 import org.apache.commons.math3.geometry.euclidean.oned.Vector1D;
 import org.apache.commons.math3.geometry.partitioning.BSPTree;
 import org.apache.commons.math3.geometry.partitioning.BoundaryProjection;
+import org.apache.commons.math3.geometry.partitioning.Hyperplane;
 import org.apache.commons.math3.geometry.partitioning.Region;
 import org.apache.commons.math3.geometry.partitioning.Region.Location;
 import org.apache.commons.math3.geometry.partitioning.RegionFactory;
@@ -1107,6 +1108,42 @@ public class PolygonsSetTest {
 
 }
 
+@Test
+public void testThinRectangle() {
+
+RegionFactory factory = new RegionFactory();
+Vector2D pA = new Vector2D(0.0,1.0);
+Vector2D pB = new Vector2D(0.0,0.0);
+Vector2D pC = new Vector2D(1.0 / 64.0, 0.0);
+Vector2D pD = new Vector2D(1.0 / 64.0, 1.0);
+
+// if tolerance is smaller than rectangle width, the rectangle is 
computed accurately
+Hyperplane[] h1 = new Line[] {
+new Line(pA, pB, 1.0 / 256),
+new Line(pB, pC, 1.0 / 256),
+new Line(pC, pD, 1.0 / 256),
+new Line(pD, pA, 1.0 / 256)
+};
+Region accuratePolygon = factory.buildConvex(h1);
+Assert.assertEquals(1.0 / 64.0, accuratePolygon.getSize(), 1.0e-10);
+Assert.assertTrue(Double.isInfinite(new 
RegionFactory().getComplement(accuratePolygon).getSize()));
+Assert.assertEquals(2 * (1.0 + 1.0 / 64.0), 
accuratePolygon.getBoundarySize(), 1.0e-10);
+
+// if tolerance is larger than rectangle width, the rectangle 
degenerates
+// as of 3.3, its two long edges cannot be distinguished anymore and 
this part of the test fails
+Hyperplane[] h2 = new Line[] {
+new Line(pA, pB, 1.0 / 16),
+new Line(pB, pC, 1.0 / 16),
+new Line(pC, pD, 1.0 / 16),
+new Line(pD, pA, 1.0 / 16)
+};
+Region degeneratedPolygon = factory.buildConvex(h2);
+Assert.assertEquals(1.0 / 64.0, degeneratedPolygon.getSize(), 1.0e-10);
+Assert.assertTrue(Double.isInfinite(new 
RegionFactory().getComplement(degeneratedPolygon).getSize()));
+Assert.assertEquals(2 * (1.0 + 1.0 / 64.0), 
degeneratedPolygon.getBoundarySize(), 1.0e-10);
+
+}
+
 private PolygonsSet buildSet(Vector2D[][] vertices) {
 ArrayList> edges = new 
ArrayList>();
 for (int i = 0; i < vertices.length; ++i) {






[1/8] [math] Added splitters in Boundary attributes.


2014-12-02

Thread
luc

Repository: commons-math
Updated Branches:
  refs/heads/master e11c00085 -> d21d3a94a


Added splitters in Boundary attributes.


Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/6525cc40
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/6525cc40
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/6525cc40

Branch: refs/heads/master
Commit: 6525cc4035fe8df3308c03f0ca9f450728e122ac
Parents: 26ee481
Author: Luc Maisonobe 
Authored: Sun Nov 30 18:09:06 2014 +0100
Committer: Luc Maisonobe 
Committed: Tue Dec 2 15:24:31 2014 +0100

--
 src/changes/changes.xml |  4 ++
 .../geometry/partitioning/AbstractRegion.java   | 67 +-
 .../partitioning/AbstractSubHyperplane.java | 67 +-
 .../partitioning/BoundaryAttribute.java | 32 +
 .../geometry/partitioning/BoundaryBuilder.java  | 23 --
 .../geometry/partitioning/Characterization.java | 67 ++
 .../math3/geometry/partitioning/NodesSet.java   | 72 +++
 .../geometry/partitioning/RegionFactory.java| 74 
 8 files changed, 338 insertions(+), 68 deletions(-)
--


http://git-wip-us.apache.org/repos/asf/commons-math/blob/6525cc40/src/changes/changes.xml
--
diff --git a/src/changes/changes.xml b/src/changes/changes.xml
index c8f0afd..46ad704 100644
--- a/src/changes/changes.xml
+++ b/src/changes/changes.xml
@@ -73,6 +73,10 @@ Users are encouraged to upgrade to this version as this 
release not
   2. A few methods in the FastMath class are in fact slower that their
   counterpart in either Math or StrictMath (cf. MATH-740 and MATH-901).
 ">
+  
+Boundary attributes in regions now provides the BSP tree nodes that
+were used to split the sub-hyperplane froming the boundary part of the 
facet. 
+  
   
 Fixed a problem with vanishing cut sub-hyperplanes during BSP tree 
merging.
   

http://git-wip-us.apache.org/repos/asf/commons-math/blob/6525cc40/src/main/java/org/apache/commons/math3/geometry/partitioning/AbstractRegion.java
--
diff --git 
a/src/main/java/org/apache/commons/math3/geometry/partitioning/AbstractRegion.java
 
b/src/main/java/org/apache/commons/math3/geometry/partitioning/AbstractRegion.java
index 3fca476..fd3dcc7 100644
--- 
a/src/main/java/org/apache/commons/math3/geometry/partitioning/AbstractRegion.java
+++ 
b/src/main/java/org/apache/commons/math3/geometry/partitioning/AbstractRegion.java
@@ -19,7 +19,9 @@ package org.apache.commons.math3.geometry.partitioning;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Comparator;
+import java.util.HashMap;
 import java.util.Iterator;
+import java.util.Map;
 import java.util.TreeSet;
 
 import org.apache.commons.math3.geometry.Point;
@@ -349,7 +351,7 @@ public abstract class AbstractRegion implement
 /** {@inheritDoc} */
 public BSPTree getTree(final boolean includeBoundaryAttributes) {
 if (includeBoundaryAttributes && (tree.getCut() != null) && 
(tree.getAttribute() == null)) {
-// we need to compute the boundary attributes
+// compute the boundary attributes
 tree.visit(new BoundaryBuilder());
 }
 return tree;
@@ -465,36 +467,65 @@ public abstract class AbstractRegion implement
  * transform to the instance
  */
 public AbstractRegion applyTransform(final Transform 
transform) {
-return buildNew(recurseTransform(getTree(false), transform));
+
+// transform the tree, except for boundary attribute splitters
+final Map, BSPTree> map = new HashMap, 
BSPTree>();
+final BSPTree transformedTree = recurseTransform(getTree(false), 
transform, map);
+
+// set up the boundary attributes splitters
+for (final Map.Entry, BSPTree> entry : map.entrySet()) {
+if (entry.getKey().getCut() != null) {
+@SuppressWarnings("unchecked")
+BoundaryAttribute original = (BoundaryAttribute) 
entry.getKey().getAttribute();
+if (original != null) {
+@SuppressWarnings("unchecked")
+BoundaryAttribute transformed = (BoundaryAttribute) 
entry.getValue().getAttribute();
+for (final BSPTree splitter : original.getSplitters()) {
+transformed.getSplitters().add(map.get(splitter));
+}
+}
+}
+}
+
+return buildNew(transformedTree);
+
 }
 
 /** Recursively transform an inside/outside BSP-tree.




[3/8] [math] Improved accuracy of internal computation.


2014-12-02

Thread
luc

Improved accuracy of internal computation.

The improvement is obtained by using high accuracy linear combinations
and by preserving cos/sin as much as possible. This last part is
important in the frequent case of lines along y axis, i.e. when angle is
π/2. We want the cosine to remain 0 and not get about 10^-17. 

Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/5f667c03
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/5f667c03
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/5f667c03

Branch: refs/heads/master
Commit: 5f667c031cdf02adbee9ef83cb71990333c58ba3
Parents: c29e3d6
Author: Luc Maisonobe 
Authored: Sun Nov 30 11:44:07 2014 +0100
Committer: Luc Maisonobe 
Committed: Tue Dec 2 15:24:31 2014 +0100

--
 .../math3/geometry/euclidean/twod/Line.java | 54 ++--
 1 file changed, 28 insertions(+), 26 deletions(-)
--


http://git-wip-us.apache.org/repos/asf/commons-math/blob/5f667c03/src/main/java/org/apache/commons/math3/geometry/euclidean/twod/Line.java
--
diff --git 
a/src/main/java/org/apache/commons/math3/geometry/euclidean/twod/Line.java 
b/src/main/java/org/apache/commons/math3/geometry/euclidean/twod/Line.java
index 70ab1ac..b40f0fa 100644
--- a/src/main/java/org/apache/commons/math3/geometry/euclidean/twod/Line.java
+++ b/src/main/java/org/apache/commons/math3/geometry/euclidean/twod/Line.java
@@ -31,6 +31,7 @@ import 
org.apache.commons.math3.geometry.partitioning.Hyperplane;
 import org.apache.commons.math3.geometry.partitioning.SubHyperplane;
 import org.apache.commons.math3.geometry.partitioning.Transform;
 import org.apache.commons.math3.util.FastMath;
+import org.apache.commons.math3.util.MathArrays;
 import org.apache.commons.math3.util.MathUtils;
 
 /** This class represents an oriented line in the 2D plane.
@@ -147,8 +148,8 @@ public class Line implements Hyperplane, 
Embedding, 
Embedding, 
Embedding, 
Embedding point) {
 Vector2D p2 = (Vector2D) point;
-return new Vector1D(cos * p2.getX() + sin * p2.getY());
+return new Vector1D(MathArrays.linearCombination(cos, p2.getX(), sin, 
p2.getY()));
 }
 
 /** {@inheritDoc} */
 public Vector2D toSpace(final Point point) {
 final double abscissa = ((Vector1D) point).getX();
-return new Vector2D(abscissa * cos - originOffset * sin,
-abscissa * sin + originOffset * cos);
+return new Vector2D(MathArrays.linearCombination(abscissa, cos, 
-originOffset, sin),
+MathArrays.linearCombination(abscissa, sin,  
originOffset, cos));
 }
 
 /** Get the intersection point of the instance and another line.
@@ -251,12 +252,12 @@ public class Line implements Hyperplane, 
Embedding, 
Embedding 0) ? -line.originOffset : 
line.originOffset);
+   (MathArrays.linearCombination(cos, line.cos, sin, line.sin) > 0 
? -line.originOffset : line.originOffset);
 }
 
 /** Get the offset (oriented distance) of a vector.
@@ -312,13 +313,13 @@ public class Line implements Hyperplane, 
Embedding point) {
 Vector2D p2 = (Vector2D) point;
-return sin * p2.getX() - cos * p2.getY() + originOffset;
+return MathArrays.linearCombination(sin, p2.getX(), -cos, p2.getY(), 
1.0, originOffset);
 }
 
 /** {@inheritDoc} */
 public boolean sameOrientationAs(final Hyperplane other) {
 final Line otherL = (Line) other;
-return (sin * otherL.sin + cos * otherL.cos) >= 0.0;
+return MathArrays.linearCombination(sin, otherL.sin, cos, otherL.cos) 
>= 0.0;
 }
 
 /** Get one point from the plane.
@@ -330,7 +331,8 @@ public class Line implements Hyperplane, 
Embedding, 
Embedding, 
Embedding, 
Embedding hyperplane) {
 final Line   line= (Line) hyperplane;
-final double rOffset = c1X * line.cos + c1Y * line.sin + c11 * 
line.originOffset;
-final double rCos= cXX * line.cos + cXY * line.sin;
-final double rSin= cYX * line.cos + cYY * line.sin;
+final double rOffset = MathArrays.linearCombination(c1X, line.cos, 
c1Y, line.sin, c11, line.originOffset);
+final double rCos= MathArrays.linearCombination(cXX, line.cos, 
cXY, line.sin);
+final double rSin= MathArrays.linearCombination(cYX, line.cos, 
cYY, line.sin);
 final double inv = 1.0 / FastMath.sqrt(rSin * rSin + rCos * 
rCos);
 return new Line(FastMath.PI + FastMath.atan2(-rSin, -rCos),
 inv * rCos, inv * rSin,






[6/8] [math] Removed development traces.


2014-12-02

Thread
luc

Removed development traces.

Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/893ef53c
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/893ef53c
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/893ef53c

Branch: refs/heads/master
Commit: 893ef53c6cb9b243ba8f28c8cad6e42c8019af0c
Parents: 84cf29e
Author: Luc Maisonobe 
Authored: Tue Dec 2 22:06:33 2014 +0100
Committer: Luc Maisonobe 
Committed: Tue Dec 2 22:06:33 2014 +0100

--
 .../commons/math3/geometry/partitioning/RegionFactory.java   | 8 
 1 file changed, 8 deletions(-)
--


http://git-wip-us.apache.org/repos/asf/commons-math/blob/893ef53c/src/main/java/org/apache/commons/math3/geometry/partitioning/RegionFactory.java
--
diff --git 
a/src/main/java/org/apache/commons/math3/geometry/partitioning/RegionFactory.java
 
b/src/main/java/org/apache/commons/math3/geometry/partitioning/RegionFactory.java
index 8cf2603..16d4472 100644
--- 
a/src/main/java/org/apache/commons/math3/geometry/partitioning/RegionFactory.java
+++ 
b/src/main/java/org/apache/commons/math3/geometry/partitioning/RegionFactory.java
@@ -21,8 +21,6 @@ import java.util.Map;
 
 import org.apache.commons.math3.geometry.Point;
 import org.apache.commons.math3.geometry.Space;
-import org.apache.commons.math3.geometry.euclidean.twod.PolygonsSet;
-import org.apache.commons.math3.geometry.euclidean.twod.Vector2D;
 import 
org.apache.commons.math3.geometry.partitioning.BSPTree.VanishingCutHandler;
 import org.apache.commons.math3.geometry.partitioning.Region.Location;
 
@@ -296,12 +294,6 @@ public class RegionFactory {
 // get a representative point in the degenerate cell
 final BSPTree cell = node.pruneAroundConvexCell(Boolean.TRUE, 
Boolean.FALSE, null);
 final Region r = region1.buildNew(cell);
-for (Vector2D[] loop : ((PolygonsSet) r).getVertices()) {
-System.out.format(java.util.Locale.US, "%n");
-for (Vector2D v : loop) {
-System.out.format(java.util.Locale.US, "%14.10f 
%14.10f%n", v.getX(), v.getY());
-}
-}
 final Point p = r.getBarycenter();
 return new BSPTree(region1.checkPoint(p) == Location.INSIDE &&
   region2.checkPoint(p) == Location.OUTSIDE);






[5/8] [math] set up a weak link between a line and its reverse to avoid duplications.


2014-12-02

Thread
luc

set up a weak link between a line and its reverse to avoid duplications.


Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/84cf29ec
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/84cf29ec
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/84cf29ec

Branch: refs/heads/master
Commit: 84cf29ecf31c67c7640f8821d4fdda625a173aa6
Parents: 6525cc4
Author: Luc Maisonobe 
Authored: Tue Dec 2 15:37:15 2014 +0100
Committer: Luc Maisonobe 
Committed: Tue Dec 2 15:37:15 2014 +0100

--
 .../math3/geometry/euclidean/twod/Line.java | 39 ++--
 1 file changed, 36 insertions(+), 3 deletions(-)
--


http://git-wip-us.apache.org/repos/asf/commons-math/blob/84cf29ec/src/main/java/org/apache/commons/math3/geometry/euclidean/twod/Line.java
--
diff --git 
a/src/main/java/org/apache/commons/math3/geometry/euclidean/twod/Line.java 
b/src/main/java/org/apache/commons/math3/geometry/euclidean/twod/Line.java
index b40f0fa..d6fd487 100644
--- a/src/main/java/org/apache/commons/math3/geometry/euclidean/twod/Line.java
+++ b/src/main/java/org/apache/commons/math3/geometry/euclidean/twod/Line.java
@@ -80,6 +80,9 @@ public class Line implements Hyperplane, 
EmbeddingThe line is oriented from p1 to p2
  * @param p1 first point
@@ -118,6 +121,7 @@ public class Line implements Hyperplane, 
Embedding, 
Embedding, 
Embedding, 
Embedding, 
Embedding, 
EmbeddingGet a line with reversed orientation with respect to the
- * instance. A new object is built, the instance is untouched.
+ * instance.
+ * 
+ * As long as neither the instance nor its reverse are modified
+ * (i.e. as long as none of the {@link #reset(Vector2D, Vector2D)},
+ * {@link #reset(Vector2D, double)}, {@link #revertSelf()},
+ * {@link #setAngle(double)} or {@link #setOriginOffset(double)}
+ * methods are called), then the line and its reverse remain linked
+ * together so that {@code line.getReverse().getReverse() == line}.
+ * When one of the line is modified, the link is deleted as both
+ * instance becomes independent.
+ * 
  * @return a new line, with orientation opposite to the instance 
orientation
  */
 public Line getReverse() {
-return new Line((angle < FastMath.PI) ? (angle + FastMath.PI) : (angle 
- FastMath.PI),
--cos, -sin, -originOffset, tolerance);
+if (reverse == null) {
+reverse = new Line((angle < FastMath.PI) ? (angle + FastMath.PI) : 
(angle - FastMath.PI),
+   -cos, -sin, -originOffset, tolerance);
+reverse.reverse = this;
+}
+return reverse;
 }
 
 /** Transform a space point into a sub-space point.
@@ -383,6 +414,7 @@ public class Line implements Hyperplane, 
Embedding, 
Embedding




[2/8] [math] Reorganized code, avoiding too many internal classes.


2014-12-02

Thread
luc

Reorganized code, avoiding too many internal classes.

Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/26ee4819
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/26ee4819
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/26ee4819

Branch: refs/heads/master
Commit: 26ee48193928f525fe0885cba6b28fdc8eff6af9
Parents: 5f667c0
Author: Luc Maisonobe 
Authored: Sun Nov 30 13:37:43 2014 +0100
Committer: Luc Maisonobe 
Committed: Tue Dec 2 15:24:31 2014 +0100

--
 .../geometry/euclidean/twod/PolygonsSet.java|   2 +-
 .../geometry/partitioning/AbstractRegion.java   | 266 +--
 .../geometry/partitioning/BoundaryBuilder.java  |  84 ++
 .../geometry/partitioning/Characterization.java | 147 ++
 .../geometry/partitioning/InsideFinder.java | 150 +++
 .../geometry/partitioning/RegionFactory.java|  47 +++-
 6 files changed, 430 insertions(+), 266 deletions(-)
--


http://git-wip-us.apache.org/repos/asf/commons-math/blob/26ee4819/src/main/java/org/apache/commons/math3/geometry/euclidean/twod/PolygonsSet.java
--
diff --git 
a/src/main/java/org/apache/commons/math3/geometry/euclidean/twod/PolygonsSet.java
 
b/src/main/java/org/apache/commons/math3/geometry/euclidean/twod/PolygonsSet.java
index fe7c463..532d6a0 100644
--- 
a/src/main/java/org/apache/commons/math3/geometry/euclidean/twod/PolygonsSet.java
+++ 
b/src/main/java/org/apache/commons/math3/geometry/euclidean/twod/PolygonsSet.java
@@ -784,7 +784,7 @@ public class PolygonsSet extends 
AbstractRegion {
 // is this an open or a closed loop ?
 final boolean open = segment.getStart() == null;
 
-while ((end != null) && (open || 
(globalStart.distance((Point) end) > 1.0e-10))) {
+while ((end != null) && (open || 
(globalStart.distance((Point) end) > getTolerance( {
 
 // search the sub-hyperplane starting where the previous one ended
 AVLTree.Node selectedNode = null;

http://git-wip-us.apache.org/repos/asf/commons-math/blob/26ee4819/src/main/java/org/apache/commons/math3/geometry/partitioning/AbstractRegion.java
--
diff --git 
a/src/main/java/org/apache/commons/math3/geometry/partitioning/AbstractRegion.java
 
b/src/main/java/org/apache/commons/math3/geometry/partitioning/AbstractRegion.java
index abddb78..3fca476 100644
--- 
a/src/main/java/org/apache/commons/math3/geometry/partitioning/AbstractRegion.java
+++ 
b/src/main/java/org/apache/commons/math3/geometry/partitioning/AbstractRegion.java
@@ -16,18 +16,15 @@
  */
 package org.apache.commons.math3.geometry.partitioning;
 
-import java.lang.reflect.Array;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Comparator;
 import java.util.Iterator;
 import java.util.TreeSet;
 
-import org.apache.commons.math3.exception.MathInternalError;
-import org.apache.commons.math3.geometry.Space;
 import org.apache.commons.math3.geometry.Point;
+import org.apache.commons.math3.geometry.Space;
 import org.apache.commons.math3.geometry.Vector;
-import org.apache.commons.math3.geometry.partitioning.Region.Location;
 
 /** Abstract class for all regions, independently of geometry type or 
dimension.
 
@@ -358,122 +355,6 @@ public abstract class AbstractRegion implement
 return tree;
 }
 
-/** Visitor building boundary shell tree.
- * 
- * The boundary shell is represented as {@link BoundaryAttribute boundary 
attributes}
- * at each internal node.
- * 
- */
-private static class BoundaryBuilder implements 
BSPTreeVisitor {
-
-/** {@inheritDoc} */
-public Order visitOrder(BSPTree node) {
-return Order.PLUS_MINUS_SUB;
-}
-
-/** {@inheritDoc} */
-public void visitInternalNode(BSPTree node) {
-
-SubHyperplane plusOutside = null;
-SubHyperplane plusInside  = null;
-
-// characterize the cut sub-hyperplane,
-// first with respect to the plus sub-tree
-@SuppressWarnings("unchecked")
-final SubHyperplane[] plusChar = (SubHyperplane[]) 
Array.newInstance(SubHyperplane.class, 2);
-characterize(node.getPlus(), node.getCut().copySelf(), plusChar);
-
-if (plusChar[0] != null && !plusChar[0].isEmpty()) {
-// plusChar[0] corresponds to a subset of the cut 
sub-hyperplane known to have
-// outside cells on its plus side, we want to check if parts 
of this subset
-// do have inside cells on their minus side
-@SuppressWarnings("unchecked")
-  



[math] Typo.


2014-12-02

Thread
luc

Repository: commons-math
Updated Branches:
  refs/heads/master d21d3a94a -> 3f13fbeff


Typo.

Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/3f13fbef
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/3f13fbef
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/3f13fbef

Branch: refs/heads/master
Commit: 3f13fbeff3fef6bce6fc71b0ff3ffa09aecf1c87
Parents: d21d3a9
Author: Luc Maisonobe 
Authored: Tue Dec 2 22:29:45 2014 +0100
Committer: Luc Maisonobe 
Committed: Tue Dec 2 22:29:45 2014 +0100

--
 src/changes/changes.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)
--


http://git-wip-us.apache.org/repos/asf/commons-math/blob/3f13fbef/src/changes/changes.xml
--
diff --git a/src/changes/changes.xml b/src/changes/changes.xml
index a4b462c..8ab9a1a 100644
--- a/src/changes/changes.xml
+++ b/src/changes/changes.xml
@@ -78,7 +78,7 @@ Users are encouraged to upgrade to this version as this 
release not
   
   
 Boundary attributes in regions now provides the BSP tree nodes that
-were used to split the sub-hyperplane froming the boundary part of the 
facet. 
+were used to split the sub-hyperplane forming the boundary part of the 
facet. 
   
   
 Fixed a problem with vanishing cut sub-hyperplanes during BSP tree 
merging.






[math] Fixed comment, the test for MATH-1174 does not fail anymore.


2014-12-02

Thread
luc

Repository: commons-math
Updated Branches:
  refs/heads/master 3f13fbeff -> 428a48533


Fixed comment, the test for MATH-1174 does not fail anymore.

Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/428a4853
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/428a4853
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/428a4853

Branch: refs/heads/master
Commit: 428a48533c711f3a27376f0eadea32c95657ea51
Parents: 3f13fbe
Author: Luc Maisonobe 
Authored: Tue Dec 2 22:35:27 2014 +0100
Committer: Luc Maisonobe 
Committed: Tue Dec 2 22:35:27 2014 +0100

--
 .../commons/math3/geometry/euclidean/twod/PolygonsSetTest.java| 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)
--


http://git-wip-us.apache.org/repos/asf/commons-math/blob/428a4853/src/test/java/org/apache/commons/math3/geometry/euclidean/twod/PolygonsSetTest.java
--
diff --git 
a/src/test/java/org/apache/commons/math3/geometry/euclidean/twod/PolygonsSetTest.java
 
b/src/test/java/org/apache/commons/math3/geometry/euclidean/twod/PolygonsSetTest.java
index 52bbbca..f965742 100644
--- 
a/src/test/java/org/apache/commons/math3/geometry/euclidean/twod/PolygonsSetTest.java
+++ 
b/src/test/java/org/apache/commons/math3/geometry/euclidean/twod/PolygonsSetTest.java
@@ -1138,7 +1138,8 @@ public class PolygonsSetTest {
 Assert.assertEquals(2 * (1.0 + 1.0 / 64.0), 
accuratePolygon.getBoundarySize(), 1.0e-10);
 
 // if tolerance is larger than rectangle width, the rectangle 
degenerates
-// as of 3.3, its two long edges cannot be distinguished anymore and 
this part of the test fails
+// as of 3.3, its two long edges cannot be distinguished anymore and 
this part of the test did fail
+// this has been fixed in 3.4 (issue MATH-1174)
 Hyperplane[] h2 = new Line[] {
 new Line(pA, pB, 1.0 / 16),
 new Line(pB, pC, 1.0 / 16),






[1/2] [math] Connect closest node instead of first node below threshold in polygons.


2014-12-03

Thread
luc

Repository: commons-math
Updated Branches:
  refs/heads/master 428a48533 -> 10b1c517c


Connect closest node instead of first node below threshold in polygons.

Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/b4fb13bc
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/b4fb13bc
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/b4fb13bc

Branch: refs/heads/master
Commit: b4fb13bca9c41e3e59a5ea8e3f8ec4bc0110ba17
Parents: 428a485
Author: Luc Maisonobe 
Authored: Wed Dec 3 10:25:44 2014 +0100
Committer: Luc Maisonobe 
Committed: Wed Dec 3 10:25:44 2014 +0100

--
 .../geometry/euclidean/twod/PolygonsSet.java| 23 +---
 1 file changed, 15 insertions(+), 8 deletions(-)
--


http://git-wip-us.apache.org/repos/asf/commons-math/blob/b4fb13bc/src/main/java/org/apache/commons/math3/geometry/euclidean/twod/PolygonsSet.java
--
diff --git 
a/src/main/java/org/apache/commons/math3/geometry/euclidean/twod/PolygonsSet.java
 
b/src/main/java/org/apache/commons/math3/geometry/euclidean/twod/PolygonsSet.java
index 8361831..dc3ef33 100644
--- 
a/src/main/java/org/apache/commons/math3/geometry/euclidean/twod/PolygonsSet.java
+++ 
b/src/main/java/org/apache/commons/math3/geometry/euclidean/twod/PolygonsSet.java
@@ -840,18 +840,25 @@ public class PolygonsSet extends 
AbstractRegion {
 private int closeVerticesConnections(final List 
segments) {
 int connected = 0;
 for (final ConnectableSegment segment : segments) {
-if (segment.getNext() == null) {
+if (segment.getNext() == null && segment.getEnd() != null) {
 final Vector2D end = segment.getEnd();
+ConnectableSegment selectedNext = null;
+double min = Double.POSITIVE_INFINITY;
 for (final ConnectableSegment candidateNext : segments) {
-if (candidateNext.getPrevious() == null &&
-Vector2D.distance(end, candidateNext.getStart()) <= 
getTolerance()) {
-// connect the two segments
-segment.setNext(candidateNext);
-candidateNext.setPrevious(segment);
-++connected;
-break;
+if (candidateNext.getPrevious() == null && 
candidateNext.getStart() != null) {
+final double distance = Vector2D.distance(end, 
candidateNext.getStart());
+if (distance < min) {
+selectedNext = candidateNext;
+min  = distance;
+}
 }
 }
+if (min <= getTolerance()) {
+// connect the two segments
+segment.setNext(selectedNext);
+selectedNext.setPrevious(segment);
+++connected;
+}
 }
 }
 return connected;






[2/2] [math] Filter out spurious vertices in polygons boundaries.


2014-12-03

Thread
luc

Filter out spurious vertices in polygons boundaries.

Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/10b1c517
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/10b1c517
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/10b1c517

Branch: refs/heads/master
Commit: 10b1c517cd5c0083cd0ad7a5f23167d66d1e59fd
Parents: b4fb13b
Author: Luc Maisonobe 
Authored: Wed Dec 3 12:20:18 2014 +0100
Committer: Luc Maisonobe 
Committed: Wed Dec 3 12:20:18 2014 +0100

--
 src/changes/changes.xml |  4 ++
 .../geometry/euclidean/twod/PolygonsSet.java| 42 +---
 .../euclidean/twod/PolygonsSetTest.java | 69 
 3 files changed, 105 insertions(+), 10 deletions(-)
--


http://git-wip-us.apache.org/repos/asf/commons-math/blob/10b1c517/src/changes/changes.xml
--
diff --git a/src/changes/changes.xml b/src/changes/changes.xml
index 8ab9a1a..869154f 100644
--- a/src/changes/changes.xml
+++ b/src/changes/changes.xml
@@ -73,6 +73,10 @@ Users are encouraged to upgrade to this version as this 
release not
   2. A few methods in the FastMath class are in fact slower that their
   counterpart in either Math or StrictMath (cf. MATH-740 and MATH-901).
 ">
+  
+Spurious vertices in the middle of otherwise straight edges are now
+filtered out when rebuilding polygons boundaries from BSP trees. 
+  
   
 Fixed a problem with too thin polygons considered to have infinite 
size.
   

http://git-wip-us.apache.org/repos/asf/commons-math/blob/10b1c517/src/main/java/org/apache/commons/math3/geometry/euclidean/twod/PolygonsSet.java
--
diff --git 
a/src/main/java/org/apache/commons/math3/geometry/euclidean/twod/PolygonsSet.java
 
b/src/main/java/org/apache/commons/math3/geometry/euclidean/twod/PolygonsSet.java
index dc3ef33..46268f5 100644
--- 
a/src/main/java/org/apache/commons/math3/geometry/euclidean/twod/PolygonsSet.java
+++ 
b/src/main/java/org/apache/commons/math3/geometry/euclidean/twod/PolygonsSet.java
@@ -34,6 +34,7 @@ import 
org.apache.commons.math3.geometry.partitioning.Hyperplane;
 import org.apache.commons.math3.geometry.partitioning.Side;
 import org.apache.commons.math3.geometry.partitioning.SubHyperplane;
 import org.apache.commons.math3.util.FastMath;
+import org.apache.commons.math3.util.Precision;
 
 /** This class represents a 2D region: a set of polygons.
  * @since 3.0
@@ -704,9 +705,9 @@ public class PolygonsSet extends 
AbstractRegion {
 }
 
 // create the segment loops
-final ArrayList> loops = new 
ArrayList>();
+final ArrayList> loops = new 
ArrayList>();
 for (ConnectableSegment s = getUnprocessed(segments); s != 
null; s = getUnprocessed(segments)) {
-final List loop = followLoop(s);
+final List loop = followLoop(s);
 if (loop != null) {
 if (loop.get(0).getStart() == null) {
 // this is an open loop, we put it on the front
@@ -722,7 +723,7 @@ public class PolygonsSet extends 
AbstractRegion {
 vertices = new Vector2D[loops.size()][];
 int i = 0;
 
-for (final List loop : loops) {
+for (final List loop : loops) {
 if (loop.size() < 2 ||
 (loop.size() == 2 && loop.get(0).getStart() == null && 
loop.get(1).getEnd() == null)) {
 // single infinite line
@@ -886,9 +887,9 @@ public class PolygonsSet extends 
AbstractRegion {
  * @return loop containing the segment (may be null if the loop is a
  * degenerated infinitely thin 2 points loop
  */
-private List followLoop(final ConnectableSegment 
defining) {
+private List followLoop(final ConnectableSegment defining) {
 
-final List loop = new 
ArrayList();
+final List loop = new ArrayList();
 loop.add(defining);
 defining.setProcessed(true);
 
@@ -909,15 +910,36 @@ public class PolygonsSet extends 
AbstractRegion {
 previous.setProcessed(true);
 previous = previous.getPrevious();
 }
+}
+
+// filter out spurious vertices
+filterSpuriousVertices(loop);
+
+if (loop.size() == 2 && loop.get(0).getStart() != null) {
+// this is a degenerated infinitely thin closed loop, we simply 
ignore it
+return null;
 } else {
-if (loop.size() == 2) {
-// this is a degener



[2/2] [math] updated download page for the next release (3.4)


2014-12-13

Thread
luc

updated download page for the next release (3.4)


Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/9f42f18f
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/9f42f18f
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/9f42f18f

Branch: refs/heads/master
Commit: 9f42f18f1544b2a7329442946c8378159a1c5513
Parents: 4ed24c8
Author: Luc Maisonobe 
Authored: Sat Dec 13 21:41:51 2014 +0100
Committer: Luc Maisonobe 
Committed: Sat Dec 13 21:41:51 2014 +0100

--
 src/site/xdoc/download_math.xml | 26 +-
 1 file changed, 13 insertions(+), 13 deletions(-)
--


http://git-wip-us.apache.org/repos/asf/commons-math/blob/9f42f18f/src/site/xdoc/download_math.xml
--
diff --git a/src/site/xdoc/download_math.xml b/src/site/xdoc/download_math.xml
index 395e406..8a2e0b1 100644
--- a/src/site/xdoc/download_math.xml
+++ b/src/site/xdoc/download_math.xml
@@ -95,32 +95,32 @@ limitations under the License.
   
 
 
-
+
   
 
   
-  commons-math3-3.3-bin.tar.gz
-  http://www.apache.org/dist/commons/math/binaries/commons-math3-3.3-bin.tar.gz.md5";>md5
-  http://www.apache.org/dist/commons/math/binaries/commons-math3-3.3-bin.tar.gz.asc";>pgp
+  commons-math3-3.4-bin.tar.gz
+  http://www.apache.org/dist/commons/math/binaries/commons-math3-3.4-bin.tar.gz.md5";>md5
+  http://www.apache.org/dist/commons/math/binaries/commons-math3-3.4-bin.tar.gz.asc";>pgp
   
   
-  commons-math3-3.3-bin.zip
-  http://www.apache.org/dist/commons/math/binaries/commons-math3-3.3-bin.zip.md5";>md5
-  http://www.apache.org/dist/commons/math/binaries/commons-math3-3.3-bin.zip.asc";>pgp
+  commons-math3-3.4-bin.zip
+  http://www.apache.org/dist/commons/math/binaries/commons-math3-3.4-bin.zip.md5";>md5
+  http://www.apache.org/dist/commons/math/binaries/commons-math3-3.4-bin.zip.asc";>pgp
   
 
   
   
 
   
-  commons-math3-3.3-src.tar.gz
-  http://www.apache.org/dist/commons/math/source/commons-math3-3.3-src.tar.gz.md5";>md5
-  http://www.apache.org/dist/commons/math/source/commons-math3-3.3-src.tar.gz.asc";>pgp
+  commons-math3-3.4-src.tar.gz
+  http://www.apache.org/dist/commons/math/source/commons-math3-3.4-src.tar.gz.md5";>md5
+  http://www.apache.org/dist/commons/math/source/commons-math3-3.4-src.tar.gz.asc";>pgp
   
   
-  commons-math3-3.3-src.zip
-  http://www.apache.org/dist/commons/math/source/commons-math3-3.3-src.zip.md5";>md5
-  http://www.apache.org/dist/commons/math/source/commons-math3-3.3-src.zip.asc";>pgp
+  commons-math3-3.4-src.zip
+  http://www.apache.org/dist/commons/math/source/commons-math3-3.4-src.zip.md5";>md5
+  http://www.apache.org/dist/commons/math/source/commons-math3-3.4-src.zip.asc";>pgp
   
 
   






[1/2] [math] fixed missing closing element


2014-12-13

Thread
luc

Repository: commons-math
Updated Branches:
  refs/heads/master 5d6e44548 -> 9f42f18f1


fixed missing closing element


Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/4ed24c87
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/4ed24c87
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/4ed24c87

Branch: refs/heads/master
Commit: 4ed24c87c593a7ae69f4310fa32a5ea1d542f8e4
Parents: 5d6e445
Author: Luc Maisonobe 
Authored: Sat Dec 13 21:40:00 2014 +0100
Committer: Luc Maisonobe 
Committed: Sat Dec 13 21:40:00 2014 +0100

--
 src/changes/changes.xml | 1 +
 1 file changed, 1 insertion(+)
--


http://git-wip-us.apache.org/repos/asf/commons-math/blob/4ed24c87/src/changes/changes.xml
--
diff --git a/src/changes/changes.xml b/src/changes/changes.xml
index 5c086ce..d241c57 100644
--- a/src/changes/changes.xml
+++ b/src/changes/changes.xml
@@ -82,6 +82,7 @@ Users are encouraged to upgrade to this version as this 
release not
   
 New classes "BicubicInterpolatingFunction" and "BicubicInterpolator" to
 replace "BicubicSplineInterpolatingFunction" and 
"BicubicSplineInterpolator".
+  
   
 Spurious vertices in the middle of otherwise straight edges are now
 filtered out when rebuilding polygons boundaries from BSP trees. 






