This is an automated email from the ASF dual-hosted git repository.
erans pushed a commit to branch master
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The following commit(s) were added to refs/heads/master by this push:
new ffcdf39f8 Update userguide.
ffcdf39f8 is described below
commit ffcdf39f8fa7ccd19c5c21a73fccb90c753592cd
Author: Gilles Sadowski <gillese...@gmail.com>
AuthorDate: Fri Apr 5 13:08:03 2024 +0200
Update userguide.
Some links are still broken (due to the refactoring).
---
src/site/xdoc/userguide/analysis.xml | 142 +++++++++++++++----------------
src/site/xdoc/userguide/distribution.xml | 4 +-
src/site/xdoc/userguide/exceptions.xml | 14 +--
src/site/xdoc/userguide/filter.xml | 6 +-
src/site/xdoc/userguide/fitting.xml | 26 +++---
src/site/xdoc/userguide/genetics.xml | 28 +++---
src/site/xdoc/userguide/leastsquares.xml | 52 +++++------
src/site/xdoc/userguide/linear.xml | 34 ++++----
src/site/xdoc/userguide/ml.xml | 22 ++---
src/site/xdoc/userguide/ode.xml | 76 ++++++++---------
src/site/xdoc/userguide/optimization.xml | 56 ++++++------
src/site/xdoc/userguide/overview.xml | 6 +-
src/site/xdoc/userguide/random.xml | 8 +-
src/site/xdoc/userguide/stat.xml | 106 +++++++++++------------
src/site/xdoc/userguide/utilities.xml | 16 ++--
15 files changed, 298 insertions(+), 298 deletions(-)
diff --git a/src/site/xdoc/userguide/analysis.xml
b/src/site/xdoc/userguide/analysis.xml
index 2def6bd0f..6bd64a27a 100644
--- a/src/site/xdoc/userguide/analysis.xml
+++ b/src/site/xdoc/userguide/analysis.xml
@@ -88,13 +88,13 @@
</subsection>
<subsection name="4.3 Root-finding" href="rootfinding">
<p>
- <a
href="../apidocs/org/apache/commons/math4/analysis/solvers/UnivariateSolver.html">
- UnivariateSolver</a>, <a
href="../apidocs/org/apache/commons/math4/analysis/solvers/UnivariateDifferentiableSolver.html">
- UnivariateDifferentiableSolver</a> and <a
href="../apidocs/org/apache/commons/math4/analysis/solvers/PolynomialSolver.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/solvers/UnivariateSolver.html">
+ UnivariateSolver</a>, <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/solvers/UnivariateDifferentiableSolver.html">
+ UnivariateDifferentiableSolver</a> and <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/solvers/PolynomialSolver.html">
PolynomialSolver</a> provide means to find roots of
- <a
href="../apidocs/org/apache/commons/math4/analysis/UnivariateFunction.html">univariate
real-valued functions</a>,
- <a
href="../apidocs/org/apache/commons/math4/analysis/differentiation/UnivariateDifferentiable.html">differentiable
univariate real-valued functions</a>,
- and <a
href="../apidocs/org/apache/commons/math4/analysis/polynomials/PolynomialFunction.html">polynomial
functions</a> respectively.
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/UnivariateFunction.html">univariate
real-valued functions</a>,
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/differentiation/UnivariateDifferentiable.html">differentiable
univariate real-valued functions</a>,
+ and <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/polynomials/PolynomialFunction.html">polynomial
functions</a> respectively.
A root is the value where the function takes the value 0.
Commons-Math
includes implementations of the several root-finding algorithms:
</p>
@@ -102,85 +102,85 @@
<tr BGCOLOR="#CCCCFF"><td colspan="5"><font size="+1">Root
solvers</font></td></tr>
<tr BGCOLOR="#EEEEFF"><font size="+1"><td>Name</td><td>Function
type</td><td>Convergence</td><td>Needs initial bracketing</td><td>Bracket side
selection</td></font></tr>
<tr>
- <td><a
href="../apidocs/org/apache/commons/math4/analysis/solvers/BisectionSolver.html">Bisection</a></td>
- <td><a
href="../apidocs/org/apache/commons/math4/analysis/UnivariateFunction.html">univariate
real-valued functions</a></td>
+ <td><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/solvers/BisectionSolver.html">Bisection</a></td>
+ <td><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/UnivariateFunction.html">univariate
real-valued functions</a></td>
<td>linear, guaranteed</td>
<td>yes</td>
<td>yes</td>
</tr>
<tr>
- <td><a
href="../apidocs/org/apache/commons/math4/analysis/solvers/BrentSolver.html">Brent-Dekker</a></td>
- <td><a
href="../apidocs/org/apache/commons/math4/analysis/UnivariateFunction.html">univariate
real-valued functions</a></td>
+ <td><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/solvers/BrentSolver.html">Brent-Dekker</a></td>
+ <td><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/UnivariateFunction.html">univariate
real-valued functions</a></td>
<td>super-linear, guaranteed</td>
<td>yes</td>
<td>no</td>
</tr>
<tr>
- <td><a
href="../apidocs/org/apache/commons/math4/analysis/solvers/BracketingNthOrderBrentSolver.html">bracketing
n<sup>th</sup> order Brent</a></td>
- <td><a
href="../apidocs/org/apache/commons/math4/analysis/UnivariateFunction.html">univariate
real-valued functions</a></td>
+ <td><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/solvers/BracketingNthOrderBrentSolver.html">bracketing
n<sup>th</sup> order Brent</a></td>
+ <td><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/UnivariateFunction.html">univariate
real-valued functions</a></td>
<td>variable order, guaranteed</td>
<td>yes</td>
<td>yes</td>
</tr>
<tr>
- <td><a
href="../apidocs/org/apache/commons/math4/analysis/solvers/IllinoisSolver.html">Illinois
Method</a></td>
- <td><a
href="../apidocs/org/apache/commons/math4/analysis/UnivariateFunction.html">univariate
real-valued functions</a></td>
+ <td><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/solvers/IllinoisSolver.html">Illinois
Method</a></td>
+ <td><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/UnivariateFunction.html">univariate
real-valued functions</a></td>
<td>super-linear, guaranteed</td>
<td>yes</td>
<td>yes</td>
</tr>
<tr>
- <td><a
href="../apidocs/org/apache/commons/math4/analysis/solvers/LaguerreSolver.html">Laguerre's
Method</a></td>
- <td><a
href="../apidocs/org/apache/commons/math4/analysis/polynomials/PolynomialFunction.html">polynomial
functions</a></td>
+ <td><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/solvers/LaguerreSolver.html">Laguerre's
Method</a></td>
+ <td><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/polynomials/PolynomialFunction.html">polynomial
functions</a></td>
<td>cubic for simple root, linear for multiple root</td>
<td>yes</td>
<td>no</td>
</tr>
<tr>
- <td><a
href="../apidocs/org/apache/commons/math4/analysis/solvers/MullerSolver.html">Muller's
Method</a> using bracketing to deal with real-valued functions</td>
- <td><a
href="../apidocs/org/apache/commons/math4/analysis/UnivariateFunction.html">univariate
real-valued functions</a></td>
+ <td><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/solvers/MullerSolver.html">Muller's
Method</a> using bracketing to deal with real-valued functions</td>
+ <td><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/UnivariateFunction.html">univariate
real-valued functions</a></td>
<td>quadratic close to roots</td>
<td>yes</td>
<td>no</td>
</tr>
<tr>
- <td><a
href="../apidocs/org/apache/commons/math4/analysis/solvers/MullerSolver2.html">Muller's
Method</a> using modulus to deal with real-valued functions</td>
- <td><a
href="../apidocs/org/apache/commons/math4/analysis/UnivariateFunction.html">univariate
real-valued functions</a></td>
+ <td><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/solvers/MullerSolver2.html">Muller's
Method</a> using modulus to deal with real-valued functions</td>
+ <td><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/UnivariateFunction.html">univariate
real-valued functions</a></td>
<td>quadratic close to root</td>
<td>yes</td>
<td>no</td>
</tr>
<tr>
- <td><a
href="../apidocs/org/apache/commons/math4/analysis/solvers/NewtonRaphsonSolver.html">Newton-Raphson's
Method</a></td>
- <td><a
href="../apidocs/org/apache/commons/math4/analysis/differentiation/UnivariateDifferentiableFunction.html">differentiable
univariate real-valued functions</a></td>
+ <td><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/solvers/NewtonRaphsonSolver.html">Newton-Raphson's
Method</a></td>
+ <td><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/differentiation/UnivariateDifferentiableFunction.html">differentiable
univariate real-valued functions</a></td>
<td>quadratic, non-guaranteed</td>
<td>no</td>
<td>no</td>
</tr>
<tr>
- <td><a
href="../apidocs/org/apache/commons/math4/analysis/solvers/PegasusSolver.html">Pegasus
Method</a></td>
- <td><a
href="../apidocs/org/apache/commons/math4/analysis/UnivariateFunction.html">univariate
real-valued functions</a></td>
+ <td><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/solvers/PegasusSolver.html">Pegasus
Method</a></td>
+ <td><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/UnivariateFunction.html">univariate
real-valued functions</a></td>
<td>super-linear, guaranteed</td>
<td>yes</td>
<td>yes</td>
</tr>
<tr>
- <td><a
href="../apidocs/org/apache/commons/math4/analysis/solvers/RegulaFalsiSolver.html">Regula
Falsi (false position) Method</a></td>
- <td><a
href="../apidocs/org/apache/commons/math4/analysis/UnivariateFunction.html">univariate
real-valued functions</a></td>
+ <td><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/solvers/RegulaFalsiSolver.html">Regula
Falsi (false position) Method</a></td>
+ <td><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/UnivariateFunction.html">univariate
real-valued functions</a></td>
<td>linear, guaranteed</td>
<td>yes</td>
<td>yes</td>
</tr>
<tr>
- <td><a
href="../apidocs/org/apache/commons/math4/analysis/solvers/RiddersSolver.html">Ridder's
Method</a></td>
- <td><a
href="../apidocs/org/apache/commons/math4/analysis/UnivariateFunction.html">univariate
real-valued functions</a></td>
+ <td><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/solvers/RiddersSolver.html">Ridder's
Method</a></td>
+ <td><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/UnivariateFunction.html">univariate
real-valued functions</a></td>
<td>super-linear</td>
<td>yes</td>
<td>no</td>
</tr>
<tr>
- <td><a
href="../apidocs/org/apache/commons/math4/analysis/solvers/SecantSolver.html">Secant
Method</a></td>
- <td><a
href="../apidocs/org/apache/commons/math4/analysis/UnivariateFunction.html">univariate
real-valued functions</a></td>
+ <td><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/solvers/SecantSolver.html">Secant
Method</a></td>
+ <td><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/UnivariateFunction.html">univariate
real-valued functions</a></td>
<td>super-linear, non-guaranteed</td>
<td>yes</td>
<td>no</td>
@@ -236,9 +236,9 @@
ill-conditioned problems is to be solved, this number can be
decreased in order
to avoid wasting time.
