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Posted to commits@commons.apache.org by tn...@apache.org on 2015/02/16 23:40:33 UTC
[63/82] [math] Update for next development iteration: commons-math4
http://git-wip-us.apache.org/repos/asf/commons-math/blob/e4e1ac23/src/site/xdoc/userguide/ode.xml
----------------------------------------------------------------------
diff --git a/src/site/xdoc/userguide/ode.xml b/src/site/xdoc/userguide/ode.xml
index a255947..37b266c 100644
--- a/src/site/xdoc/userguide/ode.xml
+++ b/src/site/xdoc/userguide/ode.xml
@@ -39,7 +39,7 @@
All integrators provide dense output. This means that besides computing the state vector
at discrete times, they also provide a cheap mean to get both the state and its derivative
between the time steps. They do so through classes extending the
- <a href="../apidocs/org/apache/commons/math3/ode/sampling/StepInterpolator.html">StepInterpolator</a>
+ <a href="../apidocs/org/apache/commons/math4/ode/sampling/StepInterpolator.html">StepInterpolator</a>
abstract class, which are made available to the user at the end of each step.
</p>
<p>
@@ -63,9 +63,9 @@
</p>
<p>
The user should describe his problem in his own classes which should implement the
- <a href="../apidocs/org/apache/commons/math3/ode/FirstOrderDifferentialEquations.html">FirstOrderDifferentialEquations</a>
+ <a href="../apidocs/org/apache/commons/math4/ode/FirstOrderDifferentialEquations.html">FirstOrderDifferentialEquations</a>
interface. Then he should pass it to the integrator he prefers among all the classes that implement
- the <a href="../apidocs/org/apache/commons/math3/ode/FirstOrderIntegrator.html">FirstOrderIntegrator</a>
+ the <a href="../apidocs/org/apache/commons/math4/ode/FirstOrderIntegrator.html">FirstOrderIntegrator</a>
interface. The following example shows how to implement the simple two-dimensional problem:
<ul>
<li>y'<sub>0</sub>(t) = ω × (c<sub>1</sub> - y<sub>1</sub>(t))</li>
@@ -115,10 +115,10 @@ dp853.integrate(ode, 0.0, y, 16.0, y); // now y contains final state at time t=1
<code>FirstOrderIntegrator.integrate</code> method, as shown by previous example. The second one
should be used when more in-depth information is needed throughout the integration process. The user
can register an object implementing the
- <a href="../apidocs/org/apache/commons/math3/ode/sampling/StepHandler.html">StepHandler</a> interface or a
- <a href="../apidocs/org/apache/commons/math3/ode/sampling/StepNormalizer.html">StepNormalizer</a> object wrapping
+ <a href="../apidocs/org/apache/commons/math4/ode/sampling/StepHandler.html">StepHandler</a> interface or a
+ <a href="../apidocs/org/apache/commons/math4/ode/sampling/StepNormalizer.html">StepNormalizer</a> object wrapping
a user-specified object implementing the
- <a href="../apidocs/org/apache/commons/math3/ode/sampling/FixedStepHandler.html">FixedStepHandler</a> interface
+ <a href="../apidocs/org/apache/commons/math4/ode/sampling/FixedStepHandler.html">FixedStepHandler</a> interface
into the integrator before calling the <code>FirstOrderIntegrator.integrate</code> method. The user object
will be called appropriately during the integration process, allowing the user to process intermediate
results. The default step handler does nothing. Considering again the previous example, we want to print the
@@ -139,7 +139,7 @@ StepHandler stepHandler = new StepHandler() {
integrator.addStepHandler(stepHandler);
</source>
<p>
- <a href="../apidocs/org/apache/commons/math3/ode/ContinuousOutputModel.html">ContinuousOutputModel</a>
+ <a href="../apidocs/org/apache/commons/math4/ode/ContinuousOutputModel.html">ContinuousOutputModel</a>
is a special-purpose step handler that is able to store all steps and to provide transparent access to
any intermediate result once the integration is over. An important feature of this class is that it
implements the <code>Serializable</code> interface. This means that a complete continuous model of the
@@ -148,10 +148,10 @@ integrator.addStepHandler(stepHandler);
Only the result of the integration is stored, there is no reference to the integrated problem by itself.
</p>
<p>
- Other default implementations of the <a href="../apidocs/org/apache/commons/math3/ode/sampling/StepHandler.html">StepHandler</a>
+ Other default implementations of the <a href="../apidocs/org/apache/commons/math4/ode/sampling/StepHandler.html">StepHandler</a>
interface are available for general needs
- (<a href="../apidocs/org/apache/commons/math3/ode/sampling/DummyStepHandler.html">DummyStepHandler</a>,
- <a href="../apidocs/org/apache/commons/math3/ode/sampling/StepNormalizer.html">StepNormalizer</a>) and custom
+ (<a href="../apidocs/org/apache/commons/math4/ode/sampling/DummyStepHandler.html">DummyStepHandler</a>,
+ <a href="../apidocs/org/apache/commons/math4/ode/sampling/StepNormalizer.html">StepNormalizer</a>) and custom
implementations can be developed for specific needs. As an example, if an application is to be
completely driven by the integration process, then most of the application code will be run inside a
step handler specific to this application.
@@ -160,11 +160,11 @@ integrator.addStepHandler(stepHandler);
Some integrators (the simple ones) use fixed steps that are set at creation time. The more efficient
integrators use variable steps that are handled internally in order to control the integration error
with respect to a specified accuracy (these integrators extend the
- <a href="../apidocs/org/apache/commons/math3/ode/AdaptiveStepsizeIntegrator.html">AdaptiveStepsizeIntegrator</a>
+ <a href="../apidocs/org/apache/commons/math4/ode/AdaptiveStepsizeIntegrator.html">AdaptiveStepsizeIntegrator</a>
abstract class). In this case, the step handler which is called after each successful step shows up
- the variable stepsize. The <a href="../apidocs/org/apache/commons/math3/ode/sampling/StepNormalizer.html">StepNormalizer</a>
+ the variable stepsize. The <a href="../apidocs/org/apache/commons/math4/ode/sampling/StepNormalizer.html">StepNormalizer</a>
class can be used to convert the variable stepsize into a fixed stepsize that can be handled by classes
- implementing the <a href="../apidocs/org/apache/commons/math3/ode/sampling/FixedStepHandler.html">FixedStepHandler</a>
+ implementing the <a href="../apidocs/org/apache/commons/math4/ode/sampling/FixedStepHandler.html">FixedStepHandler</a>
interface. Adaptive stepsize integrators can automatically compute the initial stepsize by themselves,
however the user can specify it if he prefers to retain full control over the integration or if the
automatic guess is wrong.
@@ -179,7 +179,7 @@ integrator.addStepHandler(stepHandler);
</p>
<p>
Discrete events detection is based on switching functions. The user provides
- a simple <a href="../apidocs/org/apache/commons/math3/ode/events/EventHandler.html">g(t, y)</a>
+ a simple <a href="../apidocs/org/apache/commons/math4/ode/events/EventHandler.html">g(t, y)</a>
function depending on the current time and state. The integrator will monitor
the value of the function throughout integration range and will trigger the
event when its sign changes. The magnitude of the value is almost irrelevant.
@@ -259,24 +259,24 @@ public int eventOccurred(double t, double[] y, boolean increasing) {
<table border="1" align="center">
<tr BGCOLOR="#CCCCFF"><td colspan="2"><font size="+1">Fixed Step Integrators</font></td></tr>
<tr BGCOLOR="#EEEEFF"><font size="+1"><td>Name</td><td>Order</td></font></tr>
- <tr><td><a href="../apidocs/org/apache/commons/math3/ode/nonstiff/EulerIntegrator.html">Euler</a></td><td>1</td></tr>
- <tr><td><a href="../apidocs/org/apache/commons/math3/ode/nonstiff/MidpointIntegrator.html">Midpoint</a></td><td>2</td></tr>
- <tr><td><a href="../apidocs/org/apache/commons/math3/ode/nonstiff/ClassicalRungeKuttaIntegrator.html">Classical Runge-Kutta</a></td><td>4</td></tr>
- <tr><td><a href="../apidocs/org/apache/commons/math3/ode/nonstiff/GillIntegrator.html">Gill</a></td><td>4</td></tr>
- <tr><td><a href="../apidocs/org/apache/commons/math3/ode/nonstiff/ThreeEighthesIntegrator.html">3/8</a></td><td>4</td></tr>
- <tr><td><a href="../apidocs/org/apache/commons/math3/ode/nonstiff/LutherIntegrator.html">Luther</a></td><td>6</td></tr>
+ <tr><td><a href="../apidocs/org/apache/commons/math4/ode/nonstiff/EulerIntegrator.html">Euler</a></td><td>1</td></tr>
+ <tr><td><a href="../apidocs/org/apache/commons/math4/ode/nonstiff/MidpointIntegrator.html">Midpoint</a></td><td>2</td></tr>
+ <tr><td><a href="../apidocs/org/apache/commons/math4/ode/nonstiff/ClassicalRungeKuttaIntegrator.html">Classical Runge-Kutta</a></td><td>4</td></tr>
+ <tr><td><a href="../apidocs/org/apache/commons/math4/ode/nonstiff/GillIntegrator.html">Gill</a></td><td>4</td></tr>
+ <tr><td><a href="../apidocs/org/apache/commons/math4/ode/nonstiff/ThreeEighthesIntegrator.html">3/8</a></td><td>4</td></tr>
+ <tr><td><a href="../apidocs/org/apache/commons/math4/ode/nonstiff/LutherIntegrator.html">Luther</a></td><td>6</td></tr>
</table>
</p>
<p>
<table border="1" align="center">
<tr BGCOLOR="#CCCCFF"><td colspan="3"><font size="+1">Adaptive Stepsize Integrators</font></td></tr>
<tr BGCOLOR="#EEEEFF"><font size="+1"><td>Name</td><td>Integration Order</td><td>Error Estimation Order</td></font></tr>
- <tr><td><a href="../apidocs/org/apache/commons/math3/ode/nonstiff/HighamHall54Integrator.html">Higham and Hall</a></td><td>5</td><td>4</td></tr>
- <tr><td><a href="../apidocs/org/apache/commons/math3/ode/nonstiff/DormandPrince54Integrator.html">Dormand-Prince 5(4)</a></td><td>5</td><td>4</td></tr>
- <tr><td><a href="../apidocs/org/apache/commons/math3/ode/nonstiff/DormandPrince853Integrator.html">Dormand-Prince 8(5,3)</a></td><td>8</td><td>5 and 3</td></tr>
- <tr><td><a href="../apidocs/org/apache/commons/math3/ode/nonstiff/GraggBulirschStoerIntegrator.html">Gragg-Bulirsch-Stoer</a></td><td>variable (up to 18 by default)</td><td>variable</td></tr>
- <tr><td><a href="../apidocs/org/apache/commons/math3/ode/nonstiff/AdamsBashforthIntegrator.html">Adams-Bashforth</a></td><td>variable</td><td>variable</td></tr>
- <tr><td><a href="../apidocs/org/apache/commons/math3/ode/nonstiff/AdamsMoultonIntegrator.html">Adams-Moulton</a></td><td>variable</td><td>variable</td></tr>
+ <tr><td><a href="../apidocs/org/apache/commons/math4/ode/nonstiff/HighamHall54Integrator.html">Higham and Hall</a></td><td>5</td><td>4</td></tr>
+ <tr><td><a href="../apidocs/org/apache/commons/math4/ode/nonstiff/DormandPrince54Integrator.html">Dormand-Prince 5(4)</a></td><td>5</td><td>4</td></tr>
+ <tr><td><a href="../apidocs/org/apache/commons/math4/ode/nonstiff/DormandPrince853Integrator.html">Dormand-Prince 8(5,3)</a></td><td>8</td><td>5 and 3</td></tr>
+ <tr><td><a href="../apidocs/org/apache/commons/math4/ode/nonstiff/GraggBulirschStoerIntegrator.html">Gragg-Bulirsch-Stoer</a></td><td>variable (up to 18 by default)</td><td>variable</td></tr>
+ <tr><td><a href="../apidocs/org/apache/commons/math4/ode/nonstiff/AdamsBashforthIntegrator.html">Adams-Bashforth</a></td><td>variable</td><td>variable</td></tr>
+ <tr><td><a href="../apidocs/org/apache/commons/math4/ode/nonstiff/AdamsMoultonIntegrator.html">Adams-Moulton</a></td><td>variable</td><td>variable</td></tr>
</table>
</p>
</subsection>
@@ -285,7 +285,7 @@ public int eventOccurred(double t, double[] y, boolean increasing) {
If in addition to state y(t) the user needs to compute the sensitivity of the state to
the initial state or some parameter of the ODE, he will use the classes and interfaces
from the <a
- href="../apidocs/org/apache/commons/math3/ode/jacobians/package-summary.html">org.apache.commons.ode.jacobians</a>
+ href="../apidocs/org/apache/commons/math4/ode/jacobians/package-summary.html">org.apache.commons.ode.jacobians</a>
package instead of the top level ode package. These classes compute the jacobians
dy(t)/dy<sub>0</sub> and dy(t)/dp where y<sub>0</sub> is the initial state
and p is some ODE parameter.