[math] prepared release notes for version 3.4


2014-12-13

Thread
luc

Repository: commons-math
Updated Branches:
  refs/heads/master 9f42f18f1 -> 09129d536


prepared release notes for version 3.4


Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/09129d53
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/09129d53
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/09129d53

Branch: refs/heads/master
Commit: 09129d536726fac7f94f6b641e34a34a49c9a012
Parents: 9f42f18
Author: Luc Maisonobe 
Authored: Sat Dec 13 22:04:33 2014 +0100
Committer: Luc Maisonobe 
Committed: Sat Dec 13 22:04:33 2014 +0100

--
 RELEASE-NOTES.txt   | 273 ---
 src/changes/changes.xml |   9 +-
 2 files changed, 82 insertions(+), 200 deletions(-)
--


http://git-wip-us.apache.org/repos/asf/commons-math/blob/09129d53/RELEASE-NOTES.txt
--
diff --git a/RELEASE-NOTES.txt b/RELEASE-NOTES.txt
index 16bfcde..7930ea8 100644
--- a/RELEASE-NOTES.txt
+++ b/RELEASE-NOTES.txt
@@ -1,24 +1,24 @@
 
-  Apache Commons Math 3.3 RELEASE NOTES
+  Apache Commons Math 3.4 RELEASE NOTES
 
-The Apache Commons Math team is pleased to announce the release of 
commons-math3-3.3.
+The Apache Commons Math team is pleased to announce the release of 
commons-math3-3.4-SNAPSHOT
 
-The Apache Commons Math project is a library of lightweight, self-contained 
mathematics
-and statistics components addressing the most common practical problems not 
immediately
-available in the Java programming language or commons-lang.
+The Apache Commons Math project is a library of lightweight, self-contained 
mathematics and statistics components addressing the most common practical 
problems not immediately available in the Java programming language or 
commons-lang.
 
 This is a minor release: It combines bug fixes and new features.
 Changes to existing features were made in a backwards-compatible
-way such as to allow drop-in replacement of the v3.x JAR file.
+way such as to allow drop-in replacement of the v3.3 JAR file.
 
 Most notable among the new features are:
-Framework for creating artificial neural nets, self organizing feature maps,
-computational geometry algorithms (convex hull, enclosing ball), performance
-improvements of the linear simplex solver, refactoring of curve fitters,
-low-discrepancy random generators (sobol, halton), least-squares fitting.
+new distributions (Gumbel, Laplace, Logistic, Nakagami), and
+improvements on percentiles algorithms (better handling for NaNs
+in the regular algorithm, plus a new storeless implementation).
+Bicubic splines interpolators have been fixed and new implementations
+added. There have been numerous bug fixes and several improvements
+on performances or robustness. See below for a full list)
 
-The minimum version of the Java platform required to compile and use
-Commons Math is Java 5.
+ The minimum version of the Java platform required to compile and use
+Apache Commons Math is Java 5.
 
 Users are encouraged to upgrade to this version as this release not
 only includes bug fixes but also deprecates numerous classes and
@@ -32,203 +32,80 @@ Caveat:
  and to extend the unit tests suite.
  2. A few methods in the FastMath class are in fact slower that their
  counterpart in either Math or StrictMath (cf. MATH-740 and MATH-901).
- 3. A few methods/constructors in the package o.a.c.m.geometry.partitioning
- have changed their signature in a non backwards-compatible way. The respective
- classes are intended to be package private only and are not supposed to be
- used for other purposes.
 
 Changes in this version include:
 
 New features:
-o N/A:   Added an order 6 fixed-step ODE integrator designed by H. A. 
Luther in 1968.
-o MATH-1110: Added new constructor to "OLSMultipleLinearRegression" to be able
-to specify a custom singularity threshold for QR decomposition. Thanks 
to Edward Segall.
-o MATH-1119: Added a fast single-step method for fixed-step Runge-Kutta 
integrators. 
-o MATH-1101: Improved documentation of QR decomposition handling of singular 
matrices. 
-o MATH-1053: QR decomposition can compute pseudo-inverses for tall matrices. 
Thanks to Sean Owen. 
-o MATH-820:  Field vectors now implement the visitor pattern just like real 
vectors. 
-o MATH-749:  Added MonotoneChain algorithm to compute the convex hull of a 
collection of
-points in 2D. Additionally, the AklToussaintHeuristic can be used to 
speed up the generation. 
-o MATH-1095: Added Emo Welzl algorithm to find the smallest enclosing ball of 
a collection of points. 
-o MATH-1072: Added a constructor to "AbstractListChromosome" that does not 
copy the input argument. 
-o MATH-1091: BSP tree now provides an 



[2/2] [math] Including Ekstazi profile (www.ekstazi.org) to optimize regression tests


2014-12-16

Thread
luc

Including Ekstazi profile (www.ekstazi.org) to optimize regression tests


Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/7655cb61
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/7655cb61
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/7655cb61

Branch: refs/heads/master
Commit: 7655cb61e382b9a059b75d392e59fa608e2afcd1
Parents: 8d4fd1d
Author: Milos Gligoric 
Authored: Tue Dec 16 11:19:46 2014 +0100
Committer: Luc Maisonobe 
Committed: Tue Dec 16 13:37:58 2014 +0100

--
 .gitignore |  1 +
 pom.xml| 37 +
 2 files changed, 38 insertions(+)
--


http://git-wip-us.apache.org/repos/asf/commons-math/blob/7655cb61/.gitignore
--
diff --git a/.gitignore b/.gitignore
index 3ca003a..56b85a7 100644
--- a/.gitignore
+++ b/.gitignore
@@ -7,6 +7,7 @@ target
 /build
 /lib
 /site-content
+.ekstazi
 *.class
 *.iml
 *.ipr

http://git-wip-us.apache.org/repos/asf/commons-math/blob/7655cb61/pom.xml
--
diff --git a/pom.xml b/pom.xml
index 628ec6a..46da7d8 100644
--- a/pom.xml
+++ b/pom.xml
@@ -701,6 +701,43 @@
 
   
 
+
+
+  ekstazi
+  
+
+  ekstazi
+
+  
+  
+
+  
+org.ekstazi
+ekstazi-maven-plugin
+4.4.0
+
+  true
+
+
+  
+ekstazi
+
+  select
+  restore
+
+  
+
+  
+  
+org.apache.maven.plugins
+maven-surefire-plugin
+
+  
${java.io.tmpdir}/${user.name}EkstaziExcludes
+
+  
+
+  
+
   
 
 






[1/2] [math] fixed typos in error messages translations


2014-12-16

Thread
luc

Repository: commons-math
Updated Branches:
  refs/heads/master 8d4fd1dab -> 75872ffe9


fixed typos in error messages translations


Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/75872ffe
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/75872ffe
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/75872ffe

Branch: refs/heads/master
Commit: 75872ffe9b3711683253c1d5be7ec3bb80ef1a30
Parents: 7655cb6
Author: Luc Maisonobe 
Authored: Tue Dec 16 11:48:58 2014 +0100
Committer: Luc Maisonobe 
Committed: Tue Dec 16 13:37:58 2014 +0100

--
 .../util/LocalizedFormats_fr.properties | 32 ++--
 1 file changed, 16 insertions(+), 16 deletions(-)
--


http://git-wip-us.apache.org/repos/asf/commons-math/blob/75872ffe/src/main/resources/assets/org/apache/commons/math3/exception/util/LocalizedFormats_fr.properties
--
diff --git 
a/src/main/resources/assets/org/apache/commons/math3/exception/util/LocalizedFormats_fr.properties
 
b/src/main/resources/assets/org/apache/commons/math3/exception/util/LocalizedFormats_fr.properties
index 4a78ff1..c1a7c26 100644
--- 
a/src/main/resources/assets/org/apache/commons/math3/exception/util/LocalizedFormats_fr.properties
+++ 
b/src/main/resources/assets/org/apache/commons/math3/exception/util/LocalizedFormats_fr.properties
@@ -21,8 +21,8 @@ ASSYMETRIC_EIGEN_NOT_SUPPORTED = la d\u00e9composition en 
valeurs/vecteurs propr
 AT_LEAST_ONE_COLUMN = une matrice doit comporter au moins une colonne
 AT_LEAST_ONE_ROW = une matrice doit comporter au moins une ligne
 BANDWIDTH = bande passante ({0})
-BESSEL_FUNCTION_BAD_ARGUMENT = Bessel fonction de l''ordre {0} ne peut pas 
\u00eatre calcul\u00e9 pour x = {1}
-BESSEL_FUNCTION_FAILED_CONVERGENCE = Bessel fonction de l''ordre {0} n''a pas 
r\u00e9ussi \u00e0 converger pour x = {1}
+BESSEL_FUNCTION_BAD_ARGUMENT = la fonction de Bessel \u00e0 l''ordre {0} ne 
peut pas \u00eatre calcul\u00e9e pour x = {1}
+BESSEL_FUNCTION_FAILED_CONVERGENCE = la fonction de Bessel \u00e0 l''ordre {0} 
n''a pas r\u00e9ussi \u00e0 converger pour x = {1}
 BINOMIAL_INVALID_PARAMETERS_ORDER = n doit \u00eatre sup\u00e9rieur ou 
\u00e9gal \u00e0 k pour le coefficient du bin\u00f4me (n, k), or k = {0}, n = 
{1}
 BINOMIAL_NEGATIVE_PARAMETER = n doit \u00eatre positif pour le coefficient du 
bin\u00f4me (n, k), or n = {0}
 CANNOT_CLEAR_STATISTIC_CONSTRUCTED_FROM_EXTERNAL_MOMENTS = les statistiques 
bas\u00e9es sur des moments externes ne peuvent pas \u00eatre remises \u00e0 
z\u00e9ro
@@ -70,9 +70,9 @@ EMPTY_INTERPOLATION_SAMPLE = \u00e9chantillon 
d''interpolation vide
 EMPTY_POLYNOMIALS_COEFFICIENTS_ARRAY = tableau de coefficients 
polyn\u00f4miaux vide
 EMPTY_SELECTED_COLUMN_INDEX_ARRAY = tableau des indices de colonnes 
s\u00e9lectionn\u00e9es vide
 EMPTY_SELECTED_ROW_INDEX_ARRAY = tableau des indices de lignes 
s\u00e9lectionn\u00e9es vide
-EMPTY_STRING_FOR_IMAGINARY_CHARACTER = cha\u00eene vide pour le caract\u00e8 
imaginaire
+EMPTY_STRING_FOR_IMAGINARY_CHARACTER = cha\u00eene vide pour le caract\u00e8re 
imaginaire
 ENDPOINTS_NOT_AN_INTERVAL = les bornes ne d\u00e9finissent pas un intervalle : 
[{0}, {1}]
-EQUAL_VERTICES_IN_SIMPLEX = sommets {0} et {1} \u00e9gaux dans la 
configuration du simplex
+EQUAL_VERTICES_IN_SIMPLEX = sommets {0} et {1} \u00e9gaux dans la 
configuration du simplexe
 EULER_ANGLES_SINGULARITY = singularit\u00e9 d''angles d''Euler
 EVALUATION = \u00e9valuation
 EXPANSION_FACTOR_SMALLER_THAN_ONE = facteur d''extension inf\u00e9rieur \u00e0 
un ({0})
@@ -84,9 +84,9 @@ FIRST_ELEMENT_NOT_ZERO = le premier \u00e9l\u00e9ment n''est 
pas nul : {0}
 FIRST_ROWS_NOT_INITIALIZED_YET = les {0} premi\u00e8res lignes ne sont pas 
encore initialis\u00e9es
 FRACTION_CONVERSION_OVERFLOW = D\u00e9passement de capacit\u00e9 lors de la 
conversion de {0} en fraction ({1}/{2})
 FUNCTION_NOT_DIFFERENTIABLE = la fonction n''est pas diff\u00e9rentiable
-FUNCTION_NOT_POLYNOMIAL = la fonction n''est pas p\u00f4lynomiale
-GCD_OVERFLOW_32_BITS = d\u00e9passement de capacit\u00e9 : le PGCD de {0} et 
{1} vaut 2^31
-GCD_OVERFLOW_64_BITS = d\u00e9passement de capacit\u00e9 : le PGCD de {0} et 
{1} vaut 2^63
+FUNCTION_NOT_POLYNOMIAL = la fonction n''est pas polyn\u00f4miale
+GCD_OVERFLOW_32_BITS = d\u00e9passement de capacit\u00e9 : le PGCD de {0} et 
{1} vaut 2\u00b3\u00b9
+GCD_OVERFLOW_64_BITS = d\u00e9passement de capacit\u00e9 : le PGCD de {0} et 
{1} vaut 2\u2076\u00b3
 HOLE_BETWEEN_MODELS_TIME_RANGES = trou de longueur {0} entre les domaines 
temporels des mod\u00e8les
 ILL_CONDITIONED_OPERATOR = le c



[math] Replace svn-based build number with git-based build number.