<a
-
href="../apidocs/org/apache/commons/math4/analysis/solvers/BracketedUnivariateSolver.html">Bracketed
+
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/solvers/BracketedUnivariateSolver.html">Bracketed
solvers</a> also take an <a
-
href="../apidocs/org/apache/commons/math4/analysis/solvers/AllowedSolution.html">allowed
solution</a>
+
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/solvers/AllowedSolution.html">allowed
solution</a>
enum parameter to specify which side of the final convergence
interval should be
selected as the root. It can be <code>ANY_SIDE</code>,
<code>LEFT_SIDE</code>, <code>RIGHT_SIDE</code>,
<code>BELOW_SIDE</code> or <code>ABOVE_SIDE</code>. Left and right
are used to specify the root along
@@ -372,13 +372,13 @@ double c = UnivariateSolverUtils.forceSide(100, function,
</subsection>
<subsection name="4.4 Interpolation" href="interpolation">
<p>
- A <a
href="../apidocs/org/apache/commons/math4/analysis/interpolation/UnivariateInterpolator.html">
+ A <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/interpolation/UnivariateInterpolator.html">
UnivariateInterpolator</a> is used to find a univariate real-valued
function <code>f</code> which for a given set of ordered pairs
(<code>x<sub>i</sub></code>,<code>y<sub>i</sub></code>) yields
<code>f(x<sub>i</sub>)=y<sub>i</sub></code> to the best accuracy
possible. The result
is provided as an object implementing the <a
-
href="../apidocs/org/apache/commons/math4/analysis/UnivariateFunction.html">
+
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/UnivariateFunction.html">
UnivariateFunction</a> interface. It can therefore be evaluated at
any point,
including point not belonging to the original set.
Currently, only an interpolator for generating natural cubic splines
and a polynomial
@@ -435,7 +435,7 @@ System.out println("f(" + interpolationX + ") = " +
interpolatedY);</source>
<p>
<a href="http://en.wikipedia.org/wiki/Hermite_interpolation";>Hermite
interpolation</a>
is an interpolation method that can use derivatives in addition to
function values at sample points. The <a
-
href="../apidocs/org/apache/commons/math4/analysis/interpolation/HermiteInterpolator.html">HermiteInterpolator</a>
+
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/interpolation/HermiteInterpolator.html">HermiteInterpolator</a>
class implements this method for vector-valued functions. The
sampling points can have any spacing (there are
no requirements for a regular grid) and some points may provide
derivatives while others don't provide them
(or provide derivatives to a smaller order). Points are added one at
a time, as shown in the following example:
@@ -454,13 +454,13 @@ System.out.println("derivative at x = 0.5: " +
interpolator.derivative(0.5)[0]);
// should print "interpolation polynomial: 1 + 2 x + 4 x^2 - 4 x^3 + x^4"
System.out.println("interpolation polynomial: " +
interpolator.getPolynomials()[0]);</source>
<p>
- A <a
href="../apidocs/org/apache/commons/math4/analysis/interpolation/BivariateGridInterpolator.html">
+ A <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/interpolation/BivariateGridInterpolator.html">
BivariateGridInterpolator</a> is used to find a bivariate real-valued
function <code>f</code> which for a given set of tuples
(<code>x<sub>i</sub></code>,<code>y<sub>j</sub></code>,<code>f<sub>ij</sub></code>)
yields <code>f(x<sub>i</sub>,y<sub>j</sub>)=f<sub>ij</sub></code> to
the best accuracy
possible. The result is provided as an object implementing the
- <a
href="../apidocs/org/apache/commons/math4/analysis/BivariateFunction.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/BivariateFunction.html">
BivariateFunction</a> interface. It can therefore be evaluated at
any point,
including a point not belonging to the original set.
The arrays <code>x<sub>i</sub></code> and <code>y<sub>j</sub></code>
must be
@@ -472,25 +472,25 @@ System.out.println("interpolation polynomial: " +
interpolator.getPolynomials()[
are computed from the function values sampled on a grid, as well as
the values of the
partial derivatives of the function at those grid points.
From two-dimensional data sampled on a grid, the
- <a
href="../apidocs/org/apache/commons/math4/analysis/interpolation/BicubicSplineInterpolator.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/interpolation/BicubicSplineInterpolator.html">
BicubicSplineInterpolator</a> computes a
- <a
href="../apidocs/org/apache/commons/math4/analysis/interpolation/BicubicSplineInterpolatingFunction.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/interpolation/BicubicSplineInterpolatingFunction.html">
bicubic interpolating function</a>.
Prior to computing an interpolating function, the
- <a
href="../apidocs/org/apache/commons/math4/analysis/interpolation/SmoothingPolynomialBicubicSplineInterpolator.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/interpolation/SmoothingPolynomialBicubicSplineInterpolator.html">
SmoothingPolynomialBicubicSplineInterpolator</a> class performs
smoothing of
the data by computing the polynomial that best fits each of the
one-dimensional
curves along each of the coordinate axes.
</p>
<p>
- A <a
href="../apidocs/org/apache/commons/math4/analysis/interpolation/TrivariateGridInterpolator.html">
+ A <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/interpolation/TrivariateGridInterpolator.html">
TrivariateGridInterpolator</a> is used to find a trivariate
real-valued
function <code>f</code> which for a given set of tuples
(<code>x<sub>i</sub></code>,<code>y<sub>j</sub></code>,<code>z<sub>k</sub></code>,
<code>f<sub>ijk</sub></code>)
yields
<code>f(x<sub>i</sub>,y<sub>j</sub>,z<sub>k</sub>)=f<sub>ijk</sub></code>
to the best accuracy possible. The result is provided as an object
implementing the
- <a
href="../apidocs/org/apache/commons/math4/analysis/TrivariateFunction.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/TrivariateFunction.html">
TrivariateFunction</a> interface. It can therefore be evaluated at
any point,
including a point not belonging to the original set.
The arrays <code>x<sub>i</sub></code>, <code>y<sub>j</sub></code> and
@@ -503,41 +503,41 @@ System.out.println("interpolation polynomial: " +
interpolator.getPolynomials()[
are computed from the function values sampled on a grid, as well as
the values of the
partial derivatives of the function at those grid points.
From three-dimensional data sampled on a grid, the
- <a
href="../apidocs/org/apache/commons/math4/analysis/interpolation/TricubicSplineInterpolator.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/interpolation/TricubicSplineInterpolator.html">
TricubicSplineInterpolator</a> computes a
- <a
href="../apidocs/org/apache/commons/math4/analysis/interpolation/TricubicSplineInterpolatingFunction.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/interpolation/TricubicSplineInterpolatingFunction.html">
tricubic interpolating function</a>.
</p>
</subsection>
<subsection name="4.5 Integration" href="integration">
<p>
- A <a
href="../apidocs/org/apache/commons/math4/analysis/integration/UnivariateIntegrator.html">
+ A <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/integration/UnivariateIntegrator.html">
UnivariateIntegrator</a> provides the means to numerically integrate
- <a
href="../apidocs/org/apache/commons/math4/analysis/UnivariateFunction.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/UnivariateFunction.html">
univariate real-valued functions</a>.
Commons-Math includes implementations of the following integration
algorithms: <ul>
- <li><a
href="../apidocs/org/apache/commons/math4/analysis/integration/RombergIntegrator.html">
+ <li><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/integration/RombergIntegrator.html">
Romberg's method</a></li>
- <li><a
href="../apidocs/org/apache/commons/math4/analysis/integration/SimpsonIntegrator.html">
+ <li><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/integration/SimpsonIntegrator.html">
Simpson's method</a></li>
- <li><a
href="../apidocs/org/apache/commons/math4/analysis/integration/TrapezoidIntegrator.html">
+ <li><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/integration/TrapezoidIntegrator.html">
trapezoid method</a></li>
- <li><a
href="../apidocs/org/apache/commons/math4/analysis/integration/LegendreGaussIntegrator.html">
+ <li><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/integration/LegendreGaussIntegrator.html">
Legendre-Gauss method</a></li>
</ul>
</p>
</subsection>
<subsection name="4.6 Polynomials" href="polynomials">
<p>
- The <a
href="../apidocs/org/apache/commons/math4/analysis/polynomials/package-summary.html">
+ The <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/polynomials/package-summary.html">
org.apache.commons.math4.analysis.polynomials</a> package provides
real
coefficients polynomials.
</p>
<p>
- The <a
href="../apidocs/org/apache/commons/math4/analysis/polynomials/PolynomialFunction.html">
+ The <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/polynomials/PolynomialFunction.html">
PolynomialFunction</a> class is the most general one, using
traditional
coefficients arrays. The
- <a
href="../apidocs/org/apache/commons/math4/analysis/polynomials/PolynomialsUtils.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/polynomials/PolynomialsUtils.html">
PolynomialsUtils</a> utility class provides static factory methods
to build
Chebyshev, Hermite, Jacobi, Laguerre and Legendre polynomials.