@@ -323,9 +323,9 @@ public int eventOccurred(double t, double[] y, boolean increasing) {
<p>
If the function f is too complex, the user can simply rely on internal differentiation
using finite differences to compute these local jacobians. So rather than the <a
- href="../apidocs/org/apache/commons/math3/ode/FirstOrderDifferentialEquations.html">FirstOrderDifferentialEquations</a>
+ href="../apidocs/org/apache/commons/math4/ode/FirstOrderDifferentialEquations.html">FirstOrderDifferentialEquations</a>
interface he will implement the <a
- href="../apidocs/org/apache/commons/math3/ode/jacobians/ParameterizedODE.html">ParameterizedODE</a>
+ href="../apidocs/org/apache/commons/math4/ode/jacobians/ParameterizedODE.html">ParameterizedODE</a>
interface. Considering again our example where only ω is considered a parameter, we get:
</p>
<source>
@@ -373,9 +373,9 @@ integrator.integrate(t0, y0, dy0dp, t, y, dydy0, dydp);
<p>
If the function f is simple, the user can simply provide the local jacobians
by himself. So rather than the <a
- href="../apidocs/org/apache/commons/math3/ode/FirstOrderDifferentialEquations.html">FirstOrderDifferentialEquations</a>
+ href="../apidocs/org/apache/commons/math4/ode/FirstOrderDifferentialEquations.html">FirstOrderDifferentialEquations</a>
interface he will implement the <a
- href="../apidocs/org/apache/commons/math3/ode/jacobians/ODEWithJacobians.html">ODEWithJacobians</a>
+ href="../apidocs/org/apache/commons/math4/ode/jacobians/ODEWithJacobians.html">ODEWithJacobians</a>
interface. Considering again our example where only ω is considered a parameter, we get:
</p>
<source>
http://git-wip-us.apache.org/repos/asf/commons-math/blob/e4e1ac23/src/site/xdoc/userguide/optimization.xml
----------------------------------------------------------------------
diff --git a/src/site/xdoc/userguide/optimization.xml b/src/site/xdoc/userguide/optimization.xml
index 16202d9..f691ffa 100644
--- a/src/site/xdoc/userguide/optimization.xml
+++ b/src/site/xdoc/userguide/optimization.xml
@@ -27,7 +27,7 @@
<body>
<section name="12 Optimization">
<p><em>The contents of this section currently describes deprecated classes.</em>
- Please refer to the new <a href="../apidocs/org/apache/commons/math3/optim/package-summary.html">API description</a>.
+ Please refer to the new <a href="../apidocs/org/apache/commons/math4/optim/package-summary.html">API description</a>.
</p>
<subsection name="12.1 Overview" href="overview">
@@ -57,7 +57,7 @@
</p>
<p>
The type of goal, i.e. minimization or maximization, is defined by the enumerated
- <a href="../apidocs/org/apache/commons/math3/optimization/GoalType.html">
+ <a href="../apidocs/org/apache/commons/math4/optimization/GoalType.html">
GoalType</a> which has only two values: <code>MAXIMIZE</code> and <code>MINIMIZE</code>.
</p>
<p>
@@ -66,21 +66,21 @@
are only four interfaces defining the common behavior of optimizers, one for each
supported type of objective function:
<ul>
- <li><a href="../apidocs/org/apache/commons/math3/optimization/univariate/UnivariateOptimizer.html">
+ <li><a href="../apidocs/org/apache/commons/math4/optimization/univariate/UnivariateOptimizer.html">
UnivariateOptimizer</a> for <a
- href="../apidocs/org/apache/commons/math3/analysis/UnivariateFunction.html">
+ href="../apidocs/org/apache/commons/math4/analysis/UnivariateFunction.html">
univariate real functions</a></li>
- <li><a href="../apidocs/org/apache/commons/math3/optimization/MultivariateOptimizer.html">
+ <li><a href="../apidocs/org/apache/commons/math4/optimization/MultivariateOptimizer.html">
MultivariateOptimizer</a> for <a
- href="../apidocs/org/apache/commons/math3/analysis/MultivariateFunction.html">
+ href="../apidocs/org/apache/commons/math4/analysis/MultivariateFunction.html">
multivariate real functions</a></li>
- <li><a href="../apidocs/org/apache/commons/math3/optimization/DifferentiableMultivariateOptimizer.html">
+ <li><a href="../apidocs/org/apache/commons/math4/optimization/DifferentiableMultivariateOptimizer.html">
DifferentiableMultivariateOptimizer</a> for <a
- href="../apidocs/org/apache/commons/math3/analysis/DifferentiableMultivariateFunction.html">
+ href="../apidocs/org/apache/commons/math4/analysis/DifferentiableMultivariateFunction.html">
differentiable multivariate real functions</a></li>
- <li><a href="../apidocs/org/apache/commons/math3/optimization/DifferentiableMultivariateVectorOptimizer.html">
+ <li><a href="../apidocs/org/apache/commons/math4/optimization/DifferentiableMultivariateVectorOptimizer.html">
DifferentiableMultivariateVectorOptimizer</a> for <a
- href="../apidocs/org/apache/commons/math3/analysis/DifferentiableMultivariateVectorFunction.html">
+ href="../apidocs/org/apache/commons/math4/analysis/DifferentiableMultivariateVectorFunction.html">
differentiable multivariate vectorial functions</a></li>
</ul>
</p>
@@ -88,14 +88,14 @@
<p>
Despite there are only four types of supported optimizers, it is possible to optimize
a transform a <a
- href="../apidocs/org/apache/commons/math3/analysis/MultivariateVectorFunction.html">
+ href="../apidocs/org/apache/commons/math4/analysis/MultivariateVectorFunction.html">
non-differentiable multivariate vectorial function</a> by converting it to a <a
- href="../apidocs/org/apache/commons/math3/analysis/MultivariateFunction.html">
+ href="../apidocs/org/apache/commons/math4/analysis/MultivariateFunction.html">
non-differentiable multivariate real function</a> thanks to the <a
- href="../apidocs/org/apache/commons/math3/optimization/LeastSquaresConverter.html">
+ href="../apidocs/org/apache/commons/math4/optimization/LeastSquaresConverter.html">
LeastSquaresConverter</a> helper class. The transformed function can be optimized using
any implementation of the <a
- href="../apidocs/org/apache/commons/math3/optimization/MultivariateOptimizer.html">
+ href="../apidocs/org/apache/commons/math4/optimization/MultivariateOptimizer.html">
MultivariateOptimizer</a> interface.
</p>
@@ -109,7 +109,7 @@
</subsection>
<subsection name="12.2 Univariate Functions" href="univariate">
<p>
- A <a href="../apidocs/org/apache/commons/math3/optimization/univariate/UnivariateOptimizer.html">
+ A <a href="../apidocs/org/apache/commons/math4/optimization/univariate/UnivariateOptimizer.html">
UnivariateOptimizer</a> is used to find the minimal values of a univariate real-valued
function <code>f</code>.
</p>
@@ -160,16 +160,16 @@
The <code>direct</code> package provides four solvers:
<ul>
<li>the classical <a
- href="../apidocs/org/apache/commons/math3/optimization/direct/NelderMeadSimplex.html">
+ href="../apidocs/org/apache/commons/math4/optimization/direct/NelderMeadSimplex.html">
Nelder-Mead</a> method,</li>
<li>Virginia Torczon's <a
- href="../apidocs/org/apache/commons/math3/optimization/direct/MultiDirectionalSimplex.html">
+ href="../apidocs/org/apache/commons/math4/optimization/direct/MultiDirectionalSimplex.html">
multi-directional</a> method,</li>
<li>Nikolaus Hansen's <a
- href="../apidocs/org/apache/commons/math3/optimization/direct/CMAESOptimizer.html">
+ href="../apidocs/org/apache/commons/math4/optimization/direct/CMAESOptimizer.html">
</a>Covariance Matrix Adaptation Evolution Strategy (CMA-ES),</li>
<li>Mike Powell's <a
- href="../apidocs/org/apache/commons/math3/optimization/direct/BOBYQAOptimizer.html">
+ href="../apidocs/org/apache/commons/math4/optimization/direct/BOBYQAOptimizer.html">
BOBYQA</a> method.
</li>
</ul>
@@ -177,9 +177,9 @@
<p>
The first two simplex-based methods do not handle simple bounds constraints by themselves.