2014-12-16

Thread
luc

Repository: commons-math
Updated Branches:
  refs/heads/master f9125d0b8 -> 17c903385


Replace svn-based build number with git-based build number.

Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/17c90338
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/17c90338
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/17c90338

Branch: refs/heads/master
Commit: 17c903385c1bf837de1943975550126f13fe7150
Parents: f9125d0
Author: Luc Maisonobe 
Authored: Tue Dec 16 17:00:25 2014 +0100
Committer: Luc Maisonobe 
Committed: Tue Dec 16 17:03:40 2014 +0100

--
 pom.xml | 21 +
 1 file changed, 21 insertions(+)
--


http://git-wip-us.apache.org/repos/asf/commons-math/blob/17c90338/pom.xml
--
diff --git a/pom.xml b/pom.xml
index 46da7d8..3ee5db2 100644
--- a/pom.xml
+++ b/pom.xml
@@ -390,6 +390,12 @@
 math
 
https://svn.apache.org/repos/infra/websites/production/commons/content/proper/commons-math
 
site-content
+
+
+true
+1.2.8
+${git.branch}-${git.revision}; 
${maven.build.timestamp}
+
   
 
   
@@ -514,6 +520,21 @@
   -header '<script 
type="text/javascript" 
src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>&apos;
 
   
+  
+ru.concerteza.buildnumber
+maven-jgit-buildnumber-plugin
+${math.jgit.buildnumber.version}
+
+  
+generate-resources
+
+  extract-buildnumber
+
+  
+
+
+
+  
 
   
 






[math] Added Cheng sampling procedure for beta distribution.


2014-12-16

Thread
luc

Repository: commons-math
Updated Branches:
  refs/heads/MATH-1153 [created] 9ba0a1cad


Added Cheng sampling procedure for beta distribution.

Thanks to Sergei Lebedev for the patch.

JIRA: MATH-1153

Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/9ba0a1ca
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/9ba0a1ca
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/9ba0a1ca

Branch: refs/heads/MATH-1153
Commit: 9ba0a1cadf37b0d1c68b01c706a10a042e19e1f6
Parents: d9b951c
Author: Luc Maisonobe 
Authored: Tue Dec 16 21:48:44 2014 +0100
Committer: Luc Maisonobe 
Committed: Tue Dec 16 21:48:44 2014 +0100

--
 pom.xml |   3 +
 .../math3/distribution/BetaDistribution.java| 139 +++
 .../distribution/BetaDistributionTest.java  |  74 ++
 3 files changed, 192 insertions(+), 24 deletions(-)
--


http://git-wip-us.apache.org/repos/asf/commons-math/blob/9ba0a1ca/pom.xml
--
diff --git a/pom.xml b/pom.xml
index 3ee5db2..667d36e 100644
--- a/pom.xml
+++ b/pom.xml
@@ -252,6 +252,9 @@
   Piotr Kochanski
 
 
+  Sergei Lebedev
+
+
   Bob MacCallum
 
 

http://git-wip-us.apache.org/repos/asf/commons-math/blob/9ba0a1ca/src/main/java/org/apache/commons/math3/distribution/BetaDistribution.java
--
diff --git 
a/src/main/java/org/apache/commons/math3/distribution/BetaDistribution.java 
b/src/main/java/org/apache/commons/math3/distribution/BetaDistribution.java
index 3f62f64..458fe23 100644
--- a/src/main/java/org/apache/commons/math3/distribution/BetaDistribution.java
+++ b/src/main/java/org/apache/commons/math3/distribution/BetaDistribution.java
@@ -23,6 +23,7 @@ import org.apache.commons.math3.random.Well19937c;
 import org.apache.commons.math3.special.Beta;
 import org.apache.commons.math3.special.Gamma;
 import org.apache.commons.math3.util.FastMath;
+import org.apache.commons.math3.util.Precision;
 
 /**
  * Implements the Beta distribution.
@@ -34,10 +35,12 @@ public class BetaDistribution extends 
AbstractRealDistribution {
 /**
  * Default inverse cumulative probability accuracy.
  * @since 2.1
+ * @deprecated as of 3.4, this parameter is not used anymore
  */
+@Deprecated
 public static final double DEFAULT_INVERSE_ABSOLUTE_ACCURACY = 1e-9;
 /** Serializable version identifier. */
-private static final long serialVersionUID = -1221965979403477668L;
+private static final long serialVersionUID = 20141216L;
 /** First shape parameter. */
 private final double alpha;
 /** Second shape parameter. */
@@ -46,8 +49,6 @@ public class BetaDistribution extends 
AbstractRealDistribution {
  * updated whenever alpha or beta are changed.
  */
 private double z;
-/** Inverse cumulative probability accuracy. */
-private final double solverAbsoluteAccuracy;
 
 /**
  * Build a new instance.
@@ -63,7 +64,7 @@ public class BetaDistribution extends 
AbstractRealDistribution {
  * @param beta Second shape parameter (must be positive).
  */
 public BetaDistribution(double alpha, double beta) {
-this(alpha, beta, DEFAULT_INVERSE_ABSOLUTE_ACCURACY);
+this(new Well19937c(), alpha, beta);
 }
 
 /**
@@ -82,9 +83,11 @@ public class BetaDistribution extends 
AbstractRealDistribution {
  * cumulative probability estimates (defaults to
  * {@link #DEFAULT_INVERSE_ABSOLUTE_ACCURACY}).
  * @since 2.1
+ * @deprecated as of 3.4, the inverse cumulative accuracy is not used 
anymore
  */
+@Deprecated
 public BetaDistribution(double alpha, double beta, double 
inverseCumAccuracy) {
-this(new Well19937c(), alpha, beta, inverseCumAccuracy);
+this(alpha, beta);
 }
 
 /**
@@ -96,7 +99,11 @@ public class BetaDistribution extends 
AbstractRealDistribution {
  * @since 3.3
  */
 public BetaDistribution(RandomGenerator rng, double alpha, double beta) {
-this(rng, alpha, beta, DEFAULT_INVERSE_ABSOLUTE_ACCURACY);
+super(rng);
+
+this.alpha = alpha;
+this.beta = beta;
+z = Double.NaN;
 }
 
 /**
@@ -109,17 +116,14 @@ public class BetaDistribution extends 
AbstractRealDistribution {
  * cumulative probability estimates (defaults to
  * {@link #DEFAULT_INVERSE_ABSOLUTE_ACCURACY}).
  * @since 3.1
+ * @deprecated as of 3.4, the inverse cumulative accuracy is not used 
anymore
  */
+@Deprecated
 public BetaDistribution(RandomGenerator rng,
 double alpha,
 double beta



[math] Use static internal class and method for Cheng's sampling.


2014-12-17

Thread
luc

Repository: commons-math
Updated Branches:
  refs/heads/MATH-1153 9ba0a1cad -> 84a642266


Use static internal class and method for Cheng's sampling.

The static components allow an implementation closer to the original
patch contribution, avoiding weird variables renamings.

Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/84a64226
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/84a64226
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/84a64226

Branch: refs/heads/MATH-1153
Commit: 84a642266dcebf24ed02670e26d0e41153af4f9c
Parents: 9ba0a1c
Author: Luc Maisonobe 
Authored: Wed Dec 17 11:05:56 2014 +0100
Committer: Luc Maisonobe 
Committed: Wed Dec 17 11:05:56 2014 +0100

--
 .../math3/distribution/BetaDistribution.java| 170 +++
 1 file changed, 101 insertions(+), 69 deletions(-)
--


http://git-wip-us.apache.org/repos/asf/commons-math/blob/84a64226/src/main/java/org/apache/commons/math3/distribution/BetaDistribution.java
--
diff --git 
a/src/main/java/org/apache/commons/math3/distribution/BetaDistribution.java 
b/src/main/java/org/apache/commons/math3/distribution/BetaDistribution.java
index 458fe23..d7a3f28 100644
--- a/src/main/java/org/apache/commons/math3/distribution/BetaDistribution.java
+++ b/src/main/java/org/apache/commons/math3/distribution/BetaDistribution.java
@@ -270,91 +270,123 @@ public class BetaDistribution extends 
AbstractRealDistribution {
  */
 @Override
 public double sample() {
-if (FastMath.min(alpha, beta) > 1) {
-return algorithmBB();
-} else {
-return algorithmBC();
-}
+return ChengBetaSampler.sample(random, alpha, beta);
 }
 
-/** Returns one sample using Cheng's BB algorithm, when both α and 
β are greater than 1.
- * @return sampled value
+/** Utility class implementing Cheng's algorithms for beta distribution 
sampling.
+ * 
+ * R. C. H. Cheng, "Generating beta variates with nonintegral shape 
parameters.".
+ * Communications of the ACM, 21, 317–322, 1978.
+ * 
+ * @since 3.4
  */
-private double algorithmBB() {
-final double a = FastMath.min(alpha, beta);
-final double b = FastMath.max(alpha, beta);
-final double newAlpha = a + b;
-final double newBeta = FastMath.sqrt((newAlpha - 2.) / (2. * a * b - 
newAlpha));
-final double gamma = a + 1. / newBeta;
-
-double r;
-double w;
-double t;
-do {
-final double u1 = random.nextDouble();
-final double u2 = random.nextDouble();
-final double v = newBeta * FastMath.log(u1 / (1. - u1));
-w = a * FastMath.exp(v);
-final double newZ = u1 * u1 * u2;
-r = gamma * v - 1.3862944;
-final double s = a + r - w;
-if (s + 2.609438 >= 5 * newZ) {
-break;
-}
+private static class ChengBetaSampler {
 
-t = FastMath.log(newZ);
-if (s >= t) {
-break;
-}
-} while (r + newAlpha * FastMath.log(newAlpha / (b + w)) < t);
+/** Private constructor for a utility method.
+ */
+private ChengBetaSampler() {
+}
 
-w = FastMath.min(w, Double.MAX_VALUE);
-return Precision.equals(a, alpha) ? w / (b + w) : b / (b + w);
-}
+/** Returns one sample using Cheng's BB algorithm, when both α 
and β are greater than 1.
+ * @param random random generator to use
+ * @param a0 distribution first shape parameter
+ * @param b0 distribution second shape parameter
+ * @return sampled value
+ */
+public static double algorithmBB(final RandomGenerator random, final 
double a0, final double b0) {
+final double a = FastMath.min(a0, b0);
+final double b = FastMath.max(a0, b0);
+final double alpha = a + b;
+final double beta = FastMath.sqrt((alpha - 2.) / (2. * a * b - 
alpha));
+final double gamma = a + 1. / beta;
 
-/** Returns one sample using Cheng's BC algorithm, when at least one of 
α and β is smaller than 1.
- * @return sampled value
- */
-private double algorithmBC() {
-final double a = FastMath.max(alpha, beta);
-final double b = FastMath.min(alpha, beta);
-final double newAlpha = a + b;
-final double newBeta = 1. / b;
-final double delta = 1. + a - b;
-final double k1 = delta * (0.0138889 + 0.0416667 * b) / (a * newBeta - 
0.78);
-final double k2 = 0.25 + (0.5 + 0.



[math] Removed unnecessary attribution, as per discussion on developers list.