Coefficients are
computed using exact fractions so these factory methods can build
polynomials
@@ -546,21 +546,21 @@ System.out.println("interpolation polynomial: " +
interpolator.getPolynomials()[
</subsection>
<subsection name="4.7 Differentiation" href="differentiation">
<p>
- The <a
href="../apidocs/org/apache/commons/math4/analysis/differentiation/package-summary.html">
+ The <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/differentiation/package-summary.html">
org.apache.commons.math4.analysis.differentiation</a> package
provides a general-purpose
differentiation framework.
</p>
<p>
- The core class is <a
href="../apidocs/org/apache/commons/math4/analysis/differentiation/DerivativeStructure.html">
+ The core class is <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/differentiation/DerivativeStructure.html">
DerivativeStructure</a> which holds the value and the differentials
of a function. This class
handles some arbitrary number of free parameters and arbitrary
derivation order. It is used
both as the input and the output type for the <a
-
href="../apidocs/org/apache/commons/math4/analysis/differentiation/UnivariateDifferentiableFunction.html">
+
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/differentiation/UnivariateDifferentiableFunction.html">
UnivariateDifferentiableFunction</a> interface. Any differentiable
function should implement this
interface.
</p>
<p>
- The main idea behind the <a
href="../apidocs/org/apache/commons/math4/analysis/differentiation/DerivativeStructure.html">
+ The main idea behind the <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/differentiation/DerivativeStructure.html">
DerivativeStructure</a> class is that it can be used almost as a
number (i.e. it can be added,
multiplied, its square root can be extracted or its cosine
computed... However, in addition to
computed the value itself when doing these computations, the partial
derivatives are also computed
@@ -577,7 +577,7 @@ System.out.println("interpolation polynomial: " +
interpolator.getPolynomials()[
<p>
The workflow of computation of a derivatives of an expression
<code>y=f(x)</code> is the following
one. First we configure an input parameter <code>x</code> of type <a
-
href="../apidocs/org/apache/commons/math4/analysis/differentiation/DerivativeStructure.html">
+
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/differentiation/DerivativeStructure.html">
DerivativeStructure</a> so it will drive the function to compute all
derivatives up to order 3 for
example. Then we compute <code>y=f(x)</code> normally by passing
this parameter to the f function.At
the end, we extract from <code>y</code> the value and the
derivatives we want. As we have specified
@@ -667,28 +667,28 @@ System.out.println("d2g/dxdy = " +
g.getPartialDerivative(1, 1);
System.out.println("d2g/dy2 = " + g.getPartialDerivative(0, 2);</source>
<p>
There are several ways a user can create an implementation of the <a
-
href="../apidocs/org/apache/commons/math4/analysis/differentiation/UnivariateDifferentiableFunction.html">
+
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/differentiation/UnivariateDifferentiableFunction.html">
UnivariateDifferentiableFunction</a> interface. The first method is
to simply write it directly using
- the appropriate methods from <a
href="../apidocs/org/apache/commons/math4/analysis/differentiation/DerivativeStructure.html">
+ the appropriate methods from <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/differentiation/DerivativeStructure.html">
DerivativeStructure</a> to compute addition, subtraction, sine,
cosine... This is often quite
straigthforward and there is no need to remember the rules for
differentiation: the user code only
represent the function itself, the differentials will be computed
automatically under the hood. The
second method is to write a classical <a
-
href="../apidocs/org/apache/commons/math4/analysis/UnivariateFunction.html">UnivariateFunction</a>
and to
+
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/UnivariateFunction.html">UnivariateFunction</a>
and to
pass it to an existing implementation of the <a
-
href="../apidocs/org/apache/commons/math4/analysis/differentiation/UnivariateFunctionDifferentiator.html">
+
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/differentiation/UnivariateFunctionDifferentiator.html">
UnivariateFunctionDifferentiator</a> interface to retrieve a
differentiated version of the same function.
The first method is more suited to small functions for which user
already control all the underlying code.
The second method is more suited to either large functions that
would be cumbersome to write using the
- <a
href="../apidocs/org/apache/commons/math4/analysis/differentiation/DerivativeStructure.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/differentiation/DerivativeStructure.html">
DerivativeStructure</a> API, or functions for which user does not
have control to the full underlying code
(for example functions that call external libraries).
</p>
<p>
Apache Commons Math provides one implementation of the <a
-
href="../apidocs/org/apache/commons/math4/analysis/differentiation/UnivariateFunctionDifferentiator.html">
+
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/differentiation/UnivariateFunctionDifferentiator.html">
UnivariateFunctionDifferentiator</a> interface: <a
-
href="../apidocs/org/apache/commons/math4/analysis/differentiation/FiniteDifferencesDifferentiator.html">
+
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/differentiation/FiniteDifferencesDifferentiator.html">
FiniteDifferencesDifferentiator</a>. This class creates a wrapper
that will call the user-provided function
on a grid sample and will use finite differences to compute the
derivatives. It takes care of boundaries
if the variable is not defined on the whole real line. It is
possible to use more points than strictly
@@ -726,22 +726,22 @@ for (double x = -10; x < 10; x += 0.1) {
}</source>
<p>
Note that using <a
-
href="../apidocs/org/apache/commons/math4/analysis/differentiation/FiniteDifferencesDifferentiator.html">
+
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/differentiation/FiniteDifferencesDifferentiator.html">
FiniteDifferencesDifferentiator</a>a> in order to have a <a
-
href="../apidocs/org/apache/commons/math4/analysis/differentiation/UnivariateDifferentiableFunction.html">
- UnivariateDifferentiableFunction</a> that can be provided to a <a
href="../apidocs/org/apache/commons/math4/analysis/solvers/NewtonRaphsonSolver.html">Newton-Raphson's</a>
+
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/differentiation/UnivariateDifferentiableFunction.html">
+ UnivariateDifferentiableFunction</a> that can be provided to a <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/solvers/NewtonRaphsonSolver.html">Newton-Raphson's</a>
solver is a very bad idea. The reason is that finite differences are
not really accurate and needs lots
of additional calls to the basic underlying function. If user
initially have only the basic function
available and needs to find its roots, it is <em>much</em> more
accurate and <em>much</em> more
efficient to use a solver that only requires the function values and
not the derivatives. A good choice is
- to use <a
href="../apidocs/org/apache/commons/math4/analysis/solvers/BracketingNthOrderBrentSolver.html">bracketing
+ to use <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/solvers/BracketingNthOrderBrentSolver.html">bracketing
n<sup>th</sup> order Brent</a> method, which in fact converges
faster than <a
-
href="../apidocs/org/apache/commons/math4/analysis/solvers/NewtonRaphsonSolver.html">Newton-Raphson's</a>
and
+
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/solvers/NewtonRaphsonSolver.html">Newton-Raphson's</a>
and
can be configured to a highere order (typically 5) than
Newton-Raphson which is an order 2 method.
</p>
<p>
Another implementation of the <a
-
href="../apidocs/org/apache/commons/math4/analysis/differentiation/UnivariateFunctionDifferentiator.html">
+
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/differentiation/UnivariateFunctionDifferentiator.html">
UnivariateFunctionDifferentiator</a> interface is under development
in the related project
<a href="http://commons.apache.org/sandbox/nabla/";>Apache Commons
Nabla</a>. This implementation uses
automatic code analysis and generation at binary level. However, at
time of writing
diff --git a/src/site/xdoc/userguide/distribution.xml
b/src/site/xdoc/userguide/distribution.xml
index 2f33bae80..8cb9fad8b 100644
--- a/src/site/xdoc/userguide/distribution.xml
+++ b/src/site/xdoc/userguide/distribution.xml
@@ -33,12 +33,12 @@
Commons Math provides
<ul>
<li>
- an <a
href="../apidocs/org/apache/commons/math4/legacy/distribution/EnumeratedDistribution.html">
+ an <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/distribution/EnumeratedDistribution.html">
EnumeratedDistribution</a> class that represents discrete
distributions of a finite,
enumerated set of values.
</li>
<li>
- a <a
href="../apidocs/org/apache/commons/math4/legacy/distribution/MultiVariateNormalDistribution.html">
+ a <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/distribution/MultiVariateNormalDistribution.html">
MultivariateNormalDistribution</a> interface that represents
multivariate Gaussian
distributions.
</li>
diff --git a/src/site/xdoc/userguide/exceptions.xml
b/src/site/xdoc/userguide/exceptions.xml
index 22757df48..b3331f0ca 100644
--- a/src/site/xdoc/userguide/exceptions.xml
+++ b/src/site/xdoc/userguide/exceptions.xml
@@ -53,28 +53,28 @@
<li>
<a
href="http://docs.oracle.com/javase/6/docs/api/java/lang/IllegalArgumentException.html";>
<code>IllegalArgumentException</code></a>:
- A <a
href="../apidocs/org/apache/commons/math4/exception/MathIllegalArgumentException.html">
+ A <a
href="../commons-math-legacy-exception/apidocs/org/apache/commons/math4/legacy/exception/MathIllegalArgumentException.html">
<code>MathIllegalArgumentException</code></a> is thrown when
some input
parameter fails a precondition check.
</li>
<li>
<a
href="http://docs.oracle.com/javase/6/docs/api/java/lang/IllegalStateException.html";>
<code>IllegalStateException</code></a>:
- A <a
href="../apidocs/org/apache/commons/math4/exception/MathIllegalStateException.html">
+ A <a
href="../commons-math-legacy-exception/apidocs/org/apache/commons/math4/legacy/exception/MathIllegalStateException.html">
<code>MathIllegalStateException</code></a> is thrown when some
inconsistency
has been detected.
</li>
<li>
<a
href="http://docs.oracle.com/javase/6/docs/api/java/lang/MathArithmeticException.html";>
<code>ArithmeticException</code></a>:
- A <a
href="../apidocs/org/apache/commons/math4/exception/MathArithmeticException.html">
+ A <a
href="../commons-math-legacy-exception/apidocs/org/apache/commons/math4/legacy/exception/MathArithmeticException.html">
<code>MathArithmeticException</code></a> is thrown when
conditions such as
"division by zero" or "overflow" are encountered.