However there are two adapters(<a
- href="../apidocs/org/apache/commons/math3/optimization/direct/MultivariateFunctionMappingAdapter.html">
+ href="../apidocs/org/apache/commons/math4/optimization/direct/MultivariateFunctionMappingAdapter.html">
MultivariateFunctionMappingAdapter</a> and <a
- href="../apidocs/org/apache/commons/math3/optimization/direct/MultivariateFunctionPenaltyAdapter.html">
+ href="../apidocs/org/apache/commons/math4/optimization/direct/MultivariateFunctionPenaltyAdapter.html">
MultivariateFunctionPenaltyAdapter</a>) that can be used to wrap the user function in
such a way the wrapped function is unbounded and can be used with these optimizers, despite
the fact the underlying function is still bounded and will be called only with feasible
@@ -233,15 +233,15 @@
<p>
Two optimizers are available in the general package, both devoted to least-squares
problems. The first one is based on the <a
- href="../apidocs/org/apache/commons/math3/optimization/general/GaussNewtonOptimizer.html">
+ href="../apidocs/org/apache/commons/math4/optimization/general/GaussNewtonOptimizer.html">
Gauss-Newton</a> method. The second one is the <a
- href="../apidocs/org/apache/commons/math3/optimization/general/LevenbergMarquardtOptimizer.html">
+ href="../apidocs/org/apache/commons/math4/optimization/general/LevenbergMarquardtOptimizer.html">
Levenberg-Marquardt</a> method.
</p>
<p>
In order to solve a vectorial optimization problem, the user must provide it as
an object implementing the <a
- href="../apidocs/org/apache/commons/math3/analysis/DifferentiableMultivariateVectorFunction.html">
+ href="../apidocs/org/apache/commons/math4/analysis/DifferentiableMultivariateVectorFunction.html">
DifferentiableMultivariateVectorFunction</a> interface. The object will be provided to
the <code>estimate</code> method of the optimizer, along with the target and weight arrays,
thus allowing the optimizer to compute the residuals at will. The last parameter to the
@@ -307,7 +307,7 @@
</table>
<p>
-First we need to implement the interface <a href="../apidocs/org/apache/commons/math3/analysis/DifferentiableMultivariateVectorFunction.html">DifferentiableMultivariateVectorFunction</a>.
+First we need to implement the interface <a href="../apidocs/org/apache/commons/math4/analysis/DifferentiableMultivariateVectorFunction.html">DifferentiableMultivariateVectorFunction</a>.
This requires the implementation of the method signatures:
</p>
@@ -455,7 +455,7 @@ can be seen below:
<p>
Below is the the class containing all the implementation details
-(Taken from the Apache Commons Math <b>org.apache.commons.math3.optimization.general.LevenbergMarquardtOptimizerTest</b>):
+(Taken from the Apache Commons Math <b>org.apache.commons.math4.optimization.general.LevenbergMarquardtOptimizerTest</b>):
</p>
<source>
@@ -567,17 +567,17 @@ C: 16.324008168386605
</dd></dl>
<p>
In addition to least squares solving, the <a
- href="../apidocs/org/apache/commons/math3/optimization/general/NonLinearConjugateGradientOptimizer.html">
+ href="../apidocs/org/apache/commons/math4/optimization/general/NonLinearConjugateGradientOptimizer.html">
NonLinearConjugateGradientOptimizer</a> class provides a non-linear conjugate gradient algorithm
to optimize <a
- href="../apidocs/org/apache/commons/math3/analysis/DifferentiableMultivariateFunction.html">
+ href="../apidocs/org/apache/commons/math4/analysis/DifferentiableMultivariateFunction.html">
DifferentiableMultivariateFunction</a>. Both the Fletcher-Reeves and the Polak-Ribière
search direction update methods are supported. It is also possible to set up a preconditioner
or to change the line-search algorithm of the inner loop if desired (the default one is a Brent
solver).
</p>
<p>
- The <a href="../apidocs/org/apache/commons/math3/optimization/direct/PowellOptimizer.html">
+ The <a href="../apidocs/org/apache/commons/math4/optimization/direct/PowellOptimizer.html">
PowellOptimizer</a> provides an optimization method for non-differentiable functions.
</p>
</subsection>
http://git-wip-us.apache.org/repos/asf/commons-math/blob/e4e1ac23/src/site/xdoc/userguide/overview.xml
----------------------------------------------------------------------
diff --git a/src/site/xdoc/userguide/overview.xml b/src/site/xdoc/userguide/overview.xml
index 4850965..eb8d8c1 100644
--- a/src/site/xdoc/userguide/overview.xml
+++ b/src/site/xdoc/userguide/overview.xml
@@ -73,22 +73,22 @@
<p>
Commons Math is divided into sixteen subpackages, based on functionality provided.
<ul>
- <li><a href="stat.html">org.apache.commons.math3.stat</a> - statistics, statistical tests</li>
- <li><a href="analysis.html">org.apache.commons.math3.analysis</a> - rootfinding, integration, interpolation, polynomials</li>
- <li><a href="random.html">org.apache.commons.math3.random</a> - random numbers, strings and data generation</li>
- <li><a href="special.html">org.apache.commons.math3.special</a> - special functions (Gamma, Beta) </li>
- <li><a href="linear.html">org.apache.commons.math3.linear</a> - matrices, solving linear systems </li>
- <li><a href="utilities.html">org.apache.commons.math3.util</a> - common math/stat functions extending java.lang.Math </li>
- <li><a href="complex.html">org.apache.commons.math3.complex</a> - complex numbers</li>
- <li><a href="distribution.html">org.apache.commons.math3.distribution</a> - probability distributions</li>
- <li><a href="fraction.html">org.apache.commons.math3.fraction</a> - rational numbers</li>
- <li><a href="transform.html">org.apache.commons.math3.transform</a> - transform methods (Fast Fourier)</li>
- <li><a href="geometry.html">org.apache.commons.math3.geometry</a> - geometry (Euclidean spaces and Binary Space Partitioning)</li>
- <li><a href="optimization.html">org.apache.commons.math3.optim</a> - function maximization or minimization</li>
- <li><a href="ode.html">org.apache.commons.math3.ode</a> - Ordinary Differential Equations integration</li>
- <li><a href="genetics.html">org.apache.commons.math3.genetics</a> - Genetic Algorithms</li>
- <li><a href="fitting.html">org.apache.commons.math3.fitting</a> - Curve Fitting</li>
- <li><a href="ml.html">org.apache.commons.math3.ml</a> - Machine Learning</li>
+ <li><a href="stat.html">org.apache.commons.math4.stat</a> - statistics, statistical tests</li>
+ <li><a href="analysis.html">org.apache.commons.math4.analysis</a> - rootfinding, integration, interpolation, polynomials</li>
+ <li><a href="random.html">org.apache.commons.math4.random</a> - random numbers, strings and data generation</li>
+ <li><a href="special.html">org.apache.commons.math4.special</a> - special functions (Gamma, Beta) </li>
+ <li><a href="linear.html">org.apache.commons.math4.linear</a> - matrices, solving linear systems </li>
+ <li><a href="utilities.html">org.apache.commons.math4.util</a> - common math/stat functions extending java.lang.Math </li>
+ <li><a href="complex.html">org.apache.commons.math4.complex</a> - complex numbers</li>
+ <li><a href="distribution.html">org.apache.commons.math4.distribution</a> - probability distributions</li>
+ <li><a href="fraction.html">org.apache.commons.math4.fraction</a> - rational numbers</li>
+ <li><a href="transform.html">org.apache.commons.math4.transform</a> - transform methods (Fast Fourier)</li>
+ <li><a href="geometry.html">org.apache.commons.math4.geometry</a> - geometry (Euclidean spaces and Binary Space Partitioning)</li>
+ <li><a href="optimization.html">org.apache.commons.math4.optim</a> - function maximization or minimization</li>
+ <li><a href="ode.html">org.apache.commons.math4.ode</a> - Ordinary Differential Equations integration</li>
+ <li><a href="genetics.html">org.apache.commons.math4.genetics</a> - Genetic Algorithms</li>
+ <li><a href="fitting.html">org.apache.commons.math4.fitting</a> - Curve Fitting</li>
+ <li><a href="ml.html">org.apache.commons.math4.ml</a> - Machine Learning</li>
</ul>
Package javadocs are <a href="../apidocs/index.html">here</a>
</p>
@@ -106,9 +106,9 @@
<p>
When the actual parameters provided to a method or the internal state of an object
make a computation meaningless, a
- <a href="../apidocs/org/apache/commons/math3/exception/MathIllegalArgumentException.html">
+ <a href="../apidocs/org/apache/commons/math4/exception/MathIllegalArgumentException.html">
MathIllegalArgumentException</a> or
- <a href="../apidocs/org/apache/commons/math3/exception/MathIllegalStateException.html">
+ <a href="../apidocs/org/apache/commons/math4/exception/MathIllegalStateException.html">
MathIllegalStateException</a> may be thrown. Exact conditions under which runtime
exceptions (and any other exceptions) are thrown are specified in the javadoc method
comments.
@@ -120,7 +120,7 @@
<p>
As of version 2.2, the policy for dealing with null references is as
follows: When an argument is unexpectedly null, a
- <a href="../apidocs/org/apache/commons/math3/exception/NullArgumentException.html">
+ <a href="../apidocs/org/apache/commons/math4/exception/NullArgumentException.html">
NullArgumentException</a> is raised to signal the illegal argument. Note that this
class does not inherit from the standard <code>NullPointerException</code> but is a subclass
of <code>MathIllegalArgumentException</code>.
http://git-wip-us.apache.org/repos/asf/commons-math/blob/e4e1ac23/src/site/xdoc/userguide/random.xml
----------------------------------------------------------------------
diff --git a/src/site/xdoc/userguide/random.xml b/src/site/xdoc/userguide/random.xml
index 914636b..1ea7615 100644
--- a/src/site/xdoc/userguide/random.xml
+++ b/src/site/xdoc/userguide/random.xml
@@ -67,7 +67,7 @@
<subsection name="2.2 Random numbers" href="deviates">
<p>
- The <a href="../apidocs/org/apache/commons/math3/random/RandomDataGenerator.html">
+ The <a href="../apidocs/org/apache/commons/math4/random/RandomDataGenerator.html">
RandomDataGenerator</a> class implements methods for generating random sequences
of numbers. The API contracts of these methods use the following concepts:
<dl>
@@ -86,10 +86,10 @@
ranges in the set of possible values of a random variable have
different probabilities of containing the value. Commons Math supports
generating random sequences from each of the distributions in the
- <a href="../apidocs/org/apache/commons/math3/distribution/package-summary.html">
+ <a href="../apidocs/org/apache/commons/math4/distribution/package-summary.html">
distributions</a> package.
The javadoc for the <code>nextXxx</code> methods in
- <a href="../apidocs/org/apache/commons/math3/random/RandomDataGenerator.html">
+ <a href="../apidocs/org/apache/commons/math4/random/RandomDataGenerator.html">
RandomDataGenerator</a> describes the algorithms used to generate
random deviates.