2014-12-17

Thread
luc

Repository: commons-math
Updated Branches:
  refs/heads/master 44401d183 -> 88516d95e


Removed unnecessary attribution, as per discussion on developers list.

Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/88516d95
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/88516d95
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/88516d95

Branch: refs/heads/master
Commit: 88516d95ebfa4106f52a45cff9c4c97f4ce28066
Parents: 44401d1
Author: Luc Maisonobe 
Authored: Wed Dec 17 12:01:42 2014 +0100
Committer: Luc Maisonobe 
Committed: Wed Dec 17 12:01:42 2014 +0100

--
 NOTICE.txt | 28 
 1 file changed, 28 deletions(-)
--


http://git-wip-us.apache.org/repos/asf/commons-math/blob/88516d95/NOTICE.txt
--
diff --git a/NOTICE.txt b/NOTICE.txt
index c7b078a..6a6ac87 100644
--- a/NOTICE.txt
+++ b/NOTICE.txt
@@ -78,34 +78,6 @@ Copyright (c) 2008, Frances Y. Kuo and Stephen Joe
 All rights reserved.
 ===
 
-The initial commit of the class "org.apache.commons.math3.special.BesselJ" is
-an adapted version of code translated from the netlib Fortran program, rjbesl
-http://www.netlib.org/specfun/rjbesl.  The Fortran source includes the
-following Acknowledgement
-
-   This program is based on a program written by David J. Sookne
-   (2) that computes values of the Bessel functions J or I of real
-   argument and integer order.  Modifications include the restriction
-   of the computation to the J Bessel function of non-negative real
-   argument, the extension of the computation to arbitrary positive
-   order, and the elimination of most underflow.
-
-  References: "A Note on Backward Recurrence Algorithms," Olver,
-   F. W. J., and Sookne, D. J., Math. Comp. 26, 1972,
-   pp 941-947.
-
-  "Bessel Functions of Real Argument and Integer Order,"
-   Sookne, D. J., NBS Jour. of Res. B. 77B, 1973, pp
-   125-132.
-
-  Latest modification: March 19, 1990
-
-  Author: W. J. Cody
-  Applied Mathematics Division
-  Argonne National Laboratory
-  Argonne, IL  60439
-===
-
 
 The complete text of licenses and disclaimers associated with the the original
 sources enumerated above at the time of code translation are in the LICENSE.txt






[2/5] [math] Prevent RAT plugin from complaining about spurious development files.


2014-12-17

Thread
luc

Prevent RAT plugin from complaining about spurious development files.

Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/3b58a282
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/3b58a282
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/3b58a282

Branch: refs/heads/master
Commit: 3b58a282b96cca7b330405573d148de9f6cb3b83
Parents: 2ed43de
Author: Luc Maisonobe 
Authored: Wed Dec 17 19:01:56 2014 +0100
Committer: Luc Maisonobe 
Committed: Wed Dec 17 19:01:56 2014 +0100

--
 pom.xml | 1 +
 1 file changed, 1 insertion(+)
--


http://git-wip-us.apache.org/repos/asf/commons-math/blob/3b58a282/pom.xml
--
diff --git a/pom.xml b/pom.xml
index 13b0e2a..f5ba759 100644
--- a/pom.xml
+++ b/pom.xml
@@ -614,6 +614,7 @@
 .gitignore
 .git/**
 .checkstyle
+.ekstazi/**
 
   
 






[4/5] [math] Prepare link gor 3.4 javadoc.


2014-12-17

Thread
luc

Prepare link gor 3.4 javadoc.

Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/3d97f854
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/3d97f854
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/3d97f854

Branch: refs/heads/master
Commit: 3d97f8548431751e87201c82937015390933e0ae
Parents: f9437bc
Author: Luc Maisonobe 
Authored: Wed Dec 17 19:03:14 2014 +0100
Committer: Luc Maisonobe 
Committed: Wed Dec 17 19:03:14 2014 +0100

--
 src/site/site.xml | 2 ++
 1 file changed, 2 insertions(+)
--


http://git-wip-us.apache.org/repos/asf/commons-math/blob/3d97f854/src/site/site.xml
--
diff --git a/src/site/site.xml b/src/site/site.xml
index e8b78e0..f493131 100644
--- a/src/site/site.xml
+++ b/src/site/site.xml
@@ -27,6 +27,8 @@
   
   http://commons.apache.org/math/download_math.cgi"/>
   
+  http://commons.apache.org/math/javadocs/api-3.4/index.html"/>
   http://commons.apache.org/math/javadocs/api-3.3/index.html"/>
   




[5/5] [math] Update release howto for Git-based release.


2014-12-17

Thread
luc

Update release howto for Git-based release.

Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/e27f6e71
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/e27f6e71
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/e27f6e71

Branch: refs/heads/master
Commit: e27f6e71f28e8180a391e6323057c19a2d5c628b
Parents: 3d97f85
Author: Luc Maisonobe 
Authored: Wed Dec 17 19:03:42 2014 +0100
Committer: Luc Maisonobe 
Committed: Wed Dec 17 19:03:42 2014 +0100

--
 doc/release/release.howto.txt | 177 -
 1 file changed, 115 insertions(+), 62 deletions(-)
--


http://git-wip-us.apache.org/repos/asf/commons-math/blob/e27f6e71/doc/release/release.howto.txt
--
diff --git a/doc/release/release.howto.txt b/doc/release/release.howto.txt
index 951bc2f..6bc099f 100644
--- a/doc/release/release.howto.txt
+++ b/doc/release/release.howto.txt
@@ -22,7 +22,7 @@ main site: at 
"http://commons.apache.org/releases/prepare.html"; and
 
 The files "settings-security.xml" and "settings.xml" are minimal examples
 of files used by maven to pick up authentication credentials needed to
-connect to remote servers and to cryptographically sign the artefacts.
+connect to remote servers and to cryptographically sign the artifacts.
 
 (0)
 Preliminary checks:
@@ -38,42 +38,82 @@ Preliminary checks:
 
 (1)
 As a first optional step, you can test that everything works locally, i.e.
-that the build process can create all the necessary artefacts. The command
+that the build process can create all the necessary artifacts. The command
 
   $ mvn clean deploy -Prelease -Ptest-deploy
 
-should create the artefacts in the "target/deploy".
+should create the artifacts in the "target/deploy".
 
 
 (2)
 At this point, you should commit everything that will be part of the release.
+Since [math] has switched to git as its version control system, this can be
+easily on the release manager local host in a branch. We will use the same 
branch
+for all release candidates, so the branch will be named 
MATH_3_2_RELEASE_CANDIDATES.
+The branch will only be used to store the release specific parts (i.e. the pom 
changes
+with the version number, the release date in the site and so on). Everything 
else
+and in particular code change that will remain in the component after the 
release
+must be committed to the master branch. The release candidate branch will be 
synchronised
+with master at the start of each new candidate for this particular release.
+
+The example below show a typical workflow. Just after commit A in the master 
branch, the
+release candidate branch is created starting from master. This is shown by the 
'b' in the
+second line. Then release candidate specific commits are made on the pom and a 
few other
+files, leading to a commit which will be tagged as RC1. This release candidate 
fails, and
+a few corrections need to be made on master, corresponding to commits B and C. 
Then the
+release candidate branch is synchronized by running a 'git merge' command on 
the branch.
+This is shown by the 'm' in the second line. A new commit is tagged as RC2. 
This second
+release candidate also fails, and a new correction is made on master branch, a 
new merge
+is done on the release branch, a new commit is tagged and a third release 
candidate is
+create, which succeds. Then a final tag will be added on the final commit of 
this branch
+showing the status as released.
+
+
+ A-> B > C--> D-> <- 
master branch
+  \   \\
+   b---> RC1 --m---> RC2 ---m---> RC3/final release<- release 
candidates branch
+
+This process allows to never commit release candidate specific changes to the 
master
+branch (so the pom on master always holds a SNAPSHOT version). Is also allows
+future reference to the release preserving all history.
+
+If the release candidates branch does not exist because it is the first release
+candidate, create it starting from the master branch:
+
+  $ git branch MATH_3_2_RELEASE_CANDIDATES
+
+(3)
+Switch to the release candidate branch:
+
+  $ git checkout MATH_3_2_RELEASE_CANDIDATES
+
+(4)
+If there have been changes committed in the master branch since the creation of
+the release candidate branch and if these changes must be included in the 
release
+candidate, merge master branch into release candidates branch
+
+  $ git merge master
+
+(5)
+Update the release specific files, checking you are really working on the
+release candidate branch and *not* on the master branch.
 
 In particular:
  * Update a



[3/5] [math] Candidate release date ...


2014-12-17

Thread
luc

Candidate release date ...

Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/f9437bc6
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/f9437bc6
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/f9437bc6

Branch: refs/heads/master
Commit: f9437bc64206fc4963ec511373fff06250785085
Parents: 3b58a28
Author: Luc Maisonobe 
Authored: Wed Dec 17 19:02:35 2014 +0100
Committer: Luc Maisonobe 
Committed: Wed Dec 17 19:02:35 2014 +0100

--
 src/changes/changes.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)
--


http://git-wip-us.apache.org/repos/asf/commons-math/blob/f9437bc6/src/changes/changes.xml
--
diff --git a/src/changes/changes.xml b/src/changes/changes.xml
index ba61bb4..545366d 100644
--- a/src/changes/changes.xml
+++ b/src/changes/changes.xml
@@ -50,7 +50,7 @@ If the output is not quite correct, check for invisible 
trailing spaces!
 Commons Math Release Notes
   
   
-



[1/5] [math] Setting up realistic limits for JaCoCo.


2014-12-17

Thread
luc

Repository: commons-math
Updated Branches:
  refs/heads/master 88516d95e -> e27f6e71f


Setting up realistic limits for JaCoCo.

I think we never met the previous default settings, but did not notice
it in the maven logs before.

Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/2ed43de9
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/2ed43de9
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/2ed43de9

Branch: refs/heads/master
Commit: 2ed43de903902fb93f042bcc52cd05c4f02b7cdf
Parents: 88516d9
Author: Luc Maisonobe 
Authored: Wed Dec 17 19:01:27 2014 +0100
Committer: Luc Maisonobe 
Committed: Wed Dec 17 19:01:27 2014 +0100

--
 pom.xml | 7 +++
 1 file changed, 7 insertions(+)
--


http://git-wip-us.apache.org/repos/asf/commons-math/blob/2ed43de9/pom.xml
--
diff --git a/pom.xml b/pom.xml
index 3ee5db2..13b0e2a 100644
--- a/pom.xml
+++ b/pom.xml
@@ -386,6 +386,13 @@
 
 
 0.7.0.201403182114
+0.96
+0.8
+0.8
+0.8
+0.8
+0.85
+false
 
 math
 
https://svn.apache.org/repos/infra/websites/production/commons/content/proper/commons-math






[math] Improved release process documentation with Git.


2014-12-18

Thread
luc

Repository: commons-math
Updated Branches:
  refs/heads/master e27f6e71f -> 20c577868


Improved release process documentation with Git.

Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/20c57786
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/20c57786
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/20c57786

Branch: refs/heads/master
Commit: 20c577868c2217fdaa6de70848d40c5a78340deb
Parents: e27f6e7
Author: Luc Maisonobe 
Authored: Thu Dec 18 21:11:35 2014 +0100
Committer: Luc Maisonobe 
Committed: Thu Dec 18 21:11:35 2014 +0100

--
 doc/release/release.howto.txt | 151 +++--
 1 file changed, 113 insertions(+), 38 deletions(-)
--


http://git-wip-us.apache.org/repos/asf/commons-math/blob/20c57786/doc/release/release.howto.txt
--
diff --git a/doc/release/release.howto.txt b/doc/release/release.howto.txt
index 6bc099f..74224dc 100644
--- a/doc/release/release.howto.txt
+++ b/doc/release/release.howto.txt
@@ -24,6 +24,52 @@ The files "settings-security.xml" and "settings.xml" are 
minimal examples
 of files used by maven to pick up authentication credentials needed to
 connect to remote servers and to cryptographically sign the artifacts.
 