</li>
<li>
<a
href="http://docs.oracle.com/javase/6/docs/api/java/lang/MathUnsupportedOperationException.html";>
<code>UnsupportedOperationException</code></a>:
- A <a
href="../apidocs/org/apache/commons/math4/exception/MathUnsupportedOperationException.html">
+ A <a
href="../commons-math-legacy-exception/apidocs/org/apache/commons/math4/legacy/exception/MathUnsupportedOperationException.html">
<code>MathUnsupportedOperationException</code></a> indicates
that a feature
is missing or does not make sense in the given context.
</li>
@@ -101,11 +101,11 @@
<li>Exception "context"
<p>
Every exception generated by Commons Math implements the
- <a
href="../apidocs/org/apache/commons/math4/exception/util/ExceptionContextProvider.html">
+ <a
href="../commons-math-legacy-exception/apidocs/org/apache/commons/math4/legacy/exception/util/ExceptionContextProvider.html">
ExceptionContextProvider</a> interface. A call to the
- <a
href="../apidocs/org/apache/commons/math4/exception/util/ExceptionContextProvider.html#getContext()">
+ <a
href="../commons-math-legacy-exception/apidocs/org/apache/commons/math4/legacy/exception/util/ExceptionContextProvider.html#getContext()">
getContext</a> method will return the
- <a
href="../apidocs/org/apache/commons/math4/exception/util/ExceptionContext.html">
+ <a
href="../commons-math-legacy-exception/apidocs/org/apache/commons/math4/legacy/exception/util/ExceptionContext.html">
ExceptionContext</a> instance stored in the exception, which
the
user can further customize by adding messages and/or any object.
</p>
diff --git a/src/site/xdoc/userguide/filter.xml
b/src/site/xdoc/userguide/filter.xml
index 50b0733f3..419e98c26 100644
--- a/src/site/xdoc/userguide/filter.xml
+++ b/src/site/xdoc/userguide/filter.xml
@@ -30,12 +30,12 @@
</subsection>
<subsection name="17.2 Kalman Filter" href="kalman">
<p>
- <a
href="../apidocs/org/apache/commons/math4/filter/KalmanFilter.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/filter/KalmanFilter.html">
KalmanFilter</a> provides a discrete-time filter to estimate
a stochastic linear process.</p>
- <p>A Kalman filter is initialized with a <a
href="../apidocs/org/apache/commons/math4/filter/ProcessModel.html">
- ProcessModel</a> and a <a
href="../apidocs/org/apache/commons/math4/filter/MeasurementModel.html">
+ <p>A Kalman filter is initialized with a <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/filter/ProcessModel.html">
+ ProcessModel</a> and a <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/filter/MeasurementModel.html">
MeasurementModel</a>, which contain the corresponding transformation
and noise covariance matrices.
The parameter names used in the respective models correspond to the
following names commonly used
in the mathematical literature:
diff --git a/src/site/xdoc/userguide/fitting.xml
b/src/site/xdoc/userguide/fitting.xml
index 82eff1ea7..11c2aa176 100644
--- a/src/site/xdoc/userguide/fitting.xml
+++ b/src/site/xdoc/userguide/fitting.xml
@@ -46,15 +46,15 @@
appropriate class,
</li>
<li>
- call the <a
href="../apidocs/org/apache/commons/math4/fitting/AbstractCurveFitter">fit</a>
- with a <code>Collection</code> of <a
href="../apidocs/org/apache/commons/math4/fitting/WeightedObservedPoint.html">
+ call the <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/fitting/AbstractCurveFitter">fit</a>
+ with a <code>Collection</code> of <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/fitting/WeightedObservedPoint.html">
observed data points</a> as argument, which will return an
array with the parameters that
best fit the given data points.
</li>
</ul>
The list of observed data points to be passed to <code>fit</code>
can be built by incrementally
- adding instances to an instance of <a
href="../apidocs/org/apache/commons/math4/fitting/WeightedObservedPoints.html">WeightedObservedPoints</a>,
+ adding instances to an instance of <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/fitting/WeightedObservedPoints.html">WeightedObservedPoints</a>,
and then retrieve the list of <code>WeightedObservedPoint</code> by
calling the <code>toList</code>
method on that container.
A weight can be associated with each observed point; it allows to
take into account uncertainty
@@ -81,25 +81,25 @@
Fitting of specific functions are provided through the following
classes:
<ul>
<li>
- <a
href="../apidocs/org/apache/commons/math4/fitting/PolynomialCurveFitter.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/fitting/PolynomialCurveFitter.html">
PolynomialFitter</a> fits a
- <a
href="../apidocs/org/apache/commons/math4/analysis/polynomials/PolynomialFunction.Parametric.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/polynomials/PolynomialFunction.Parametric.html">
polynomial</a> function.
</li>
<li>
- <a
href="../apidocs/org/apache/commons/math4/fitting/HarmonicCurveFitter.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/fitting/HarmonicCurveFitter.html">
HarmonicFitter</a> fits a
- <a
href="../apidocs/org/apache/commons/math4/analysis/function/HarmonicOscillator.Parametric.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/function/HarmonicOscillator.Parametric.html">
harmonic</a> function.
- An instance of the inner class <a
href="../apidocs/org/apache/commons/math4/fitting/HarmonicCurveFitter.ParameterGuesser.html">
+ An instance of the inner class <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/fitting/HarmonicCurveFitter.ParameterGuesser.html">
ParameterGuesser</a> can be used to retrieve initial values
for the fitting procedure.
</li>
<li>
- <a
href="../apidocs/org/apache/commons/math4/fitting/GaussianCurveFitter.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/fitting/GaussianCurveFitter.html">
GaussianFitter</a> fits a
- <a
href="../apidocs/org/apache/commons/math4/analysis/function/Gaussian.Parametric.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/function/Gaussian.Parametric.html">
Gaussian</a> function.
- An instance of the inner class <a
href="../apidocs/org/apache/commons/math4/fitting/GaussianCurveFitter.ParameterGuesser.html">
+ An instance of the inner class <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/fitting/GaussianCurveFitter.ParameterGuesser.html">
ParameterGuesser</a> can be used to retrieve initial values
for the fitting procedure.
</li>
</ul>
@@ -129,11 +129,11 @@ final double[] coeff = fitter.fit(obs.toList());
<subsection name="13.3 General Case" href="general">
<p>
- The <a
href="../apidocs/org/apache/commons/math4/fitting/AbstractCurveFitter.html">
+ The <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/fitting/AbstractCurveFitter.html">
AbstractCurveFitter</a> class provides the basic functionality for
implementing other
curve fitting classes.
Users must provide their own implementation of the curve template as
a class that implements
- the <a
href="../apidocs/org/apache/commons/math4/analysis/ParametricUnivariateFunction.html">
+ the <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/ParametricUnivariateFunction.html">
ParametricUnivariateFunction</a> interface.
</p>
</subsection>
diff --git a/src/site/xdoc/userguide/genetics.xml
b/src/site/xdoc/userguide/genetics.xml
index bf4c17ce0..a8e723899 100644
--- a/src/site/xdoc/userguide/genetics.xml
+++ b/src/site/xdoc/userguide/genetics.xml
@@ -31,15 +31,15 @@
</subsection>
<subsection name="16.2 GA Framework">
<p>
- <a
href="../apidocs/org/apache/commons/math4/genetics/GeneticAlgorithm.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/genetics/GeneticAlgorithm.html">
GeneticAlgorithm</a> provides an execution framework for Genetic
Algorithms (GA).
- <a href="../apidocs/org/apache/commons/math4/genetics/Population.html">
- Populations,</a> consisting of <a
href="../apidocs/org/apache/commons/math4/genetics/Chromosome.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/genetics/Population.html">
+ Populations,</a> consisting of <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/genetics/Chromosome.html">
Chromosomes</a> are evolved by the <code>GeneticAlgorithm</code> until a
- <a
href="../apidocs/org/apache/commons/math4/genetics/StoppingCondition.html">
- StoppingCondition</a> is reached. Evolution is determined by <a
href="../apidocs/org/apache/commons/math4/genetics/SelectionPolicy.html">
- SelectionPolicy</a>, <a
href="../apidocs/org/apache/commons/math4/genetics/MutationPolicy.html">
- MutationPolicy</a> and <a
href="../apidocs/org/apache/commons/math4/genetics/Fitness.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/genetics/StoppingCondition.html">
+ StoppingCondition</a> is reached. Evolution is determined by <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/genetics/SelectionPolicy.html">
+ SelectionPolicy</a>, <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/genetics/MutationPolicy.html">
+ MutationPolicy</a> and <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/genetics/Fitness.html">
Fitness</a>.