</dd>
@@ -166,11 +166,11 @@ for (int i = 0; i < 1000; i++) {
Some algorithms require random vectors instead of random scalars. When the
components of these vectors are uncorrelated, they may be generated simply
one at a time and packed together in the vector. The <a
- href="../apidocs/org/apache/commons/math3/random/UncorrelatedRandomVectorGenerator.html">
+ href="../apidocs/org/apache/commons/math4/random/UncorrelatedRandomVectorGenerator.html">
UncorrelatedRandomVectorGenerator</a> class simplifies this
process by setting the mean and deviation of each component once and
generating complete vectors. When the components are correlated however,
- generating them is much more difficult. The <a href="../apidocs/org/apache/commons/math3/random/CorrelatedRandomVectorGenerator.html">
+ generating them is much more difficult. The <a href="../apidocs/org/apache/commons/math4/random/CorrelatedRandomVectorGenerator.html">
CorrelatedRandomVectorGenerator</a> class provides this service. In this
case, the user must set up a complete covariance matrix instead of a simple
standard deviations vector. This matrix gathers both the variance and the
@@ -219,10 +219,10 @@ RealMatrix covariance = MatrixUtils.createRealMatrix(cov); </source>
<p>
In addition to multivariate normal distributions, correlated vectors from multivariate uniform
distributions can be generated by creating a
- <a href="../apidocs/org/apache/commons/math3/random/UniformRandomGenerator.html">UniformRandomGenerator</a>
+ <a href="../apidocs/org/apache/commons/math4/random/UniformRandomGenerator.html">UniformRandomGenerator</a>
in place of the
<code>GaussianRandomGenerator</code> above. More generally, any
- <a href="../apidocs/org/apache/commons/math3/random/NormalizedRandomGenerator.html">NormalizedRandomGenerator</a>
+ <a href="../apidocs/org/apache/commons/math4/random/NormalizedRandomGenerator.html">NormalizedRandomGenerator</a>
may be used.
</p>
<p><dl>
@@ -234,8 +234,8 @@ RealMatrix covariance = MatrixUtils.createRealMatrix(cov); </source>
is completely deterministic), their unique properties give them an important advantage for quasi-Monte Carlo simulations.<br/>
Currently, the following low-discrepancy sequences are supported:
<ul>
- <li><a href="../apidocs/org/apache/commons/math3/random/SobolSequenceGenerator.html">Sobol sequence</a> (pre-configured up to dimension 1000)</li>
- <li><a href="../apidocs/org/apache/commons/math3/random/HaltonSequenceGenerator.html">Halton sequence</a> (pre-configured up to dimension 40)</li>
+ <li><a href="../apidocs/org/apache/commons/math4/random/SobolSequenceGenerator.html">Sobol sequence</a> (pre-configured up to dimension 1000)</li>
+ <li><a href="../apidocs/org/apache/commons/math4/random/HaltonSequenceGenerator.html">Halton sequence</a> (pre-configured up to dimension 40)</li>
</ul>
<source>
// Create a Sobol sequence generator for 2-dimensional vectors
@@ -369,41 +369,41 @@ double[] randomVector = generator.nextVector();
generation utilities and to provide a generic means to replace
<code>java.util.Random</code> in applications, a random generator
adaptor framework has been added to commons-math. The
- <a href="../apidocs/org/apache/commons/math3/random/RandomGenerator.html">
+ <a href="../apidocs/org/apache/commons/math4/random/RandomGenerator.html">
RandomGenerator</a> interface abstracts the public interface of
<code>java.util.Random</code> and any implementation of this
interface can be used as the source of random data for the commons-math
data generation classes. An abstract base class,
- <a href="../apidocs/org/apache/commons/math3/random/AbstractRandomGenerator.html">
+ <a href="../apidocs/org/apache/commons/math4/random/AbstractRandomGenerator.html">
AbstractRandomGenerator</a> is provided to make implementation easier.
This class provides default implementations of "derived" data generation
methods based on the primitive, <code>nextDouble()</code>.
To support generic replacement of <code>java.util.Random</code>, the
- <a href="../apidocs/org/apache/commons/math3/random/RandomAdaptor.html">
+ <a href="../apidocs/org/apache/commons/math4/random/RandomAdaptor.html">
RandomAdaptor</a> class is provided, which extends
<code>java.util.Random</code> and wraps and delegates calls to
a <code>RandomGenerator</code> instance.
</p>
<p>Commons-math provides by itself several implementations of the <a
- href="../apidocs/org/apache/commons/math3/random/RandomGenerator.html">
+ href="../apidocs/org/apache/commons/math4/random/RandomGenerator.html">
RandomGenerator</a> interface:
<ul>
- <li><a href="../apidocs/org/apache/commons/math3/random/JDKRandomGenerator.html">JDKRandomGenerator</a>
+ <li><a href="../apidocs/org/apache/commons/math4/random/JDKRandomGenerator.html">JDKRandomGenerator</a>
that extends the JDK provided generator</li>
- <li><a href="../apidocs/org/apache/commons/math3/random/AbstractRandomGenerator.html">
+ <li><a href="../apidocs/org/apache/commons/math4/random/AbstractRandomGenerator.html">
AbstractRandomGenerator</a> as a helper for users generators</li>
- <li><a href="../apidocs/org/apache/commons/math3/random/BitStreamGenerator.html">
+ <li><a href="../apidocs/org/apache/commons/math4/random/BitStreamGenerator.html">
BitStreamGenerator</a> which is an abstract class for several generators and
which in turn is extended by:
<ul>
- <li><a href="../apidocs/org/apache/commons/math3/random/MersenneTwister.html">MersenneTwister</a></li>
- <li><a href="../apidocs/org/apache/commons/math3/random/Well512a.html">Well512a</a></li>
- <li><a href="../apidocs/org/apache/commons/math3/random/Well1024a.html">Well1024a</a></li>
- <li><a href="../apidocs/org/apache/commons/math3/random/Well19937a.html">Well19937a</a></li>
- <li><a href="../apidocs/org/apache/commons/math3/random/Well19937c.html">Well19937c</a></li>
- <li><a href="../apidocs/org/apache/commons/math3/random/Well44497a.html">Well44497a</a></li>
- <li><a href="../apidocs/org/apache/commons/math3/random/Well44497b.html">Well44497b</a></li>
+ <li><a href="../apidocs/org/apache/commons/math4/random/MersenneTwister.html">MersenneTwister</a></li>
+ <li><a href="../apidocs/org/apache/commons/math4/random/Well512a.html">Well512a</a></li>
+ <li><a href="../apidocs/org/apache/commons/math4/random/Well1024a.html">Well1024a</a></li>
+ <li><a href="../apidocs/org/apache/commons/math4/random/Well19937a.html">Well19937a</a></li>
+ <li><a href="../apidocs/org/apache/commons/math4/random/Well19937c.html">Well19937c</a></li>
+ <li><a href="../apidocs/org/apache/commons/math4/random/Well44497a.html">Well44497a</a></li>
+ <li><a href="../apidocs/org/apache/commons/math4/random/Well44497b.html">Well44497b</a></li>
</ul>
</li>
</ul>
@@ -474,21 +474,21 @@ double[] randomVector = generator.nextVector();
<table border="1" align="center">
<tr BGCOLOR="#CCCCFF"><td colspan="2"><font size="+1">Example of performances</font></td></tr>
<tr BGCOLOR="#EEEEFF"><font size="+1"><td>Name</td><td>generation rate (relative to MersenneTwister)</td></font></tr>
- <tr><td><a href="../apidocs/org/apache/commons/math3/random/MersenneTwister.html">MersenneTwister</a></td><td>1</td></tr>
- <tr><td><a href="../apidocs/org/apache/commons/math3/random/JDKRandomGenerator.html">JDKRandomGenerator</a></td><td>between 0.96 and 1.16</td></tr>
- <tr><td><a href="../apidocs/org/apache/commons/math3/random/Well512a.html">Well512a</a></td><td>between 0.85 and 0.88</td></tr>
- <tr><td><a href="../apidocs/org/apache/commons/math3/random/Well1024a.html">Well1024a</a></td><td>between 0.63 and 0.73</td></tr>
- <tr><td><a href="../apidocs/org/apache/commons/math3/random/Well19937a.html">Well19937a</a></td><td>between 0.70 and 0.71</td></tr>
- <tr><td><a href="../apidocs/org/apache/commons/math3/random/Well19937c.html">Well19937c</a></td><td>between 0.57 and 0.71</td></tr>
- <tr><td><a href="../apidocs/org/apache/commons/math3/random/Well44497a.html">Well44497a</a></td><td>between 0.69 and 0.71</td></tr>
- <tr><td><a href="../apidocs/org/apache/commons/math3/random/Well44497b.html">Well44497b</a></td><td>between 0.65 and 0.71</td></tr>
+ <tr><td><a href="../apidocs/org/apache/commons/math4/random/MersenneTwister.html">MersenneTwister</a></td><td>1</td></tr>
+ <tr><td><a href="../apidocs/org/apache/commons/math4/random/JDKRandomGenerator.html">JDKRandomGenerator</a></td><td>between 0.96 and 1.16</td></tr>
+ <tr><td><a href="../apidocs/org/apache/commons/math4/random/Well512a.html">Well512a</a></td><td>between 0.85 and 0.88</td></tr>
+ <tr><td><a href="../apidocs/org/apache/commons/math4/random/Well1024a.html">Well1024a</a></td><td>between 0.63 and 0.73</td></tr>
+ <tr><td><a href="../apidocs/org/apache/commons/math4/random/Well19937a.html">Well19937a</a></td><td>between 0.70 and 0.71</td></tr>
+ <tr><td><a href="../apidocs/org/apache/commons/math4/random/Well19937c.html">Well19937c</a></td><td>between 0.57 and 0.71</td></tr>
+ <tr><td><a href="../apidocs/org/apache/commons/math4/random/Well44497a.html">Well44497a</a></td><td>between 0.69 and 0.71</td></tr>
+ <tr><td><a href="../apidocs/org/apache/commons/math4/random/Well44497b.html">Well44497b</a></td><td>between 0.65 and 0.71</td></tr>
</table>
</p>
<p>
So for most simulation problems, the better generators like <a
- href="../apidocs/org/apache/commons/math3/random/Well19937c.html">Well19937c</a> and <a
- href="../apidocs/org/apache/commons/math3/random/Well44497b.html">Well44497b</a> are probably very good choices.
+ href="../apidocs/org/apache/commons/math4/random/Well19937c.html">Well19937c</a> and <a
+ href="../apidocs/org/apache/commons/math4/random/Well44497b.html">Well44497b</a> are probably very good choices.
</p>
<p>
http://git-wip-us.apache.org/repos/asf/commons-math/blob/e4e1ac23/src/site/xdoc/userguide/stat.xml
----------------------------------------------------------------------
diff --git a/src/site/xdoc/userguide/stat.xml b/src/site/xdoc/userguide/stat.xml
index b93e0e1..6035727 100644
--- a/src/site/xdoc/userguide/stat.xml
+++ b/src/site/xdoc/userguide/stat.xml
@@ -62,12 +62,12 @@
</p>
<p>
The top level interface is
- <a href="../apidocs/org/apache/commons/math3/stat/descriptive/UnivariateStatistic.html">
+ <a href="../apidocs/org/apache/commons/math4/stat/descriptive/UnivariateStatistic.html">
UnivariateStatistic</a>.