+Since [math] has switched to git as its version control system, release 
preparation
+can be done easily on the release manager local host in a branch. We will use a
+temporary branch for all release candidates, and delete it afterwards, so the 
branch
+will be simply named release-candidates. The branch will only be used to store 
the
+release specific parts (i.e. the pom changes with the version number, the 
release date
+in the site and so on). Everything else and in particular code change that 
will remain
+in the component after the release must be committed to the master branch. The 
release
+candidate branch will be synchronized with master at the start of each new 
candidate for
+this particular release. Once the release is done, the branch will be merged 
back to
+master and deleted. Of course, this will not delete the history, only the name
+release-candidates pointing to the head of this branch will disappear and can 
be reused
+for next version.
+
+The example below show a typical workflow. Just after commit A in the master 
branch, the
+release-candidate branch is created starting from master. This is shown by the 
'b' in the
+second line. Then release candidate specific commits are made on the pom and a 
few other
+files, leading to a commit which will be tagged as RC1. This release candidate 
fails, and
+a few corrections need to be made on master, corresponding to commits B and C. 
Then the
+release candidate branch is synchronized by running a 'git merge' command on 
the branch.
+This is shown by the 'm' in the second line. A new commit is tagged as RC2. 
This second
+release candidate also fails, and a new correction is made on master branch, a 
new merge
+is done on the release branch, a new commit is tagged and a third release 
candidate is
+create, which succeeds. Then a final tag will be added on the final commit of 
this branch
+showing the status as released. Then the files are cleaned to prepare for next 
version
+(pom getting again a SNAPSHOT suffix, changes.xml getting a new placeholder 
for changes)
+and the cleaned branch is merged back to master. Once the branch has been 
merged, it is not
+useful anymore so it is deleted, hence the name release-candidate can be used 
again for
+the release branch of the next version.
+
+
+ A---> B --> C--> 
D--m><- master branch
+  \   \\/
+   b---> RC1 --m---> RC2 ---m---> RC3/final release --> cleaning --X   
<- release-candidates branch
+
+This process allows:
+
+ - to never commit release candidate specific changes to the master
+   branch (so the pom on master always holds a SNAPSHOT version),
+ - to preserve future reference to the release
+ - to allow parallel work on master during the release
+ - if necessary to have multiple release managers or help on the
+   release as the release-candidates branch is shared
+ - to abort a release by deleting the branch early if some
+   larger change is needed on master
+
+
 (0)
 Preliminary checks:
  * All Java files must contain a license header. The "RAT" maven plugin will
@@ -46,57 +92,37 @@ should create the artifacts in the "target/deploy".
 
 
 (2)
-At this point, you should commit everything that will be part of the release.
-Since [math] has switched to git as its version 



[math] Added the command to check Git tag GPG signature


2014-12-18

Thread
luc

Repository: commons-math
Updated Branches:
  refs/heads/master 20c577868 -> 1a9697311


Added the command to check Git tag GPG signature

Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/1a969731
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/1a969731
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/1a969731

Branch: refs/heads/master
Commit: 1a969731191b215163681d324acca0c836437c61
Parents: 20c5778
Author: Luc Maisonobe 
Authored: Thu Dec 18 21:28:04 2014 +0100
Committer: Luc Maisonobe 
Committed: Thu Dec 18 21:28:04 2014 +0100

--
 doc/release/release.howto.txt | 10 --
 1 file changed, 8 insertions(+), 2 deletions(-)
--


http://git-wip-us.apache.org/repos/asf/commons-math/blob/1a969731/doc/release/release.howto.txt
--
diff --git a/doc/release/release.howto.txt b/doc/release/release.howto.txt
index 74224dc..7823b0d 100644
--- a/doc/release/release.howto.txt
+++ b/doc/release/release.howto.txt
@@ -203,12 +203,16 @@ Then, assuming the first candidate, the suffix will be 
"RC1" (this should
 be the  same as in the "" in the "pom.xml"), and the command
 will be:
 
-  $ git tag -s -m "Creating Commons Math v3.2 RC1 tag." MATH_3_2_RC1
+  $ git tag -s -m "Creating Apache Commons Math v3.2 RC1 tag." MATH_3_2_RC1
 
 If you have several GPG keys, you may prefer to use "-u keyId" to select a 
specific
 key for signing the tag instead of "-s" which select automatically one key
 from the configured e-mail address.
 
+Check the tag GPG signature:
+
+  $ git tag -v MATH_3_2_RC1
+
 Push everything (including the tag!) on the Apache repository:
 
   $ git push --tags
@@ -316,8 +320,10 @@ Call to vote by sending a message to the "dev" ML with 
subject
 "[VOTE][RC1] Release Commons Math 3.2". You can use the following example as
 a starting point, replacing the URLs with the appropriate ones:
 --
-Tag:
+Tag (and how to check its GPG signature):
   git clone https://git-wip-us.apache.org/repos/asf/commons-math.git --branch 
MATH_3_2_RC1
+  cd commons-math
+  git tag -v MATH_3_2_RC1
 
 Site:
   http://people.apache.org/builds/commons/math/3.2/RC1/






Git Push Summary


2014-12-18

Thread
luc

Repository: commons-math
Updated Tags:  refs/tags/MATH_3_4_RC1 [created] f38f96a0b





[math] creating release candidate


2014-12-18

Thread
luc

Repository: commons-math
Updated Branches:
  refs/heads/release-candidates [created] cf4a9d70c


creating release candidate


Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo
Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/cf4a9d70
Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/cf4a9d70
Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/cf4a9d70

Branch: refs/heads/release-candidates
Commit: cf4a9d70c9ac24dd7196995390171150e4e56451
Parents: 1a96973
Author: Luc Maisonobe 
Authored: Thu Dec 18 21:19:05 2014 +0100
Committer: Luc Maisonobe 
Committed: Thu Dec 18 21:29:08 2014 +0100

--
 RELEASE-NOTES.txt | 27 +--
 pom.xml   |  4 ++--
 2 files changed, 23 insertions(+), 8 deletions(-)
--


http://git-wip-us.apache.org/repos/asf/commons-math/blob/cf4a9d70/RELEASE-NOTES.txt
--
diff --git a/RELEASE-NOTES.txt b/RELEASE-NOTES.txt
index 7930ea8..7bcdbe3 100644
--- a/RELEASE-NOTES.txt
+++ b/RELEASE-NOTES.txt
@@ -1,9 +1,11 @@
 
   Apache Commons Math 3.4 RELEASE NOTES
 
-The Apache Commons Math team is pleased to announce the release of 
commons-math3-3.4-SNAPSHOT
+The Apache Commons Math team is pleased to announce the release of 
commons-math3-3.4
 
-The Apache Commons Math project is a library of lightweight, self-contained 
mathematics and statistics components addressing the most common practical 
problems not immediately available in the Java programming language or 
commons-lang.
+The Apache Commons Math project is a library of lightweight, self-contained 
mathematics
+and statistics components addressing the most common practical problems not 
immediately
+available in the Java programming language or commons-lang.
 
 This is a minor release: It combines bug fixes and new features.
 Changes to existing features were made in a backwards-compatible
@@ -13,11 +15,12 @@ Most notable among the new features are:
 new distributions (Gumbel, Laplace, Logistic, Nakagami), and
 improvements on percentiles algorithms (better handling for NaNs
 in the regular algorithm, plus a new storeless implementation).
-Bicubic splines interpolators have been fixed and new implementations
-added. There have been numerous bug fixes and several improvements
-on performances or robustness. See below for a full list)
+Bicubic and tricubic interpolators have been fixed and new
+implementations added. There have been numerous bug fixes and
+several improvements on performances or robustness. See below
+for a full list.
 
- The minimum version of the Java platform required to compile and use
+The minimum version of the Java platform required to compile and use
 Apache Commons Math is Java 5.
 
 Users are encouraged to upgrade to this version as this release not
@@ -36,6 +39,12 @@ Caveat:
 Changes in this version include:
 
 New features:
+o MATH-1066:  Added Bessel functions of the first kind, based on NetLib 
implementation. Thanks to Brian Wignall. 
+o MATH-1180:  Method to create a sequence of integers (in 
"o.a.c.m.util.MathArrays"). 
+o MATH-1172:  New class "SimpleCurveFitter": Boiler-plate code to allow 
fitting of
+a user-defined parametric function. 
+o MATH-1173:  New classes "TricubicInterpolatingFunction" and 
"TricubicInterpolator" to
+replace "TricubicSplineInterpolatingFunction" and 
"TricubicSplineInterpolator". 
 o MATH-1166:  New classes "BicubicInterpolatingFunction" and 
"BicubicInterpolator" to
 replace "BicubicSplineInterpolatingFunction" and 
"BicubicSplineInterpolator". 
 o   Boundary attributes in regions now provides the BSP tree nodes that
@@ -53,6 +62,12 @@ o MATH-418:  Added implementation of PSquare algorithm to 
estimate percentiles w
 storing data in memory (i.e. as StorelessUnivariateStatistic). Thanks 
to Venkatesha Murthy. 
 
 Fixed Bugs:
+o MATH-1142:  Improve performance of kalman gain calculation in "KalmanFilter" 
by
+directly solving a linear system rather than computing the matrix
+inverse. Thanks to Arne Schwarz. 
+o MATH-1181:  Fixed integer overflow in KolmogorovSmirnovTest causing 2-sample 
test
+to use exact method when the product of the sample sizes exceeds 
+Integer.MAX_VALUE, resulting in effectively hung execution. 
 o MATH-1178:  Fixed example in userguide ("stat" section). Thanks to Dmitriy. 
 o MATH-1175:  Fixed inverse cumulative probability of 0 in 
"LaplaceDistribution". Thanks to Karsten Loesing. 
 o MATH-1174:  Fixed a problem with too thin polygons considered to have 
infinite size. 

http://git-wip-us.apache.org/repos/asf/commons-math/blob/cf4a9d70/pom.xml
---



svn commit: r933283 [3/8] - /websites/production/commons/content/proper/commons-math/


2014-12-18

Thread
luc

Modified: 
websites/production/commons/content/proper/commons-math/checkstyle.html
==
--- websites/production/commons/content/proper/commons-math/checkstyle.html 
(original)
+++ websites/production/commons/content/proper/commons-math/checkstyle.html Thu 
Dec 18 23:11:03 2014
@@ -1,13 +1,13 @@
 
 
 http://www.w3.org/1999/xhtml"; xml:lang="en" lang="en">
   
 
 
-
+
 
 Math - Checkstyle Results
 
@@ -40,8 +40,8 @@
http://commons.apache.org/proper/commons-math/";>Apache Commons Math 
™
  
 
-Last Published: 18 October 2014
-  | Version: 
3.4-SNAPSHOT
+Last Published: 18 December 2014
+  | Version: 3.4
   


@@ -82,6 +82,10 @@
 Latest API docs (development)



+ 
+Javadoc (3.4 release)
+   
+   

  
 Javadoc (3.3 release)

@@ -366,7 +370,7 @@
 Warnings 
 Errors 
 
-914
+927
 0
 0
 0

Modified: websites/production/commons/content/proper/commons-math/checkstyle.rss
==
Binary files - no diff available.

Modified: 
websites/production/commons/content/proper/commons-math/clirr-report.html
==
--- websites/production/commons/content/proper/commons-math/clirr-report.html 
(original)
+++ websites/production/commons/content/proper/commons-math/clirr-report.html 
Thu Dec 18 23:11:03 2014
@@ -1,13 +1,13 @@
 
 
 http://www.w3.org/1999/xhtml"; xml:lang="en" lang="en">
   
 
 
-
+
 
 Math - Clirr Results
 
@@ -40,8 +40,8 @@
http://commons.apache.org/proper/commons-math/";>Apache Commons Math 
™
  
 
-Last Published: 18 October 2014
-  | Version: 
3.4-SNAPSHOT
+Last Published: 18 December 2014
+  | Version: 3.4
   


@@ -82,6 +82,10 @@
 Latest API docs (development)



+ 
+Javadoc (3.4 release)
+   
+   

  
 Javadoc (3.3 release)

@@ -358,7 +362,7 @@
 Clirr Results
 The following document contains the results of http://clirr.sourceforge.net/";>Clirr.
 