</p>
<p>
@@ -62,10 +62,10 @@
<ul><li>Apply configured <code>SelectionPolicy</code> to select a
pair of parents
from <code>current</code></li>
<li>With probability =
- <a
href="../apidocs/org/apache/commons/math4/genetics/GeneticAlgorithm.html#getCrossoverRate()">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/genetics/GeneticAlgorithm.html#getCrossoverRate()">
getCrossoverRate()</a>, apply configured
<code>CrossoverPolicy</code> to parents</li>
<li>With probability =
- <a
href="../apidocs/org/apache/commons/math4/genetics/GeneticAlgorithm.html#getMutationRate()">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/genetics/GeneticAlgorithm.html#getMutationRate()">
getMutationRate()</a>,
apply configured <code>MutationPolicy</code> to each of the
offspring</li>
<li>Add offspring individually to nextGeneration,
@@ -104,27 +104,27 @@ Chromosome bestFinal =
finalPopulation.getFittestChromosome();
<table>
<tr><th>Parameter</th><th>value in example</th><th>meaning</th></tr>
<tr><td>crossoverPolicy</td>
- <td><a
href="../apidocs/org/apache/commons/math4/genetics/OnePointCrossover.html">OnePointCrossover</a></td>
+ <td><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/genetics/OnePointCrossover.html">OnePointCrossover</a></td>
<td>A random crossover point is selected and the first part from each
parent is copied to the corresponding
child, and the second parts are copied crosswise.</td></tr>
<tr><td>crossoverRate</td>
<td>1</td>
<td>Always apply crossover</td></tr>
<tr><td>mutationPolicy</td>
- <td><a
href="../apidocs/org/apache/commons/math4/genetics/RandomKeyMutation.html">RandomKeyMutation</a></td>
+ <td><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/genetics/RandomKeyMutation.html">RandomKeyMutation</a></td>
<td>Changes a randomly chosen element of the array representation to a
random value uniformly distributed in [0,1].</td></tr>
<tr><td>mutationRate</td>
<td>.1</td>
<td>Apply mutation with probability 0.1 - that is, 10% of the
time.</td></tr>
<tr><td>selectionPolicy</td>
- <td><a
href="../apidocs/org/apache/commons/math4/genetics/TournamentSelection.html">TournamentSelection</a></td>
+ <td><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/genetics/TournamentSelection.html">TournamentSelection</a></td>
<td>Each of the two selected chromosomes is selected based on an n-ary
tournament -- this is done by drawing
n random chromosomes without replacement from the population, and then
selecting the fittest chromosome among them.</td></tr>
</table><br/>
The algorithm starts with an <code>initial</code> population of
<code>Chromosomes.</code> and executes until
- the specified <a
href="../apidocs/org/apache/commons/math4/genetics/StoppingCondition.html">StoppingCondition</a>
+ the specified <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/genetics/StoppingCondition.html">StoppingCondition</a>
is reached. In the example above, a
- <a
href="../apidocs/org/apache/commons/math4/genetics/FixedGenerationCount.html">FixedGenerationCount</a>
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/genetics/FixedGenerationCount.html">FixedGenerationCount</a>
stopping condition is used, which means the algorithm proceeds through
a fixed number of generations.
</p>
</subsection>
diff --git a/src/site/xdoc/userguide/leastsquares.xml
b/src/site/xdoc/userguide/leastsquares.xml
index 6153de3e6..d6cd9a99d 100644
--- a/src/site/xdoc/userguide/leastsquares.xml
+++ b/src/site/xdoc/userguide/leastsquares.xml
@@ -41,9 +41,9 @@
</p>
<p>
Two engines devoted to least-squares problems are available. The
first one is
- based on the <a
href="../apidocs/org/apache/commons/math4/fitting/leastsquares/GaussNewtonOptimizer.html">
+ based on the <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/fitting/leastsquares/GaussNewtonOptimizer.html">
Gauss-Newton</a> method. The second one is the <a
-
href="../apidocs/org/apache/commons/math4/fitting/leastsquares/LevenbergMarquardtOptimizer.html">
+
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/fitting/leastsquares/LevenbergMarquardtOptimizer.html">
Levenberg-Marquardt</a> method.
</p>
</subsection>
@@ -67,12 +67,12 @@
</p>
<p>
The elements of the list above can be provided as an implementation
of the
- <a
href="../apidocs/org/apache/commons/math4/fitting/leastsquares/LeastSquaresProblem.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/fitting/leastsquares/LeastSquaresProblem.html">
LeastSquaresProblem</a> interface. However, this is cumbersome to do
directly, so some helper
classes are available. The first helper is a mutable builder:
- <a
href="../apidocs/org/apache/commons/math4/fitting/leastsquares/LeastSquaresBuilder.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/fitting/leastsquares/LeastSquaresBuilder.html">
LeastSquaresBuilder</a>. The second helper is an utility factory:
- <a
href="../apidocs/org/apache/commons/math4/fitting/leastsquares/LeastSquaresFactory.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/fitting/leastsquares/LeastSquaresFactory.html">
LeastSquaresFactory</a>.
</p>
<p>
@@ -109,13 +109,13 @@
be available. There are two ways to provide this:
<ul>
<li>provide one
- <a
href="../apidocs/org/apache/commons/math4/analysis/MultivariateVectorFunction.html">MultivariateVectorFunction</a>
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/MultivariateVectorFunction.html">MultivariateVectorFunction</a>
instance for computing the components values and one
- <a
href="../apidocs/org/apache/commons/math4/analysis/MultivariateMatrixFunction.html">MultivariateMatrixFunction</a>
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/MultivariateMatrixFunction.html">MultivariateMatrixFunction</a>
instance for computing the components derivatives (i.e. the
Jacobian matrix) with
respect to the parameters,</li>
<li>or provide one
- <a
href="../apidocs/org/apache/commons/math4/fitting/leastsquares/MultivariateJacobianFunction.html">MultivariateJacobianFunction</a>
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/fitting/leastsquares/MultivariateJacobianFunction.html">MultivariateJacobianFunction</a>
instance for computing both the components values and their
derivatives simultaneously.</li>
</ul>
The first alternative is best suited for models which are not
computationally intensive
@@ -125,16 +125,16 @@
</p>
<p>
The <code>point</code> parameter of the <code>value</code> methods
in the
- <a
href="../apidocs/org/apache/commons/math4/analysis/MultivariateVectorFunction.html">MultivariateVectorFunction</a>,
- <a
href="../apidocs/org/apache/commons/math4/analysis/MultivariateMatrixFunction.html">MultivariateMatrixFunction</a>,
- or <a
href="../apidocs/org/apache/commons/math4/fitting/leastsquares/MultivariateJacobianFunction.html">MultivariateJacobianFunction</a>
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/MultivariateVectorFunction.html">MultivariateVectorFunction</a>,
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/MultivariateMatrixFunction.html">MultivariateMatrixFunction</a>,
+ or <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/fitting/leastsquares/MultivariateJacobianFunction.html">MultivariateJacobianFunction</a>
interfaces will contain the parameters p<sub>k</sub>. The values
will be the model components
model<sub>i</sub> and the derivatives will be the derivatives of the
model components
with respect to the parameters dmodel<sub>i</sub>/dp<sub>k</sub>.
</p>
<p>
There are no requirements on how to compute value and derivatives.
The
- <a
href="../apidocs/org/apache/commons/math4/analysis/differentiation/DerivativeStructure.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/differentiation/DerivativeStructure.html">
DerivativeStructure</a> class may be useful to compute analytically
derivatives in
difficult cases, but this class is not mandated by the API which
only expects the derivatives
as a Jacobian matrix containing primitive double entries.
@@ -147,7 +147,7 @@
if the model functions are themselves separated, i.e. it can be used
only with the first
alternative above. Setting up the <code>lazyEvaluation</code> flag
to <code>true</code> in the builder
or factory and setting up the model function as one
- <a
href="../apidocs/org/apache/commons/math4/fitting/leastsquares/MultivariateJacobianFunction.html">MultivariateJacobianFunction</a>
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/fitting/leastsquares/MultivariateJacobianFunction.html">MultivariateJacobianFunction</a>
instance at the same time will trigger an illegal state exception
telling that the model function
misses required functionality.
</p>
@@ -164,7 +164,7 @@
</p>
<p>
Both ways are achieved by setting up a
- <a
href="../apidocs/org/apache/commons/math4/fitting/leastsquares/ParameterValidator.html">ParameterValidator</a>
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/fitting/leastsquares/ParameterValidator.html">ParameterValidator</a>
instance. The input of the value and jacobian model functions will
always be the output of
the parameter validator if one exists.
</p>
@@ -217,26 +217,26 @@
</p>
<p>
Convergence checking is delegated to a dedicated interface from the
<code>optim</code>
- package: <a
href="../apidocs/org/apache/commons/math4/optim/ConvergenceChecker.html">
+ package: <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/optim/ConvergenceChecker.html">
ConvergenceChecker</a>, parameterized with either the specific
- <a
href="../apidocs/org/apache/commons/math4/fitting/leastsquares/LeastSquaresProblem.Evaluation.html">Evaluation</a>
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/fitting/leastsquares/LeastSquaresProblem.Evaluation.html">Evaluation</a>
class used for least squares problems or the general
- <a
href="../apidocs/org/apache/commons/math4/optim/PointVectorValuePair.html">PointVectorValuePair</a>.
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/optim/PointVectorValuePair.html">PointVectorValuePair</a>.
Each time convergence is checked, both the previous
and the current evaluations of the least squares problem are
provided, so the checker can
compare them and decide whereas convergence has been reached or not.
The predefined convergence
checker implementations that can be useful for least squares fitting
are:
<ul>
- <li><a
href="../apidocs/org/apache/commons/math4/fitting/leastsquares/EvaluationRmsChecker.html">EvaluationRmsChecker</a>,
+ <li><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/fitting/leastsquares/EvaluationRmsChecker.html">EvaluationRmsChecker</a>,
which uses only the normalized cost (square-root of the sum of
squared of the residuals,
divided by the number of measurements),</li>
- <li><a
href="../apidocs/org/apache/commons/math4/optim/SimpleVectorValueChecker.html">SimpleVectorValueChecker</a>,
+ <li><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/optim/SimpleVectorValueChecker.html">SimpleVectorValueChecker</a>,
which uses the model components themselves (<em>not</em> the
residuals),</li>
- <li><a
href="../apidocs/org/apache/commons/math4/optim/SimplePointChecker.html">SimplePointChecker<PointVectorValuePair></a>,
+ <li><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/optim/SimplePointChecker.html">SimplePointChecker<PointVectorValuePair></a>,
which uses the parameters.</li>
</ul>
Of course, users can also provide their own implementation of the
- <a
href="../apidocs/org/apache/commons/math4/optim/ConvergenceChecker.html">ConvergenceChecker</a>
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/optim/ConvergenceChecker.html">ConvergenceChecker</a>
interface.