This interface, implemented by all statistics, consists of
<code>evaluate()</code> methods that take double[] arrays as arguments
and return the value of the statistic. This interface is extended by
- <a href="../apidocs/org/apache/commons/math3/stat/descriptive/StorelessUnivariateStatistic.html">
+ <a href="../apidocs/org/apache/commons/math4/stat/descriptive/StorelessUnivariateStatistic.html">
StorelessUnivariateStatistic</a>, which adds <code>increment(),</code>
<code>getResult()</code> and associated methods to support
"storageless" implementations that maintain counters, sums or other
@@ -76,9 +76,9 @@
</p>
<p>
Abstract implementations of the top level interfaces are provided in
- <a href="../apidocs/org/apache/commons/math3/stat/descriptive/AbstractUnivariateStatistic.html">
+ <a href="../apidocs/org/apache/commons/math4/stat/descriptive/AbstractUnivariateStatistic.html">
AbstractUnivariateStatistic</a> and
- <a href="../apidocs/org/apache/commons/math3/stat/descriptive/AbstractStorelessUnivariateStatistic.html">
+ <a href="../apidocs/org/apache/commons/math4/stat/descriptive/AbstractStorelessUnivariateStatistic.html">
AbstractStorelessUnivariateStatistic</a> respectively.
</p>
<p>
@@ -88,9 +88,9 @@
compute the statistic). There are several ways to instantiate and use statistics.
Statistics can be instantiated and used directly, but it is generally more convenient
(and efficient) to access them using the provided aggregates,
- <a href="../apidocs/org/apache/commons/math3/stat/descriptive/DescriptiveStatistics.html">
+ <a href="../apidocs/org/apache/commons/math4/stat/descriptive/DescriptiveStatistics.html">
DescriptiveStatistics</a> and
- <a href="../apidocs/org/apache/commons/math3/stat/descriptive/SummaryStatistics.html">
+ <a href="../apidocs/org/apache/commons/math4/stat/descriptive/SummaryStatistics.html">
SummaryStatistics.</a>
</p>
<p>
@@ -108,18 +108,18 @@
<table>
<tr><th>Aggregate</th><th>Statistics Included</th><th>Values stored?</th>
<th>"Rolling" capability?</th></tr><tr><td>
- <a href="../apidocs/org/apache/commons/math3/stat/descriptive/DescriptiveStatistics.html">
+ <a href="../apidocs/org/apache/commons/math4/stat/descriptive/DescriptiveStatistics.html">
DescriptiveStatistics</a></td><td>min, max, mean, geometric mean, n,
sum, sum of squares, standard deviation, variance, percentiles, skewness,
kurtosis, median</td><td>Yes</td><td>Yes</td></tr><tr><td>
- <a href="../apidocs/org/apache/commons/math3/stat/descriptive/SummaryStatistics.html">
+ <a href="../apidocs/org/apache/commons/math4/stat/descriptive/SummaryStatistics.html">
SummaryStatistics</a></td><td>min, max, mean, geometric mean, n,
sum, sum of squares, standard deviation, variance</td><td>No</td><td>No</td></tr>
</table>
</p>
<p>
<code>SummaryStatistics</code> can be aggregated using
- <a href="../apidocs/org/apache/commons/math3/stat/descriptive/AggregateSummaryStatistics.html">
+ <a href="../apidocs/org/apache/commons/math4/stat/descriptive/AggregateSummaryStatistics.html">
AggregateSummaryStatistics.</a> This class can be used to concurrently
gather statistics for multiple datasets as well as for a combined sample
including all of the data.
@@ -133,19 +133,19 @@
<p>
Neither <code>DescriptiveStatistics</code> nor <code>SummaryStatistics</code>
is thread-safe.
- <a href="../apidocs/org/apache/commons/math3/stat/descriptive/SynchronizedDescriptiveStatistics.html">
+ <a href="../apidocs/org/apache/commons/math4/stat/descriptive/SynchronizedDescriptiveStatistics.html">
SynchronizedDescriptiveStatistics</a> and
- <a href="../apidocs/org/apache/commons/math3/stat/descriptive/SynchronizedSummaryStatistics.html">
+ <a href="../apidocs/org/apache/commons/math4/stat/descriptive/SynchronizedSummaryStatistics.html">
SynchronizedSummaryStatistics</a>, respectively, provide thread-safe
versions for applications that require concurrent access to statistical
aggregates by multiple threads.
- <a href="../apidocs/org/apache/commons/math3/stat/descriptive/SynchronizedMultiVariateSummaryStatistics.html">
+ <a href="../apidocs/org/apache/commons/math4/stat/descriptive/SynchronizedMultiVariateSummaryStatistics.html">
SynchronizedMultivariateSummaryStatistics</a> provides thread-safe
<code>MultivariateSummaryStatistics.</code>
</p>
<p>
There is also a utility class,
- <a href="../apidocs/org/apache/commons/math3/stat/StatUtils.html">
+ <a href="../apidocs/org/apache/commons/math4/stat/StatUtils.html">
StatUtils</a>, that provides static methods for computing statistics
directly from double[] arrays.
</p>
@@ -243,7 +243,7 @@ DescriptiveStatistics stats = new SynchronizedDescriptiveStatistics();
The first is to use an <code>AggregateSummaryStatistics</code> instance
to accumulate overall statistics contributed by <code>SummaryStatistics</code>
instances created using
- <a href="../apidocs/org/apache/commons/math3/stat/descriptive/AggregateSummaryStatistics.html#createContributingStatistics()">
+ <a href="../apidocs/org/apache/commons/math4/stat/descriptive/AggregateSummaryStatistics.html#createContributingStatistics()">
AggregateSummaryStatistics.createContributingStatistics()</a>:
<source>
// Create a AggregateSummaryStatistics instance to accumulate the overall statistics
@@ -264,7 +264,7 @@ double totalSampleSum = aggregate.getSum();
<code>SummaryStatistics</code> instance maintained by the aggregate and each value addition updates the
aggregate as well as the subsample. For applications that can wait to do the aggregation until all values
have been added, a static
- <a href="../apidocs/org/apache/commons/math3/stat/descriptive/AggregateSummaryStatistics.html#aggregate(java.util.Collection)">
+ <a href="../apidocs/org/apache/commons/math4/stat/descriptive/AggregateSummaryStatistics.html#aggregate(java.util.Collection)">
aggregate</a> method is available, as shown in the following example.
This method should be used when aggregation needs to be done across threads.
<source>
@@ -292,7 +292,7 @@ double totalSampleSum = aggregatedStats.getSum();
</subsection>
<subsection name="1.3 Frequency distributions">
<p>
- <a href="../apidocs/org/apache/commons/math3/stat/Frequency.html">
+ <a href="../apidocs/org/apache/commons/math4/stat/Frequency.html">
Frequency</a>
provides a simple interface for maintaining counts and percentages of discrete
values.
@@ -356,7 +356,7 @@ System.out.println(f.getCumPct("z")); // displays 1
</subsection>
<subsection name="1.4 Simple regression">
<p>
- <a href="../apidocs/org/apache/commons/math3/stat/regression/SimpleRegression.html">
+ <a href="../apidocs/org/apache/commons/math4/stat/regression/SimpleRegression.html">
SimpleRegression</a> provides ordinary least squares regression with
one independent variable estimating the linear model:
</p>
@@ -392,7 +392,7 @@ System.out.println(f.getCumPct("z")); // displays 1
"compute" method that updates all statistics. Each of the getters performs
the necessary computations to return the requested statistic.</li>
<li> The intercept term may be suppressed by passing <code>false</code> to the
- <a href="../apidocs/org/apache/commons/math3/stat/regression/SimpleRegression.html#SimpleRegression(boolean)">
+ <a href="../apidocs/org/apache/commons/math4/stat/regression/SimpleRegression.html#SimpleRegression(boolean)">
SimpleRegression(boolean)</a> constructor. When the <code>hasIntercept</code>
property is false, the model is estimated without a constant term and
<code>getIntercept()</code> returns <code>0</code>.</li>
@@ -510,9 +510,9 @@ System.out.println(regression.getInterceptStdErr() );
</subsection>
<subsection name="1.5 Multiple linear regression">
<p>
- <a href="../apidocs/org/apache/commons/math3/stat/regression/OLSMultipleLinearRegression.html">
+ <a href="../apidocs/org/apache/commons/math4/stat/regression/OLSMultipleLinearRegression.html">
OLSMultipleLinearRegression</a> and
- <a href="../apidocs/org/apache/commons/math3/stat/regression/GLSMultipleLinearRegression.html">
+ <a href="../apidocs/org/apache/commons/math4/stat/regression/GLSMultipleLinearRegression.html">
GLSMultipleLinearRegression</a> provide least squares regression to fit the linear model:
</p>
<p>
@@ -524,9 +524,9 @@ System.out.println(regression.getInterceptStdErr() );
of <b>error terms</b> or <b>residuals</b>.
</p>
<p>
- <a href="../apidocs/org/apache/commons/math3/stat/regression/OLSMultipleLinearRegression.html">
+ <a href="../apidocs/org/apache/commons/math4/stat/regression/OLSMultipleLinearRegression.html">
OLSMultipleLinearRegression</a> provides Ordinary Least Squares Regression, and
- <a href="../apidocs/org/apache/commons/math3/stat/regression/GLSMultipleLinearRegression.html">
+ <a href="../apidocs/org/apache/commons/math4/stat/regression/GLSMultipleLinearRegression.html">
GLSMultipleLinearRegression</a> implements Generalized Least Squares. See the javadoc for these
classes for details on the algorithms and formulas used.
</p>
@@ -534,11 +534,11 @@ System.out.println(regression.getInterceptStdErr() );
Data for OLS models can be loaded in a single double[] array, consisting of concatenated rows of data, each containing
the regressand (Y) value, followed by regressor values; or using a double[][] array with rows corresponding to
observations. GLS models also require a double[][] array representing the covariance matrix of the error terms. See
- <a href="../apidocs/org/apache/commons/math3/stat/regression/AbstractMultipleLinearRegression.html#newSampleData(double[], int, int)">
+ <a href="../apidocs/org/apache/commons/math4/stat/regression/AbstractMultipleLinearRegression.html#newSampleData(double[], int, int)">
AbstractMultipleLinearRegression#newSampleData(double[],int,int)</a>,
- <a href="../apidocs/org/apache/commons/math3/stat/regression/OLSMultipleLinearRegression.html#newSampleData(double[], double[][])">
+ <a href="../apidocs/org/apache/commons/math4/stat/regression/OLSMultipleLinearRegression.html#newSampleData(double[], double[][])">
OLSMultipleLinearRegression#newSampleData(double[], double[][])</a> and
- <a href="../apidocs/org/apache/commons/math3/stat/regression/GLSMultipleLinearRegression.html#newSampleData(double[], double[][], double[][])">
+ <a href="../apidocs/org/apache/commons/math4/stat/regression/GLSMultipleLinearRegression.html#newSampleData(double[], double[][], double[][])">
GLSMultipleLinearRegression#newSampleData(double[],double[][],double[][])</a> for details.