-Current Version: 3.4-SNAPSHOT
+Current Version: 3.4
 Comparison Version: 3.3
 
 Summary
@@ -368,13 +372,13 @@
 Number
 
  Error
-7
+0
 
  Warning
 0
 
  Info
-58
+84
 
 Details
 
@@ -384,60 +388,70 @@
 Class
 Method / Field
 
-
-In method 'public BicubicSplineInterpolatingFunction(double[], double[], 
double[][], double[][], double[][], double[][])' the number of arguments has 
changed
-org.apache.commons.math3.analysis.interpolation.BicubicSplineInterpolatingFunction
-public BicubicSplineInterpolatingFunction(double[], double[], double[][], 
double[][], double[][], double[][])
+
+Class 
org.apache.commons.math3.analysis.interpolation.AkimaSplineInterpolator 
added
+org.apache.commons.math3.analysis.interpolation.AkimaSplineInterpolator
+
 
-
-Method 'public double partialDerivativeX(double, double)' has been 
removed
-org.apache.commons.math3.analysis.interpolation.BicubicSplineInterpolatingFunction
-public double partialDerivativeX(double, double)
+
+Class 
org.apache.commons.math3.analysis.interpolation.BicubicInterpolatingFunction 
added
+org.apache.commons.math3.analysis.interpolation.BicubicInterpolatingFunction
+
 
-
-Method 'public double partialDerivativeXX(double, double)' has been 
removed
-org.apache.commons.math3.analysis.interpolation.BicubicSplineInterpolatingFunction
-public double partialDerivativeXX(double, double)
+
+Class org.apache.commons.math3.analysis.interpolation.BicubicInterpolator 
added
+org.apache.commons.math3.analysis.interpolation.BicubicInterpolator
+
 
-
-Method 'public double partialDerivativeXY(double, double)' has been 
removed
+
+Method 'public BicubicSplineInterpolatingFunction(double[], double[], 
double[][], double[][], double[][], double[][], boolean)' has been added
 org.apache.commons.math3.analysis.interpol



svn commit: r933283 [4/8] - /websites/production/commons/content/proper/commons-math/


2014-12-18

Thread
luc

Modified: 
websites/production/commons/content/proper/commons-math/jdepend-report.html
==
--- websites/production/commons/content/proper/commons-math/jdepend-report.html 
(original)
+++ websites/production/commons/content/proper/commons-math/jdepend-report.html 
Thu Dec 18 23:11:03 2014
@@ -1,13 +1,13 @@
 
 
 http://www.w3.org/1999/xhtml"; xml:lang="en" lang="en">
   
 
 
-
+
 
 Math - JDepend Report Metrics
 
@@ -40,8 +40,8 @@
http://commons.apache.org/proper/commons-math/";>Apache Commons Math 
™
  
 
-Last Published: 18 October 2014
-  | Version: 
3.4-SNAPSHOT
+Last Published: 18 December 2014
+  | Version: 3.4
   


@@ -82,6 +82,10 @@
 Latest API docs (development)



+ 
+Javadoc (3.4 release)
+   
+   

  
 Javadoc (3.3 release)

@@ -385,11 +389,11 @@
 41
 27
 14
-25
+26
 5
 34.0%
-17.0%
-49.0%
+16.0%
+50.0%
 1
 
 org.apache.commons.math3.analysis.differentiation
@@ -437,14 +441,14 @@
 1
 
 org.apache.commons.math3.analysis.interpolation
-23
-19
+39
+35
 4
 1
 15
-17.0%
+10.0%
 94.0%
-11.0%
+4.0%
 1
 
 org.apache.commons.math3.analysis.polynomials
@@ -528,10 +532,10 @@
 6
 4
 2
-48
+50
 4
 33.0%
-8.0%
+7.0%
 58.96%
 1
 
@@ -547,8 +551,8 @@
 1
 
 org.apache.commons.math3.fitting
+25
 24
-23
 1
 1
 13
@@ -558,14 +562,14 @@
 1
 
 org.apache.commons.math3.fitting.leastsquares
-29
+30
 21
-8
+9
 1
 8
-28.0%
+30.02%
 89.0%
-16.0%
+19.0%
 1
 
 org.apache.commons.math3.fraction
@@ -639,10 +643,10 @@
 18
 0
 3
-14
+13
 0.0%
-82.0%
-18.0%
+81.0%
+19.0%
 1
 
 org.apache.commons.math3.geometry.euclidean.twod.hull
@@ -668,25 +672,25 @@
 1
 
 org.apache.commons.math3.geometry.partitioning
-31
-22
-9
+38
+28
+10
 7
 6
-29.0%
+26.0%
 46.0%
-25.0%
+28.0%
 1
 
 org.apache.commons.math3.geometry.partitioning.utilities
 5
 5
 0
-1
+0
 3
 0.0%
-75.0%
-25.0%
+100.0%
+0.0%
 1
 
 org.apache.commons.math3.geometry.spherical.oned
@@ -1031,14 +1035,14 @@
 1
 
 org.apache.commons.math3.special
-5
-5
+7
+7
 0
 1
-3
+6
 0.0%
-75.0%
-25.0%
+86.0%
+14.0%
 1
 
 org.apache.commons.math3.stat
@@ -1218,11 +1222,11 @@
 Instability
 Distance
 
-25
+26
 5
 34.0%
-17.0%
-49.0%
+16.0%
+50.0%
 
 
 Abstract Classes
@@ -1232,7 +1236,7 @@
 
 org.apache.commons.math3.analysis.BivariateFunctionorg.apache.commons.math3.analysis.DifferentiableMultivariateFunctionorg.apache.commons.math3.analysis.DifferentiableMultivariateVectorFunctionorg.apache.commons.math3.analysis.DifferentiableUnivariateFunctionorg.apache.commons.math3.analysis.DifferentiableUnivariateMatrixFunctionorg.apache.commons.math3.analysis.DifferentiableUnivariateVectorFunctionorg.apache.commons.math3.analysis.MultivariateFunctionorg.apache.commons.math3.analysis.MultivariateMatrixFunctionorg.apache.commons.math3.analysis.MultivariateVectorFunctionorg.apache.commons.math3.analysis.ParametricUnivariateFunctionorg.apache.commons.math3.analysis.TrivariateFunctionorg.apache.commons.math3.analysis.UnivariateFunctionorg.apache.commons.math3.analysis.UnivariateMatrixFunctionorg.apache.commons.math3.analysis.UnivariateVectorFunction
 org.apache.commons.math3.analysis.FunctionUtilsorg.apache.commons.math3.analysis.FunctionUtils$1org.apache.commons.math3.analysis.FunctionUtils$10org.apache.commons.math3.analysis.FunctionUtils$11org.apache.commons.math3.analysis.FunctionUtils$12org.apache.commons.math3.analysis.FunctionUtils$13org.apache.commons.math3.analysis.FunctionUtils$14org.apache.commons.math3.analysis.FunctionUtils$14$1org.apache.commons.math3.analysis.FunctionUtils$15org.apache.commons.math3.analysis.FunctionUtils$16org.apache.commons.math3.analysis.FunctionUtils$16$1org.apache.commons.math3.analysis.FunctionUtils$16$2org.apache.commons.math3.analysis.FunctionUtils$17org.apache.commons.math3.analysis.FunctionUtils$18org.apache.commons.math3.analysis.FunctionUtils$18$1org.apache.commons.math3.analysis.FunctionUtils$19org.apache.commons.math3.analysis.FunctionUtils$2org.apache.commons.math3.analysis.Func
 tionUtils$3org.apache.commons.math3.analysis.FunctionUtils$3$1org.apache.commons.math3.analysis.FunctionUtils$4org.apache.commons.math3.analysis.FunctionUtils$5org.apache.commons.math3.analysis.FunctionUtils$6org.apache.commons.math3.analysis.FunctionUtils$6$1org.apache.commons.math3.analysis.FunctionUtils$7org.apache.commons.math3.analysis.FunctionUtils$8org.apache.commons.math3.analysis.FunctionUtils$9or



svn commit: r933283 [5/8] - /websites/production/commons/content/proper/commons-math/


2014-12-18

Thread
luc

Modified: 
websites/production/commons/content/proper/commons-math/rat-report.html
==
--- websites/production/commons/content/proper/commons-math/rat-report.html 
(original)
+++ websites/production/commons/content/proper/commons-math/rat-report.html Thu 
Dec 18 23:11:03 2014
@@ -1,13 +1,13 @@
 
 
 http://www.w3.org/1999/xhtml"; xml:lang="en" lang="en">
   
 
 
-
+
 
 Math - Rat (Release Audit Tool) results
 
@@ -40,8 +40,8 @@
http://commons.apache.org/proper/commons-math/";>Apache Commons Math 
™
  
 
-Last Published: 18 October 2014
-  | Version: 
3.4-SNAPSHOT
+Last Published: 18 December 2014
+  | Version: 3.4
   


@@ -82,6 +82,10 @@
 Latest API docs (development)



+ 
+Javadoc (3.4 release)
+   
+   

  
 Javadoc (3.3 release)

@@ -363,13 +367,13 @@
 *
 Summary
 ---
-Generated at: 2014-10-18T17:25:08+02:00
+Generated at: 2014-12-18T23:57:44+01:00
 Notes: 5
 Binaries: 22
 Archives: 0
-Standards: 1596
+Standards: 1617
 
-Apache Licensed: 1596
+Apache Licensed: 1617
 Generated Documents: 0
 
 JavaDocs are generated and so license header is optional
@@ -391,1629 +395,1650 @@ Archives:
   Binary files (which do not require AL headers) will be marked B
   Compressed archives will be marked A
   Notices, licenses etc will be marked N
-  ALfindbugs-exclude-filter.xml
-  ALsiteMods/pom.xml
-  ALsiteMods/site.css
-  ALsiteMods/site.xml
-  ALpom.xml
-  ALdoc/release/settings-security.xml
-  ALdoc/release/settings.xml
-  ALdoc/release/release.howto.txt
-  ALdoap_math.rdf
-  ALbuild.xml
-  N LICENSE.txt
-  ALmath-RC.sh
-  ALclirr-ignored.xml
   ALtest-jar.xml
-  N RELEASE-NOTES.txt
+  B src/userguide/resources/monalisa.png
+  B src/userguide/resources/feather-small.gif
   ALsrc/userguide/pom.xml
-  AL
src/userguide/java/org/apache/commons/math3/userguide/LowDiscrepancyGeneratorComparison.java
-  ALsrc/userguide/java/org/apache/commons/math3/userguide/ExampleUtils.java
+  AL
src/userguide/java/org/apache/commons/math3/userguide/sofm/ChineseRingsClassifier.java
+  AL
src/userguide/java/org/apache/commons/math3/userguide/sofm/ChineseRings.java
+  AL
src/userguide/java/org/apache/commons/math3/userguide/geometry/GeometryExample.java
   AL
src/userguide/java/org/apache/commons/math3/userguide/genetics/RandomPolygonMutation.java
   AL
src/userguide/java/org/apache/commons/math3/userguide/genetics/PolygonChromosome.java
-  AL
src/userguide/java/org/apache/commons/math3/userguide/genetics/HelloWorldExample.java
-  AL
src/userguide/java/org/apache/commons/math3/userguide/genetics/ImageEvolutionExample.java
   AL
src/userguide/java/org/apache/commons/math3/userguide/genetics/Polygon.java
-  AL
src/userguide/java/org/apache/commons/math3/userguide/geometry/GeometryExample.java
-  AL
src/userguide/java/org/apache/commons/math3/userguide/filter/CannonballExample.java
+  AL
src/userguide/java/org/apache/commons/math3/userguide/genetics/ImageEvolutionExample.java
+  AL
src/userguide/java/org/apache/commons/math3/userguide/genetics/HelloWorldExample.java
   AL
src/userguide/java/org/apache/commons/math3/userguide/filter/ConstantVoltageExample.java
-  AL
src/userguide/java/org/apache/commons/math3/userguide/sofm/ChineseRings.java
-  AL
src/userguide/java/org/apache/commons/math3/userguide/sofm/ChineseRingsClassifier.java
+  AL
src/userguide/java/org/apache/commons/math3/userguide/filter/CannonballExample.java
   AL
src/userguide/java/org/apache/commons/math3/userguide/RealDistributionComparison.java
+  AL
src/userguide/java/org/apache/commons/math3/userguide/LowDiscrepancyGeneratorComparison.java
+  ALsrc/userguide/java/org/apache/commons/math3/userguide/ExampleUtils.java
   AL
src/userguide/java/org/apache/commons/math3/userguide/ClusterAlgorithmComparison.java
-  B src/userguide/resources/feather-small.gif
-  B src/userguide/resources/monalisa.png
-  N src/test/maxima/special/RealFunctionValidation/README.txt
-  AL
src/test/maxima/special/RealFunctionValidation/RealFunctionValidation.sh
-  AL
src/test/maxima/special/RealFunctionValidation/RealFunctionValidation.java
+  B 
src/test/resources/org/apache/commons/math3/opt


    
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