</p>
</subsection>
@@ -246,9 +246,9 @@
Once the least squares problem has been created, using either the
builder or the factory,
it is passed to an optimization engine for solving. Two engines
devoted to least-squares
problems are available. The first one is
- based on the <a
href="../apidocs/org/apache/commons/math4/fitting/leastsquares/GaussNewtonOptimizer.html">
+ based on the <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/fitting/leastsquares/GaussNewtonOptimizer.html">
Gauss-Newton</a> method. The second one is the <a
-
href="../apidocs/org/apache/commons/math4/fitting/leastsquares/LevenbergMarquardtOptimizer.html">
+
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/fitting/leastsquares/LevenbergMarquardtOptimizer.html">
Levenberg-Marquardt</a> method. For both increased readability and
in order to leverage
possible future changes in the configuration, it is recommended to
use the fluent-style API to
build and configure the optimizers. This means creating a first
temporary version of the optimizer
@@ -286,12 +286,12 @@
<p>
The <a
-
href="../apidocs/org/apache/commons/math4/fitting/leastsquares/LeastSquaresOptimizer.Optimum.html">
+
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/fitting/leastsquares/LeastSquaresOptimizer.Optimum.html">
LeastSquaresOptimizer.Optimum</a> class is a specialized
- <a
href="../apidocs/org/apache/commons/math4/fitting/leastsquares/LeastSquaresProblem.Evaluation.html">Evaluation</a>
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/fitting/leastsquares/LeastSquaresProblem.Evaluation.html">Evaluation</a>
with additional methods te retrieve the number of evaluations and
number of iterations performed.
The most important methods are inherited from the
- <a
href="../apidocs/org/apache/commons/math4/fitting/leastsquares/LeastSquaresProblem.Evaluation.html">Evaluation</a>
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/fitting/leastsquares/LeastSquaresProblem.Evaluation.html">Evaluation</a>
class and correspond to the point (i.e. the parameters), cost,
Jacobian, RMS, covariance ...
</p>
</subsection>
diff --git a/src/site/xdoc/userguide/linear.xml
b/src/site/xdoc/userguide/linear.xml
index 8d05eb767..6ba4e342a 100644
--- a/src/site/xdoc/userguide/linear.xml
+++ b/src/site/xdoc/userguide/linear.xml
@@ -35,7 +35,7 @@
</subsection>
<subsection name="3.2 Real matrices" href="real_matrices">
<p>
- The <a
href="../apidocs/org/apache/commons/math4/linear/RealMatrix.html">
+ The <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/linear/RealMatrix.html">
RealMatrix</a> interface represents a matrix with real numbers as
entries. The following basic matrix operations are supported:
<ul>
@@ -72,18 +72,18 @@ RealMatrix pInverse = new
LUDecomposition(p).getSolver().getInverse();
</p>
<p>
The three main implementations of the interface are <a
-
href="../apidocs/org/apache/commons/math4/linear/Array2DRowRealMatrix.html">
+
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/linear/Array2DRowRealMatrix.html">
Array2DRowRealMatrix</a> and <a
- href="../apidocs/org/apache/commons/math4/linear/BlockRealMatrix.html">
+
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/linear/BlockRealMatrix.html">
BlockRealMatrix</a> for dense matrices (the second one being more
suited to
dimensions above 50 or 100) and <a
-
href="../apidocs/org/apache/commons/math4/linear/SparseRealMatrix.html">
+
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/linear/SparseRealMatrix.html">
SparseRealMatrix</a> for sparse matrices.
</p>
</subsection>
<subsection name="3.3 Real vectors" href="real_vectors">
<p>
- The <a
href="../apidocs/org/apache/commons/math4/linear/RealVector.html">
+ The <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/linear/RealVector.html">
RealVector</a> interface represents a vector with real numbers as
entries. The following basic matrix operations are supported:
<ul>
@@ -96,7 +96,7 @@ RealMatrix pInverse = new
LUDecomposition(p).getSolver().getInverse();
</ul>
</p>
<p>
- The <a
href="../apidocs/org/apache/commons/math4/linear/RealVectorFormat.html">
+ The <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/linear/RealVectorFormat.html">
RealVectorFormat</a> class handles input/output of vectors in a
customizable
textual format.
</p>
@@ -104,7 +104,7 @@ RealMatrix pInverse = new
LUDecomposition(p).getSolver().getInverse();
<subsection name="3.4 Solving linear systems" href="solve">
<p>
The <code>solve()</code> methods of the <a
-
href="../apidocs/org/apache/commons/math4/linear/DecompositionSolver.html">DecompositionSolver</a>
+
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/linear/DecompositionSolver.html">DecompositionSolver</a>
interface support solving linear systems of equations of the form
AX=B, either
in linear sense or in least square sense. A <code>RealMatrix</code>
instance is
used to represent the coefficient matrix of the system. Solving the
system is a
@@ -157,11 +157,11 @@ RealVector solution = solver.solve(constants);
<table border="1" align="center">
<tr BGCOLOR="#CCCCFF"><td colspan="3"><font size="+1">Decomposition
algorithms</font></td></tr>
<tr BGCOLOR="#EEEEFF"><font size="+1"><td>Name</td><td>coefficients
matrix</td><td>problem type</td></font></tr>
- <tr><td><a
href="../apidocs/org/apache/commons/math4/linear/LUDecomposition.html">LU</a></td><td>square</td><td>exact
solution only</td></tr>
- <tr><td><a
href="../apidocs/org/apache/commons/math4/linear/CholeskyDecomposition.html">Cholesky</a></td><td>symmetric
positive definite</td><td>exact solution only</td></tr>
- <tr><td><a
href="../apidocs/org/apache/commons/math4/linear/QRDecomposition.html">QR</a></td><td>any</td><td>least
squares solution</td></tr>
- <tr><td><a
href="../apidocs/org/apache/commons/math4/linear/EigenDecomposition.html">eigen
decomposition</a></td><td>square</td><td>exact solution only</td></tr>
- <tr><td><a
href="../apidocs/org/apache/commons/math4/linear/SingularValueDecomposition.html">SVD</a></td><td>any</td><td>least
squares solution</td></tr>
+ <tr><td><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/linear/LUDecomposition.html">LU</a></td><td>square</td><td>exact
solution only</td></tr>
+ <tr><td><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/linear/CholeskyDecomposition.html">Cholesky</a></td><td>symmetric
positive definite</td><td>exact solution only</td></tr>
+ <tr><td><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/linear/QRDecomposition.html">QR</a></td><td>any</td><td>least
squares solution</td></tr>
+ <tr><td><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/linear/EigenDecomposition.html">eigen
decomposition</a></td><td>square</td><td>exact solution only</td></tr>
+ <tr><td><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/linear/SingularValueDecomposition.html">SVD</a></td><td>any</td><td>least
squares solution</td></tr>
</table>
</p>
<p>
@@ -196,13 +196,13 @@ RealVector solution = solver.solve(constants);
<subsection name="3.6 Non-real fields (complex, fractions ...)"
href="field">
<p>
In addition to the real field, matrices and vectors using non-real <a
- href="../apidocs/org/apache/commons/math4/FieldElement.html">field
elements</a> can be used.
+
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/FieldElement.html">field
elements</a> can be used.
The fields already supported by the library are:
<ul>
- <li><a
href="../apidocs/org/apache/commons/math4/complex/Complex.html">Complex</a></li>
- <li><a
href="../apidocs/org/apache/commons/math4/fraction/Fraction.html">Fraction</a></li>
- <li><a
href="../apidocs/org/apache/commons/math4/fraction/BigFraction.html">BigFraction</a></li>
- <li><a
href="../apidocs/org/apache/commons/math4/util/BigReal.html">BigReal</a></li>
+ <li><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/complex/Complex.html">Complex</a></li>
+ <li><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/fraction/Fraction.html">Fraction</a></li>
+ <li><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/fraction/BigFraction.html">BigFraction</a></li>
+ <li><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/util/BigReal.html">BigReal</a></li>
</ul>
</p>
</subsection>
diff --git a/src/site/xdoc/userguide/ml.xml b/src/site/xdoc/userguide/ml.xml
index ed063bf85..705d777ed 100644
--- a/src/site/xdoc/userguide/ml.xml
+++ b/src/site/xdoc/userguide/ml.xml
@@ -33,30 +33,30 @@
</subsection>
<subsection name="16.2 Clustering algorithms and distance measures"
href="clustering">
<p>
- The <a
href="../apidocs/org/apache/commons/math4/ml/clustering/Clusterer.html">
+ The <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/ml/clustering/Clusterer.html">
Clusterer</a> class represents a clustering algorithm.
The following algorithms are available:
<ul>
- <li><a
href="../apidocs/org/apache/commons/math4/ml/clustering/KMeansPlusPlusClusterer.html">KMeans++</a>:
+ <li><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/ml/clustering/KMeansPlusPlusClusterer.html">KMeans++</a>:
It is based on the well-known kMeans algorithm, but uses a different
method for
choosing the initial values (or "seeds") and thus avoids cases where
KMeans sometimes
results in poor clusterings. KMeans/KMeans++ clustering aims to
partition n observations
into k clusters in such that each point belongs to the cluster with
the nearest center.
</li>
- <li><a
href="../apidocs/org/apache/commons/math4/ml/clustering/FuzzyKMeansClusterer.html">Fuzzy-KMeans</a>:
+ <li><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/ml/clustering/FuzzyKMeansClusterer.html">Fuzzy-KMeans</a>:
A variation of the classical K-Means algorithm, with the major
difference that a single
data point is not uniquely assigned to a single cluster. Instead,
each point i has a set
of weights u<sub>ij</sub> which indicate the degree of membership to
the cluster j. The fuzzy
variant does not require initial values for the cluster centers and
is thus more robust, although
slower than the original kMeans algorithm.
</li>
- <li><a
href="../apidocs/org/apache/commons/math4/ml/clustering/DBSCANClusterer.html">DBSCAN</a>:
+ <li><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/ml/clustering/DBSCANClusterer.html">DBSCAN</a>:
Density-based spatial clustering of applications with noise (DBSCAN)
finds a number of
clusters starting from the estimated density distribution of
corresponding nodes. The
main advantages over KMeans/KMeans++ are that DBSCAN does not
require the specification
of an initial number of clusters and can find arbitrarily shaped
clusters.
</li>
- <li><a
href="../apidocs/org/apache/commons/math4/ml/clustering/MultiKMeansPlusPlusClusterer.html">Multi-KMeans++</a>:
+ <li><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/ml/clustering/MultiKMeansPlusPlusClusterer.html">Multi-KMeans++</a>:
Multi-KMeans++ is a meta algorithm that basically performs n runs
using KMeans++ and then
chooses the best clustering (i.e., the one with the lowest distance
variance over all clusters)
from those runs.