</p>
<p>
@@ -616,16 +616,16 @@ regression.newSampleData(y, x, omega);
<subsection name="1.6 Rank transformations">
<p>
Some statistical algorithms require that input data be replaced by ranks.
- The <a href="../apidocs/org/apache/commons/math3/stat/ranking/package-summary.html">
- org.apache.commons.math3.stat.ranking</a> package provides rank transformation.
- <a href="../apidocs/org/apache/commons/math3/stat/ranking/RankingAlgorithm.html">
+ The <a href="../apidocs/org/apache/commons/math4/stat/ranking/package-summary.html">
+ org.apache.commons.math4.stat.ranking</a> package provides rank transformation.
+ <a href="../apidocs/org/apache/commons/math4/stat/ranking/RankingAlgorithm.html">
RankingAlgorithm</a> defines the interface for ranking.
- <a href="../apidocs/org/apache/commons/math3/stat/ranking/NaturalRanking.html">
+ <a href="../apidocs/org/apache/commons/math4/stat/ranking/NaturalRanking.html">
NaturalRanking</a> provides an implementation that has two configuration options.
<ul>
- <li><a href="../apidocs/org/apache/commons/math3/stat/ranking/TiesStrategy.html">
+ <li><a href="../apidocs/org/apache/commons/math4/stat/ranking/TiesStrategy.html">
Ties strategy</a> deterimines how ties in the source data are handled by the ranking</li>
- <li><a href="../apidocs/org/apache/commons/math3/stat/ranking/NaNStrategy.html">
+ <li><a href="../apidocs/org/apache/commons/math4/stat/ranking/NaNStrategy.html">
NaN strategy</a> determines how NaN values in the source data are handled.</li>
</ul>
</p>
@@ -649,24 +649,24 @@ new NaturalRanking(NaNStrategy.REMOVED,TiesStrategy.SEQUENTIAL).rank(exampleData
values larger than any other value (including <code>Double.POSITIVE_INFINITY</code>). The
default <code>TiesStrategy</code> is <code>TiesStrategy.AVERAGE,</code> which assigns tied
values the average of the ranks applicable to the sequence of ties. See the
- <a href="../apidocs/org/apache/commons/math3/stat/ranking/NaturalRanking.html">
- NaturalRanking</a> for more examples and <a href="../apidocs/org/apache/commons/math3/stat/ranking/TiesStrategy.html">
- TiesStrategy</a> and <a href="../apidocs/org/apache/commons/math3/stat/ranking/NaNStrategy.html">NaNStrategy</a>
+ <a href="../apidocs/org/apache/commons/math4/stat/ranking/NaturalRanking.html">
+ NaturalRanking</a> for more examples and <a href="../apidocs/org/apache/commons/math4/stat/ranking/TiesStrategy.html">
+ TiesStrategy</a> and <a href="../apidocs/org/apache/commons/math4/stat/ranking/NaNStrategy.html">NaNStrategy</a>
for details on these configuration options.
</p>
</subsection>
<subsection name="1.7 Covariance and correlation">
<p>
- The <a href="../apidocs/org/apache/commons/math3/stat/correlation/package-summary.html">
- org.apache.commons.math3.stat.correlation</a> package computes covariances
+ The <a href="../apidocs/org/apache/commons/math4/stat/correlation/package-summary.html">
+ org.apache.commons.math4.stat.correlation</a> package computes covariances
and correlations for pairs of arrays or columns of a matrix.
- <a href="../apidocs/org/apache/commons/math3/stat/correlation/Covariance.html">
+ <a href="../apidocs/org/apache/commons/math4/stat/correlation/Covariance.html">
Covariance</a> computes covariances,
- <a href="../apidocs/org/apache/commons/math3/stat/correlation/PearsonsCorrelation.html">
+ <a href="../apidocs/org/apache/commons/math4/stat/correlation/PearsonsCorrelation.html">
PearsonsCorrelation</a> provides Pearson's Product-Moment correlation coefficients,
- <a href="../apidocs/org/apache/commons/math3/stat/correlation/SpearmansCorrelation.html">
+ <a href="../apidocs/org/apache/commons/math4/stat/correlation/SpearmansCorrelation.html">
SpearmansCorrelation</a> computes Spearman's rank correlation and
- <a href="../apidocs/org/apache/commons/math3/stat/correlation/KendallsCorrelation.html">
+ <a href="../apidocs/org/apache/commons/math4/stat/correlation/KendallsCorrelation.html">
KendallsCorrelation</a> computes Kendall's tau rank correlation.
</p>
<p>
@@ -682,21 +682,21 @@ new NaturalRanking(NaNStrategy.REMOVED,TiesStrategy.SEQUENTIAL).rank(exampleData
defaults to <code>true.</code>
</li>
<li>
- <a href="../apidocs/org/apache/commons/math3/stat/correlation/PearsonsCorrelation.html">
+ <a href="../apidocs/org/apache/commons/math4/stat/correlation/PearsonsCorrelation.html">
PearsonsCorrelation</a> computes correlations defined by the formula <br/>
<code>cor(X, Y) = sum[(x<sub>i</sub> - E(X))(y<sub>i</sub> - E(Y))] / [(n - 1)s(X)s(Y)]</code><br/>
where <code>E(X)</code> and <code>E(Y)</code> are means of <code>X</code> and <code>Y</code>
and <code>s(X)</code>, <code>s(Y)</code> are standard deviations.
</li>
<li>
- <a href="../apidocs/org/apache/commons/math3/stat/correlation/SpearmansCorrelation.html">
+ <a href="../apidocs/org/apache/commons/math4/stat/correlation/SpearmansCorrelation.html">
SpearmansCorrelation</a> applies a rank transformation to the input data and computes Pearson's
correlation on the ranked data. The ranking algorithm is configurable. By default,
- <a href="../apidocs/org/apache/commons/math3/stat/ranking/NaturalRanking.html">
+ <a href="../apidocs/org/apache/commons/math4/stat/ranking/NaturalRanking.html">
NaturalRanking</a> with default strategies for handling ties and NaN values is used.
</li>
<li>
- <a href="../apidocs/org/apache/commons/math3/stat/correlation/KendallsCorrelation.html">
+ <a href="../apidocs/org/apache/commons/math4/stat/correlation/KendallsCorrelation.html">
KendallsCorrelation</a> computes the association between two measured quantities. A tau test
is a non-parametric hypothesis test for statistical dependence based on the tau coefficient.
</li>
@@ -818,8 +818,8 @@ new KendallsCorrelation().correlation(x, y)
</subsection>
<subsection name="1.8 Statistical tests">
<p>
- The <a href="../apidocs/org/apache/commons/math3/stat/inference/">
- org.apache.commons.math3.stat.inference</a> package provides implementations for
+ The <a href="../apidocs/org/apache/commons/math4/stat/inference/">
+ org.apache.commons.math4.stat.inference</a> package provides implementations for
<a href="http://www.itl.nist.gov/div898/handbook/prc/section2/prc22.htm">
Student's t</a>,
<a href="http://www.itl.nist.gov/div898/handbook/eda/section3/eda35f.htm">
@@ -838,23 +838,23 @@ new KendallsCorrelation().correlation(x, y)
<code>Chi-Square</code>, <code>G</code>, <code>One-Way ANOVA</code>, <code>Mann-Whitney U</code>
<code>Wilcoxon signed rank</code>, and <code>Kolmogorov-Smirnov</code> tests.
The respective test classes are
- <a href="../apidocs/org/apache/commons/math3/stat/inference/TTest.html">
+ <a href="../apidocs/org/apache/commons/math4/stat/inference/TTest.html">
TTest</a>,
- <a href="../apidocs/org/apache/commons/math3/stat/inference/ChiSquareTest.html">
+ <a href="../apidocs/org/apache/commons/math4/stat/inference/ChiSquareTest.html">
ChiSquareTest</a>,
- <a href="../apidocs/org/apache/commons/math3/stat/inference/GTest.html">
+ <a href="../apidocs/org/apache/commons/math4/stat/inference/GTest.html">
GTest</a>,
- <a href="../apidocs/org/apache/commons/math3/stat/inference/OneWayAnova.html">
+ <a href="../apidocs/org/apache/commons/math4/stat/inference/OneWayAnova.html">
OneWayAnova</a>,
- <a href="../apidocs/org/apache/commons/math3/stat/inference/MannWhitneyUTest.html">
+ <a href="../apidocs/org/apache/commons/math4/stat/inference/MannWhitneyUTest.html">
MannWhitneyUTest</a>,
- <a href="../apidocs/org/apache/commons/math3/stat/inference/WilcoxonSignedRankTest.html">
+ <a href="../apidocs/org/apache/commons/math4/stat/inference/WilcoxonSignedRankTest.html">
WilcoxonSignedRankTest</a>,
- <a href="../apidocs/org/apache/commons/math3/stat/inference/BinomialTest.html">
+ <a href="../apidocs/org/apache/commons/math4/stat/inference/BinomialTest.html">
BinomialTest</a> and
- <a href="../apidocs/org/apache/commons/math3/stat/inference/KolmogorovSmirnovTest.html">
+ <a href="../apidocs/org/apache/commons/math4/stat/inference/KolmogorovSmirnovTest.html">
KolmogorovSmirnovTest</a>.
- The <a href="../apidocs/org/apache/commons/math3/stat/inference/TestUtils.html">
+ The <a href="../apidocs/org/apache/commons/math4/stat/inference/TestUtils.html">
TestUtils</a> class provides static methods to get test instances or
to compute test statistics directly. The examples below all use the
static methods in <code>TestUtils</code> to execute tests. To get
@@ -937,7 +937,7 @@ System.out.println(TestUtils.t(mu, observed));
<code>mu.</code>
</dd>
<dd>To compare the mean of a dataset described by a
- <a href="../apidocs/org/apache/commons/math3/stat/descriptive/StatisticalSummary.html">
+ <a href="../apidocs/org/apache/commons/math4/stat/descriptive/StatisticalSummary.html">
StatisticalSummary</a> to a fixed value:
<source>
double[] observed ={1d, 2d, 3d};
http://git-wip-us.apache.org/repos/asf/commons-math/blob/e4e1ac23/src/site/xdoc/userguide/transform.xml
----------------------------------------------------------------------
diff --git a/src/site/xdoc/userguide/transform.xml b/src/site/xdoc/userguide/transform.xml
index 1499eb5..56cdec0 100644
--- a/src/site/xdoc/userguide/transform.xml
+++ b/src/site/xdoc/userguide/transform.xml
@@ -30,13 +30,13 @@
This package provides a few transformers for signal analysis. All transformers
provide both direct and inverse transforms.
<ul>
- <li><a href="../apidocs/org/apache/commons/math3/transform/FastFourierTransformer.html">
+ <li><a href="../apidocs/org/apache/commons/math4/transform/FastFourierTransformer.html">
FastFourierTransformer</a> (produces <code>Complex</code> results)</li>
- <li><a href="../apidocs/org/apache/commons/math3/transform/FastCosineTransformer.html">
+ <li><a href="../apidocs/org/apache/commons/math4/transform/FastCosineTransformer.html">
FastCosineTransformer</a> (produces real results)</li>
- <li><a href="../apidocs/org/apache/commons/math3/transform/FastSineTransformer.html">
+ <li><a href="../apidocs/org/apache/commons/math4/transform/FastSineTransformer.html">
FastSineTransformer</a> (produces real results)</li>
- <li><a href="../apidocs/org/apache/commons/math3/transform/FastHadamardTransformer.html">
+ <li><a href="../apidocs/org/apache/commons/math4/transform/FastHadamardTransformer.html">
FastHadamardTransformer</a> (produces real results)</li>
</ul>
</p>
http://git-wip-us.apache.org/repos/asf/commons-math/blob/e4e1ac23/src/site/xdoc/userguide/utilities.xml
----------------------------------------------------------------------
diff --git a/src/site/xdoc/userguide/utilities.xml b/src/site/xdoc/userguide/utilities.xml
index a03c2f3..e166e77 100644
--- a/src/site/xdoc/userguide/utilities.xml
+++ b/src/site/xdoc/userguide/utilities.xml
@@ -30,8 +30,8 @@
<subsection name="6.1 Overview" href="overview">
<p>
- The <a href="../apidocs/org/apache/commons/math3/util/package-summary.html">
- org.apache.commons.math3.util</a> package collects a group of array utilities,
+ The <a href="../apidocs/org/apache/commons/math4/util/package-summary.html">
+ org.apache.commons.math4.util</a> package collects a group of array utilities,
value transformers, and numerical routines used by implementation classes in
commons-math.
</p>
@@ -43,7 +43,7 @@
array implementation was developed and is provided for reuse in the
<code>util</code> package. The core functionality provided is described in
the documentation for the interface,
- <a href="../apidocs/org/apache/commons/math3/util/DoubleArray.html">
+ <a href="../apidocs/org/apache/commons/math4/util/DoubleArray.html">
DoubleArray</a>. This interface adds one method,
<code>addElementRolling(double)</code> to basic list accessors.
The <code>addElementRolling</code> method adds an element
@@ -51,7 +51,7 @@
in the list.
</p>
<p>
- The <a href="../apidocs/org/apache/commons/math3/util/ResizableDoubleArray.html">
+ The <a href="../apidocs/org/apache/commons/math4/util/ResizableDoubleArray.html">
ResizableDoubleArray</a> class provides a configurable, array-backed
implementation of the <code>DoubleArray</code> interface.
When <code>addElementRolling</code> is invoked, the underlying
@@ -65,7 +65,7 @@
automatically, with frequency / effect driven by the configuration
properties <code>expansionMode</code>, <code>expansionFactor</code> and
<code>contractionCriteria.</code> See
- <a href="../apidocs/org/apache/commons/math3/util/ResizableDoubleArray.html">
+ <a href="../apidocs/org/apache/commons/math4/util/ResizableDoubleArray.html">
ResizableDoubleArray</a>
for details.
</p>
@@ -73,7 +73,7 @@
<subsection name="6.3 int/double hash map" href="int_double_hash_map">
<p>
- The <a href="../apidocs/org/apache/commons/math3/util/OpenIntToDoubleHashMap.html">
+ The <a href="../apidocs/org/apache/commons/math4/util/OpenIntToDoubleHashMap.html">
OpenIntToDoubleHashMap</a> class provides a specialized hash map
implementation for int/double. This implementation has a much smaller memory
overhead than standard <code>java.util.HashMap</code> class. It uses open addressing
@@ -84,7 +84,7 @@
<subsection name="6.4 Continued Fractions" href="continued_fractions">
<p>
- The <a href="../apidocs/org/apache/commons/math3/util/ContinuedFraction.html">
+ The <a href="../apidocs/org/apache/commons/math4/util/ContinuedFraction.html">
ContinuedFraction</a> class provides a generic way to create and evaluate
continued fractions. The easiest way to create a continued fraction is
to subclass <code>ContinuedFraction</code> and override the
@@ -148,7 +148,7 @@
<subsection name="6.5 Binomial coefficients, factorials, Stirling numbers and other common math functions" href="binomial_coefficients_factorials_and_other_common_math_functions">
<p>
A collection of reusable math functions is provided in the
- <a href="../apidocs/org/apache/commons/math3/util/ArithmeticUtils.html">ArithmeticUtils</a>
+ <a href="../apidocs/org/apache/commons/math4/util/ArithmeticUtils.html">ArithmeticUtils</a>
utility class. ArithmeticUtils currently includes methods to compute the following: <ul>
<li>
Binomial coefficients -- "n choose k" available as an (exact) long value,
@@ -234,7 +234,7 @@
</subsection>
<subsection name="6.7 Miscellaneous" href="miscellaneous">
- The <a href="../apidocs/org/apache/commons/math3/util/MultidimensionalCounter.html">
+ The <a href="../apidocs/org/apache/commons/math4/util/MultidimensionalCounter.html">
MultidimensionalCounter</a> is a utility class that converts a set of indices
(identifying points in a multidimensional space) to a single index (e.g. identifying
a location in a one-dimensional array.
http://git-wip-us.apache.org/repos/asf/commons-math/blob/e4e1ac23/src/test/R/KolmogorovSmirnovTestCases.R
----------------------------------------------------------------------
diff --git a/src/test/R/KolmogorovSmirnovTestCases.R b/src/test/R/KolmogorovSmirnovTestCases.R
index 6b70155..f66b253 100644
--- a/src/test/R/KolmogorovSmirnovTestCases.R
+++ b/src/test/R/KolmogorovSmirnovTestCases.R
@@ -15,7 +15,7 @@
#
#------------------------------------------------------------------------------
# R source file to validate KolmogorovSmirnov tests in
-# org.apache.commons.math3.stat.inference.KolmogorovSmirnovTest
+# org.apache.commons.math4.stat.inference.KolmogorovSmirnovTest
#
# To run the test, install R, put this file and testFunctions
# into the same directory, launch R from this directory and then enter
http://git-wip-us.apache.org/repos/asf/commons-math/blob/e4e1ac23/src/test/R/LevyDistributionTestCases.R
----------------------------------------------------------------------
diff --git a/src/test/R/LevyDistributionTestCases.R b/src/test/R/LevyDistributionTestCases.R
index 7a6651f..9e9238e 100644
--- a/src/test/R/LevyDistributionTestCases.R
+++ b/src/test/R/LevyDistributionTestCases.R
@@ -15,7 +15,7 @@
#
#------------------------------------------------------------------------------
# R source file to validate Lévy distribution tests in
-# org.apache.commons.math3.distribution.LevyDistributionTest
+# org.apache.commons.math4.distribution.LevyDistributionTest
#
# To run the test, install R, put this file and testFunctions
# into the same directory, launch R from this directory and then enter
http://git-wip-us.apache.org/repos/asf/commons-math/blob/e4e1ac23/src/test/R/gumbelTestCases.R
----------------------------------------------------------------------
diff --git a/src/test/R/gumbelTestCases.R b/src/test/R/gumbelTestCases.R
index 727c2a0..f243860 100644
--- a/src/test/R/gumbelTestCases.R
+++ b/src/test/R/gumbelTestCases.R
@@ -15,7 +15,7 @@
#
#------------------------------------------------------------------------------
# R source file to validate Gumbel distribution tests in
-# org.apache.commons.math3.distribution.GumbelDistributionTest
+# org.apache.commons.math4.distribution.GumbelDistributionTest
#
# To run the test, install R, put this file and testFunctions
# into the same directory, launch R from this directory and then enter
http://git-wip-us.apache.org/repos/asf/commons-math/blob/e4e1ac23/src/test/R/laplaceTestCases.R
----------------------------------------------------------------------
diff --git a/src/test/R/laplaceTestCases.R b/src/test/R/laplaceTestCases.R
index ec1f186..b4d4620 100644
--- a/src/test/R/laplaceTestCases.R
+++ b/src/test/R/laplaceTestCases.R
@@ -15,7 +15,7 @@
#
#------------------------------------------------------------------------------
# R source file to validate Laplace distribution tests in
-# org.apache.commons.math3.distribution.LaplaceDistributionTest
+# org.apache.commons.math4.distribution.LaplaceDistributionTest
#
# To run the test, install R, put this file and testFunctions
# into the same directory, launch R from this directory and then enter
http://git-wip-us.apache.org/repos/asf/commons-math/blob/e4e1ac23/src/test/R/logisticsTestCases.R
----------------------------------------------------------------------
diff --git a/src/test/R/logisticsTestCases.R b/src/test/R/logisticsTestCases.R
index 97e3cf1..f555fea 100644
--- a/src/test/R/logisticsTestCases.R
+++ b/src/test/R/logisticsTestCases.R
@@ -15,7 +15,7 @@
#
#------------------------------------------------------------------------------
# R source file to validate Logistics distribution tests in
-# org.apache.commons.math3.distribution.LogisticsDistributionTest
+# org.apache.commons.math4.distribution.LogisticsDistributionTest
#
# To run the test, install R, put this file and testFunctions
# into the same directory, launch R from this directory and then enter
http://git-wip-us.apache.org/repos/asf/commons-math/blob/e4e1ac23/src/test/R/nakagamiTestCases.R
----------------------------------------------------------------------
diff --git a/src/test/R/nakagamiTestCases.R b/src/test/R/nakagamiTestCases.R
index 033de7e..e1dd2be 100644
--- a/src/test/R/nakagamiTestCases.R
+++ b/src/test/R/nakagamiTestCases.R
@@ -15,7 +15,7 @@
#
#------------------------------------------------------------------------------
# R source file to validate Nakagami distribution tests in
-# org.apache.commons.math3.distribution.NakagamiDistributionTest
+# org.apache.commons.math4.distribution.NakagamiDistributionTest
#
# To run the test, install R, put this file and testFunctions
# into the same directory, launch R from this directory and then enter
http://git-wip-us.apache.org/repos/asf/commons-math/blob/e4e1ac23/src/test/java/org/apache/commons/math4/ExtendedFieldElementAbstractTest.java
----------------------------------------------------------------------
diff --git a/src/test/java/org/apache/commons/math4/ExtendedFieldElementAbstractTest.java b/src/test/java/org/apache/commons/math4/ExtendedFieldElementAbstractTest.java
index 76e9cd5..03b5a1a 100644
--- a/src/test/java/org/apache/commons/math4/ExtendedFieldElementAbstractTest.java
+++ b/src/test/java/org/apache/commons/math4/ExtendedFieldElementAbstractTest.java
@@ -14,12 +14,13 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-package org.apache.commons.math3;
+package org.apache.commons.math4;
-import org.apache.commons.math3.random.RandomGenerator;
-import org.apache.commons.math3.random.Well1024a;
-import org.apache.commons.math3.util.FastMath;
-import org.apache.commons.math3.util.MathArrays;
+import org.apache.commons.math4.RealFieldElement;
+import org.apache.commons.math4.random.RandomGenerator;
+import org.apache.commons.math4.random.Well1024a;
+import org.apache.commons.math4.util.FastMath;
+import org.apache.commons.math4.util.MathArrays;
import org.junit.Assert;
import org.junit.Test;
http://git-wip-us.apache.org/repos/asf/commons-math/blob/e4e1ac23/src/test/java/org/apache/commons/math4/PerfTestUtils.java
----------------------------------------------------------------------
diff --git a/src/test/java/org/apache/commons/math4/PerfTestUtils.java b/src/test/java/org/apache/commons/math4/PerfTestUtils.java
index 4558305..75afa60 100644
--- a/src/test/java/org/apache/commons/math4/PerfTestUtils.java
+++ b/src/test/java/org/apache/commons/math4/PerfTestUtils.java
@@ -14,14 +14,15 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-package org.apache.commons.math3;
+package org.apache.commons.math4;
import java.util.Random;
import java.util.concurrent.Callable;
-import org.apache.commons.math3.stat.descriptive.SummaryStatistics;
-import org.apache.commons.math3.stat.descriptive.StatisticalSummary;
-import org.apache.commons.math3.exception.MathIllegalStateException;
-import org.apache.commons.math3.exception.util.LocalizedFormats;
+
+import org.apache.commons.math4.exception.MathIllegalStateException;
+import org.apache.commons.math4.exception.util.LocalizedFormats;
+import org.apache.commons.math4.stat.descriptive.StatisticalSummary;
+import org.apache.commons.math4.stat.descriptive.SummaryStatistics;
/**
* Simple benchmarking utilities.