@@ -74,11 +74,11 @@
between two points (either data points or cluster centers).
The following distance measures are available:
<ul>
- <li><a
href="../apidocs/org/apache/commons/math4/ml/distance/CanberraDistance.html">Canberra
distance</a></li>
- <li><a
href="../apidocs/org/apache/commons/math4/ml/distance/ChebyshevDistance.html">ChebyshevDistance
distance</a></li>
- <li><a
href="../apidocs/org/apache/commons/math4/ml/distance/EuclideanDistance.html">EuclideanDistance
distance</a></li>
- <li><a
href="../apidocs/org/apache/commons/math4/ml/distance/ManhattanDistance.html">ManhattanDistance
distance</a></li>
- <li><a
href="../apidocs/org/apache/commons/math4/ml/distance/EarthMoversDistance.html">Earth
Mover's distance</a></li>
+ <li><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/ml/distance/CanberraDistance.html">Canberra
distance</a></li>
+ <li><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/ml/distance/ChebyshevDistance.html">ChebyshevDistance
distance</a></li>
+ <li><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/ml/distance/EuclideanDistance.html">EuclideanDistance
distance</a></li>
+ <li><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/ml/distance/ManhattanDistance.html">ManhattanDistance
distance</a></li>
+ <li><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/ml/distance/EarthMoversDistance.html">Earth
Mover's distance</a></li>
</ul>
</p>
</subsection>
@@ -90,7 +90,7 @@
10 different clusters based on their euclidean distance.
</p>
<p>
- The cluster algorithms expect a list of <a
href="../apidocs/org/apache/commons/math4/ml/cluster/Clusterable.html">Clusterable</a>
+ The cluster algorithms expect a list of <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/ml/cluster/Clusterable.html">Clusterable</a>
as input. Typically, we don't want to pollute our domain objects with
interfaces from helper APIs.
Hence, we first create a wrapper object:
<source>
diff --git a/src/site/xdoc/userguide/ode.xml b/src/site/xdoc/userguide/ode.xml
index 6a8cd536e..49d4be63f 100644
--- a/src/site/xdoc/userguide/ode.xml
+++ b/src/site/xdoc/userguide/ode.xml
@@ -38,7 +38,7 @@
All integrators provide dense output. This means that besides
computing the state vector
at discrete times, they also provide a cheap means 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/math4/ode/sampling/StepInterpolator.html">StepInterpolator</a>
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/ode/sampling/StepInterpolator.html">StepInterpolator</a>
abstract class, which are made available to the user at the end of
each step.
</p>
<p>
@@ -83,11 +83,11 @@
</p>
<p>
The user should describe his problem in his own classes which should
implement the
- <a
href="../apidocs/org/apache/commons/math4/ode/FirstOrderDifferentialEquations.html">FirstOrderDifferentialEquations</a>
- interface (or <a
href="../apidocs/org/apache/commons/math4/ode/FirstOrderFieldDifferentialEquations.html">FirstOrderFieldDifferentialEquations</a>
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/ode/FirstOrderDifferentialEquations.html">FirstOrderDifferentialEquations</a>
+ interface (or <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/ode/FirstOrderFieldDifferentialEquations.html">FirstOrderFieldDifferentialEquations</a>
interface). Then they should pass it to the integrator they prefer
among all the classes that implement
- the <a
href="../apidocs/org/apache/commons/math4/ode/FirstOrderIntegrator.html">FirstOrderIntegrator</a>
- interface (or the <a
href="../apidocs/org/apache/commons/math4/ode/FirstOrderFieldIntegrator.html">FirstOrderFieldIntegrator</a>
+ the <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/ode/FirstOrderIntegrator.html">FirstOrderIntegrator</a>
+ interface (or the <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/ode/FirstOrderFieldIntegrator.html">FirstOrderFieldIntegrator</a>
interface). The following example shows how to implement the simple
two-dimensional problem using double primitives:
<ul>
<li>y'<sub>0</sub>(t) = ω × (c<sub>1</sub> -
y<sub>1</sub>(t))</li>
@@ -137,10 +137,10 @@ 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/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
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/ode/sampling/StepHandler.html">StepHandler</a>
interface or a
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/ode/sampling/StepNormalizer.html">StepNormalizer</a>
object wrapping
a user-specified object implementing the
- <a
href="../apidocs/org/apache/commons/math4/ode/sampling/FixedStepHandler.html">FixedStepHandler</a>
interface
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/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
@@ -161,7 +161,7 @@ StepHandler stepHandler = new StepHandler() {
integrator.addStepHandler(stepHandler);
</source>
<p>
- <a
href="../apidocs/org/apache/commons/math4/ode/ContinuousOutputModel.html">ContinuousOutputModel</a>
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/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
@@ -170,10 +170,10 @@ 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/math4/ode/sampling/StepHandler.html">StepHandler</a>
+ Other default implementations of the <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/ode/sampling/StepHandler.html">StepHandler</a>
interface are available for general needs
- (<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
+ (<a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/ode/sampling/DummyStepHandler.html">DummyStepHandler</a>,
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/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.
@@ -182,12 +182,12 @@ 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
of the main state with respect to a specified accuracy (these
integrators extend the
- <a
href="../apidocs/org/apache/commons/math4/ode/AdaptiveStepsizeIntegrator.html">AdaptiveStepsizeIntegrator</a>
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/ode/AdaptiveStepsizeIntegrator.html">AdaptiveStepsizeIntegrator</a>
abstract class). The secondary equations are explicitly ignored for
step size control, in order to get reproducible
results regardless of the secondary equations being integrated or
not. The step handler which is called after each
- successful step shows up the variable stepsize. The <a
href="../apidocs/org/apache/commons/math4/ode/sampling/StepNormalizer.html">StepNormalizer</a>
+ successful step shows up the variable stepsize. The <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/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/math4/ode/sampling/FixedStepHandler.html">FixedStepHandler</a>
+ implementing the <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/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 they prefer to retain full
control over the integration or if the
automatic guess is wrong.
@@ -202,7 +202,7 @@ integrator.addStepHandler(stepHandler);
</p>
<p>
Discrete events detection is based on switching functions. The user
provides
- a simple <a
href="../apidocs/org/apache/commons/math4/ode/events/EventHandler.html">g(t,
y)</a>
+ a simple <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/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.
@@ -282,24 +282,24 @@ 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/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>
+ <tr><td><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/ode/nonstiff/EulerIntegrator.html">Euler</a></td><td>1</td></tr>
+ <tr><td><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/ode/nonstiff/MidpointIntegrator.html">Midpoint</a></td><td>2</td></tr>
+ <tr><td><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/ode/nonstiff/ClassicalRungeKuttaIntegrator.html">Classical
Runge-Kutta</a></td><td>4</td></tr>
+ <tr><td><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/ode/nonstiff/GillIntegrator.html">Gill</a></td><td>4</td></tr>
+ <tr><td><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/ode/nonstiff/ThreeEighthesIntegrator.html">3/8</a></td><td>4</td></tr>
+ <tr><td><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/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/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>
+ <tr><td><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/ode/nonstiff/HighamHall54Integrator.html">Higham
and Hall</a></td><td>5</td><td>4</td></tr>
+ <tr><td><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/ode/nonstiff/DormandPrince54Integrator.html">Dormand-Prince
5(4)</a></td><td>5</td><td>4</td></tr>
+ <tr><td><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/ode/nonstiff/DormandPrince853Integrator.html">Dormand-Prince
8(5,3)</a></td><td>8</td><td>5 and 3</td></tr>
+ <tr><td><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/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="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/ode/nonstiff/AdamsBashforthIntegrator.html">Adams-Bashforth</a></td><td>variable</td><td>variable</td></tr>
+ <tr><td><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/ode/nonstiff/AdamsMoultonIntegrator.html">Adams-Moulton</a></td><td>variable</td><td>variable</td></tr>
</table>
</p>
</subsection>
@@ -311,7 +311,7 @@ public int eventOccurred(double t, double[] y, boolean
increasing) {
appended to the main state before the integration starts. Then the
integration will propagate the compound
state composed of both the main state and its partial derivatives.
At the end of the integration, the Jacobian
matrices are extracted from the integrated secondary state. The <a
-
href="../apidocs/org/apache/commons/math4/ode/JacobianMatrices.html">JacobianMatrices</a>
class can do most of
+
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/ode/JacobianMatrices.html">JacobianMatrices</a>
class can do most of
this as long as the local derivatives are provided to it. It will
set up the variational equations, register
them as secondary equations into the ODE, and it will set up the
initial values and retrieve the intermediate
and final values as Jacobian matrices.
@@ -321,7 +321,7 @@ public int eventOccurred(double t, double[] y, boolean
increasing) {
elements array. The first 6 elements will be the original state, the
next 36 elements will represent the 6x6
Jacobian matrix of the final state with respect to the initial
state, and the remaining 18 elements will
represent the 6x3 Jacobian matrix of the final state with respect to
the 3 parameters. The <a
-
href="../apidocs/org/apache/commons/math4/ode/JacobianMatrices.html">JacobianMatrices</a>
class does the mapping
+
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/ode/JacobianMatrices.html">JacobianMatrices</a>
class does the mapping
between the 60 elements compound state and the Jacobian matrices and
sets up the correcsponding secondary equations.
</p>
<p>
@@ -333,22 +333,22 @@ public int eventOccurred(double t, double[] y, boolean
increasing) {
<p>
What remains of user responsibility is to provide the local
Jacobians df(t, y, p)/dy and df(t, y, p)/dp<sub>k</sub>
corresponding the the main ODE y'=f(t, y, p). The main ODE is as
usual provided by the user as a class implementing
- the <a
href="../apidocs/org/apache/commons/math4/ode/FirstOrderDifferentialEquations.html">FirstOrderDifferentialEquations</a>
+ the <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/ode/FirstOrderDifferentialEquations.html">FirstOrderDifferentialEquations</a>
interface or a sub-interface.