http://git-wip-us.apache.org/repos/asf/commons-math/blob/e4e1ac23/src/test/java/org/apache/commons/math4/Retry.java
----------------------------------------------------------------------
diff --git a/src/test/java/org/apache/commons/math4/Retry.java b/src/test/java/org/apache/commons/math4/Retry.java
index 0d5f2ab..7289ab6 100644
--- a/src/test/java/org/apache/commons/math4/Retry.java
+++ b/src/test/java/org/apache/commons/math4/Retry.java
@@ -15,7 +15,7 @@
* limitations under the License.
*/
-package org.apache.commons.math3;
+package org.apache.commons.math4;
import java.lang.annotation.*;
http://git-wip-us.apache.org/repos/asf/commons-math/blob/e4e1ac23/src/test/java/org/apache/commons/math4/RetryRunner.java
----------------------------------------------------------------------
diff --git a/src/test/java/org/apache/commons/math4/RetryRunner.java b/src/test/java/org/apache/commons/math4/RetryRunner.java
index d02741c..a2c2bc1 100644
--- a/src/test/java/org/apache/commons/math4/RetryRunner.java
+++ b/src/test/java/org/apache/commons/math4/RetryRunner.java
@@ -15,7 +15,7 @@
* limitations under the License.
*/
-package org.apache.commons.math3;
+package org.apache.commons.math4;
import org.junit.runners.BlockJUnit4ClassRunner;
import org.junit.runners.model.FrameworkMethod;
http://git-wip-us.apache.org/repos/asf/commons-math/blob/e4e1ac23/src/test/java/org/apache/commons/math4/RetryRunnerTest.java
----------------------------------------------------------------------
diff --git a/src/test/java/org/apache/commons/math4/RetryRunnerTest.java b/src/test/java/org/apache/commons/math4/RetryRunnerTest.java
index f7fa1e0..193d11a 100644
--- a/src/test/java/org/apache/commons/math4/RetryRunnerTest.java
+++ b/src/test/java/org/apache/commons/math4/RetryRunnerTest.java
@@ -15,12 +15,11 @@
* limitations under the License.
*/
-package org.apache.commons.math3;
+package org.apache.commons.math4;
import java.util.Random;
-import org.apache.commons.math3.exception.MathIllegalStateException;
-
+import org.apache.commons.math4.exception.MathIllegalStateException;
import org.junit.Test;
import org.junit.runner.RunWith;
http://git-wip-us.apache.org/repos/asf/commons-math/blob/e4e1ac23/src/test/java/org/apache/commons/math4/TestUtils.java
----------------------------------------------------------------------
diff --git a/src/test/java/org/apache/commons/math4/TestUtils.java b/src/test/java/org/apache/commons/math4/TestUtils.java
index 4dddf56..109e64d 100644
--- a/src/test/java/org/apache/commons/math4/TestUtils.java
+++ b/src/test/java/org/apache/commons/math4/TestUtils.java
@@ -15,7 +15,7 @@
* limitations under the License.
*/
-package org.apache.commons.math3;
+package org.apache.commons.math4;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
@@ -24,16 +24,16 @@ import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
import java.text.DecimalFormat;
-
-import org.apache.commons.math3.complex.Complex;
-import org.apache.commons.math3.complex.ComplexFormat;
-import org.apache.commons.math3.distribution.RealDistribution;
-import org.apache.commons.math3.linear.FieldMatrix;
-import org.apache.commons.math3.linear.RealMatrix;
-import org.apache.commons.math3.linear.RealVector;
-import org.apache.commons.math3.stat.inference.ChiSquareTest;
-import org.apache.commons.math3.util.FastMath;
-import org.apache.commons.math3.util.Precision;
+import org.apache.commons.math4.FieldElement;
+import org.apache.commons.math4.complex.Complex;
+import org.apache.commons.math4.complex.ComplexFormat;
+import org.apache.commons.math4.distribution.RealDistribution;
+import org.apache.commons.math4.linear.FieldMatrix;
+import org.apache.commons.math4.linear.RealMatrix;
+import org.apache.commons.math4.linear.RealVector;
+import org.apache.commons.math4.stat.inference.ChiSquareTest;
+import org.apache.commons.math4.util.FastMath;
+import org.apache.commons.math4.util.Precision;
import org.junit.Assert;
/**
http://git-wip-us.apache.org/repos/asf/commons-math/blob/e4e1ac23/src/test/java/org/apache/commons/math4/analysis/FunctionUtilsTest.java
----------------------------------------------------------------------
diff --git a/src/test/java/org/apache/commons/math4/analysis/FunctionUtilsTest.java b/src/test/java/org/apache/commons/math4/analysis/FunctionUtilsTest.java
index 5e2bc96..f1c649a 100644
--- a/src/test/java/org/apache/commons/math4/analysis/FunctionUtilsTest.java
+++ b/src/test/java/org/apache/commons/math4/analysis/FunctionUtilsTest.java
@@ -15,30 +15,37 @@
* limitations under the License.
*/
-package org.apache.commons.math3.analysis;
-
-import org.apache.commons.math3.analysis.differentiation.DerivativeStructure;
-import org.apache.commons.math3.analysis.differentiation.MultivariateDifferentiableFunction;
-import org.apache.commons.math3.analysis.differentiation.UnivariateDifferentiableFunction;
-import org.apache.commons.math3.analysis.function.Add;
-import org.apache.commons.math3.analysis.function.Constant;
-import org.apache.commons.math3.analysis.function.Cos;
-import org.apache.commons.math3.analysis.function.Cosh;
-import org.apache.commons.math3.analysis.function.Divide;
-import org.apache.commons.math3.analysis.function.Identity;
-import org.apache.commons.math3.analysis.function.Inverse;
-import org.apache.commons.math3.analysis.function.Log;
-import org.apache.commons.math3.analysis.function.Max;
-import org.apache.commons.math3.analysis.function.Min;
-import org.apache.commons.math3.analysis.function.Minus;
-import org.apache.commons.math3.analysis.function.Multiply;
-import org.apache.commons.math3.analysis.function.Pow;
-import org.apache.commons.math3.analysis.function.Power;
-import org.apache.commons.math3.analysis.function.Sin;
-import org.apache.commons.math3.analysis.function.Sinc;
-import org.apache.commons.math3.exception.NotStrictlyPositiveException;
-import org.apache.commons.math3.exception.NumberIsTooLargeException;
-import org.apache.commons.math3.util.FastMath;
+package org.apache.commons.math4.analysis;
+
+import org.apache.commons.math4.analysis.BivariateFunction;
+import org.apache.commons.math4.analysis.DifferentiableMultivariateFunction;
+import org.apache.commons.math4.analysis.DifferentiableUnivariateFunction;
+import org.apache.commons.math4.analysis.FunctionUtils;
+import org.apache.commons.math4.analysis.MultivariateFunction;
+import org.apache.commons.math4.analysis.MultivariateVectorFunction;
+import org.apache.commons.math4.analysis.UnivariateFunction;
+import org.apache.commons.math4.analysis.differentiation.DerivativeStructure;
+import org.apache.commons.math4.analysis.differentiation.MultivariateDifferentiableFunction;
+import org.apache.commons.math4.analysis.differentiation.UnivariateDifferentiableFunction;
+import org.apache.commons.math4.analysis.function.Add;
+import org.apache.commons.math4.analysis.function.Constant;
+import org.apache.commons.math4.analysis.function.Cos;
+import org.apache.commons.math4.analysis.function.Cosh;
+import org.apache.commons.math4.analysis.function.Divide;
+import org.apache.commons.math4.analysis.function.Identity;
+import org.apache.commons.math4.analysis.function.Inverse;
+import org.apache.commons.math4.analysis.function.Log;
+import org.apache.commons.math4.analysis.function.Max;
+import org.apache.commons.math4.analysis.function.Min;
+import org.apache.commons.math4.analysis.function.Minus;
+import org.apache.commons.math4.analysis.function.Multiply;
+import org.apache.commons.math4.analysis.function.Pow;
+import org.apache.commons.math4.analysis.function.Power;
+import org.apache.commons.math4.analysis.function.Sin;
+import org.apache.commons.math4.analysis.function.Sinc;
+import org.apache.commons.math4.exception.NotStrictlyPositiveException;
+import org.apache.commons.math4.exception.NumberIsTooLargeException;
+import org.apache.commons.math4.util.FastMath;
import org.junit.Assert;
import org.junit.Test;
http://git-wip-us.apache.org/repos/asf/commons-math/blob/e4e1ac23/src/test/java/org/apache/commons/math4/analysis/MonitoredFunction.java
----------------------------------------------------------------------
diff --git a/src/test/java/org/apache/commons/math4/analysis/MonitoredFunction.java b/src/test/java/org/apache/commons/math4/analysis/MonitoredFunction.java
index e38dc11..b2a9e9d 100644
--- a/src/test/java/org/apache/commons/math4/analysis/MonitoredFunction.java
+++ b/src/test/java/org/apache/commons/math4/analysis/MonitoredFunction.java
@@ -14,7 +14,9 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-package org.apache.commons.math3.analysis;
+package org.apache.commons.math4.analysis;
+
+import org.apache.commons.math4.analysis.UnivariateFunction;
/**
* Wrapper class for counting functions calls.