</p>
<p>
If the ODE is simple enough that the user can implement df(t, y,
p)/dy directly, then instead of providing an
implementation of the <a
-
href="../apidocs/org/apache/commons/math4/ode/FirstOrderDifferentialEquations.html">FirstOrderDifferentialEquations</a>
+
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/ode/FirstOrderDifferentialEquations.html">FirstOrderDifferentialEquations</a>
interface only, the user should rather provide an implementation of
the <a
-
href="../apidocs/org/apache/commons/math4/ode/MainStateJacobianProvider.html">MainStateJacobianProvider</a>
interface,
+
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/ode/MainStateJacobianProvider.html">MainStateJacobianProvider</a>
interface,
which extends the previous interface by adding a method to compute
df(t, y, p)/dy. The user class is used as a
- constructor parameter of the <a
href="../apidocs/org/apache/commons/math4/ode/JacobianMatrices.html">JacobianMatrices</a>
+ constructor parameter of the <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/ode/JacobianMatrices.html">JacobianMatrices</a>
class. If the ODE is too complex or the user simply does not bother
implementing df(t, y, p)/dy directly, then
the ODE can still be implemented using the simple <a
-
href="../apidocs/org/apache/commons/math4/ode/FirstOrderDifferentialEquations.html">FirstOrderDifferentialEquations</a>
+
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/ode/FirstOrderDifferentialEquations.html">FirstOrderDifferentialEquations</a>
interface and given as such to another constructor of the <a
-
href="../apidocs/org/apache/commons/math4/ode/JacobianMatrices.html">JacobianMatrices</a>
class, but in this case an array
+
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/ode/JacobianMatrices.html">JacobianMatrices</a>
class, but in this case an array
hy must also be provided that will contain the step size to use form
each component of the main state vector y, and
the Jacobian f(t, y, p)/dy will be computed internally using finite
differences. This will of course trigger more evaluations
of the ODE at each step and will suffer from finite differences
errors, but it is much simpler to implement from a user
@@ -356,10 +356,10 @@ public int eventOccurred(double t, double[] y, boolean
increasing) {
</p>
<p>
The parameters are identified by a name (a simple user-defined
string), which are also specified at <a
-
href="../apidocs/org/apache/commons/math4/ode/JacobianMatrices.html">JacobianMatrices</a>
class construction. If the ODE
+
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/ode/JacobianMatrices.html">JacobianMatrices</a>
class construction. If the ODE
is simple enough that the user can implement df(t, y,
p)/dp<sub>k</sub> directly for some of the parameters p<sub>k</sub>,
then they can provide one or more classes implementing the <a
-
href="../apidocs/org/apache/commons/math4/ode/ParameterJacobianProvider.html">ParameterJacobianProvider</a>
interface by
+
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/ode/ParameterJacobianProvider.html">ParameterJacobianProvider</a>
interface by
calling the JacobianMatrices.addParameterJacobianProvide method. The
parameters are handled one at a time, but all the calls to
ParameterJacobianProvider.computeParameterJacobian will be grouped
in one sequence after the call to
MainStateJacobianProvider.computeMainStateJacobian
This feature can be used when all the derivatives share a lot of
costly computation. In this case, the user
diff --git a/src/site/xdoc/userguide/optimization.xml
b/src/site/xdoc/userguide/optimization.xml
index 39d6110cf..64077e31b 100644
--- a/src/site/xdoc/userguide/optimization.xml
+++ b/src/site/xdoc/userguide/optimization.xml
@@ -26,7 +26,7 @@
<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/math4/optim/package-summary.html">API
+ Please refer to the new <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/optim/package-summary.html">API
description</a>.
</p>
<p>Least squares optimizers are not in this package anymore, they have
been moved
@@ -61,7 +61,7 @@
</p>
<p>
The type of goal, i.e. minimization or maximization, is defined by the
enumerated
- <a
href="../apidocs/org/apache/commons/math4/optimization/GoalType.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/optimization/GoalType.html">
GoalType</a> which has only two values: <code>MAXIMIZE</code> and
<code>MINIMIZE</code>.
</p>
<p>
@@ -70,21 +70,21 @@
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/math4/optimization/univariate/UnivariateOptimizer.html">
+ <li><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/optimization/univariate/UnivariateOptimizer.html">
UnivariateOptimizer</a> for <a
-
href="../apidocs/org/apache/commons/math4/analysis/UnivariateFunction.html">
+
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/UnivariateFunction.html">
univariate real functions</a></li>
- <li><a
href="../apidocs/org/apache/commons/math4/optimization/MultivariateOptimizer.html">
+ <li><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/optimization/MultivariateOptimizer.html">
MultivariateOptimizer</a> for <a
-
href="../apidocs/org/apache/commons/math4/analysis/MultivariateFunction.html">
+
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/MultivariateFunction.html">
multivariate real functions</a></li>
- <li><a
href="../apidocs/org/apache/commons/math4/optimization/DifferentiableMultivariateOptimizer.html">
+ <li><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/optimization/DifferentiableMultivariateOptimizer.html">
DifferentiableMultivariateOptimizer</a> for <a
-
href="../apidocs/org/apache/commons/math4/analysis/DifferentiableMultivariateFunction.html">
+
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/DifferentiableMultivariateFunction.html">
differentiable multivariate real functions</a></li>
- <li><a
href="../apidocs/org/apache/commons/math4/optimization/DifferentiableMultivariateVectorOptimizer.html">
+ <li><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/optimization/DifferentiableMultivariateVectorOptimizer.html">
DifferentiableMultivariateVectorOptimizer</a> for <a
-
href="../apidocs/org/apache/commons/math4/analysis/DifferentiableMultivariateVectorFunction.html">
+
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/DifferentiableMultivariateVectorFunction.html">
differentiable multivariate vectorial functions</a></li>
</ul>
</p>
@@ -92,14 +92,14 @@
<p>
Despite there are only four types of supported optimizers, it is
possible to optimize
a transform a <a
-
href="../apidocs/org/apache/commons/math4/analysis/MultivariateVectorFunction.html">
+
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/MultivariateVectorFunction.html">
non-differentiable multivariate vectorial function</a> by converting
it to a <a
-
href="../apidocs/org/apache/commons/math4/analysis/MultivariateFunction.html">
+
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/MultivariateFunction.html">
non-differentiable multivariate real function</a> thanks to the <a
-
href="../apidocs/org/apache/commons/math4/optimization/LeastSquaresConverter.html">
+
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/optimization/LeastSquaresConverter.html">
LeastSquaresConverter</a> helper class. The transformed function can
be optimized using
any implementation of the <a
-
href="../apidocs/org/apache/commons/math4/optimization/MultivariateOptimizer.html">
+
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/optimization/MultivariateOptimizer.html">
MultivariateOptimizer</a> interface.
</p>
@@ -113,7 +113,7 @@
</subsection>
<subsection name="12.2 Univariate Functions" href="univariate">
<p>
- A <a
href="../apidocs/org/apache/commons/math4/optimization/univariate/UnivariateOptimizer.html">
+ A <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/optimization/univariate/UnivariateOptimizer.html">
UnivariateOptimizer</a> is used to find the minimal values of a
univariate real-valued
function <code>f</code>.
</p>
@@ -164,16 +164,16 @@
The <code>direct</code> package provides four solvers:
<ul>
<li>the classical <a
-
href="../apidocs/org/apache/commons/math4/optimization/direct/NelderMeadSimplex.html">
+
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/optimization/direct/NelderMeadSimplex.html">
Nelder-Mead</a> method,</li>
<li>Virginia Torczon's <a
-
href="../apidocs/org/apache/commons/math4/optimization/direct/MultiDirectionalSimplex.html">
+
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/optimization/direct/MultiDirectionalSimplex.html">
multi-directional</a> method,</li>
<li>Nikolaus Hansen's <a
-
href="../apidocs/org/apache/commons/math4/optimization/direct/CMAESOptimizer.html">
+
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/optimization/direct/CMAESOptimizer.html">
</a>Covariance Matrix Adaptation Evolution Strategy
(CMA-ES),</li>
<li>Mike Powell's <a
-
href="../apidocs/org/apache/commons/math4/optimization/direct/BOBYQAOptimizer.html">
+
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/optimization/direct/BOBYQAOptimizer.html">
BOBYQA</a> method.
</li>
</ul>
@@ -181,9 +181,9 @@
<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/math4/optimization/direct/MultivariateFunctionMappingAdapter.html">
+
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/optimization/direct/MultivariateFunctionMappingAdapter.html">
MultivariateFunctionMappingAdapter</a> and <a
-
href="../apidocs/org/apache/commons/math4/optimization/direct/MultivariateFunctionPenaltyAdapter.html">
+
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/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
@@ -237,15 +237,15 @@
<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/math4/optimization/general/GaussNewtonOptimizer.html">
+
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/optimization/general/GaussNewtonOptimizer.html">
Gauss-Newton</a> method. The second one is the <a
-
href="../apidocs/org/apache/commons/math4/optimization/general/LevenbergMarquardtOptimizer.html">
+
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/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/math4/analysis/DifferentiableMultivariateVectorFunction.html">
+
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/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
@@ -311,7 +311,7 @@
</table>
<p>
-First we need to implement the interface <a
href="../apidocs/org/apache/commons/math4/analysis/DifferentiableMultivariateVectorFunction.html">DifferentiableMultivariateVectorFunction</a>.
+First we need to implement the interface <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/analysis/DifferentiableMultivariateVectorFunction.html">DifferentiableMultivariateVectorFunction</a>.
This requires the implementation of the method signatures:
</p>
@@ -571,17 +571,17 @@ C: 16.324008168386605
</dd></dl>
<p>
In addition to least squares solving, the <a
-
href="../apidocs/org/apache/commons/math4/optimization/general/NonLinearConjugateGradientOptimizer.html">
+
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/optimization/general/NonLinearConjugateGradientOptimizer.html">
NonLinearConjugateGradientOptimizer</a> class provides a non-linear
conjugate gradient algorithm
to optimize <a
-
href="../apidocs/org/apache/commons/math4/analysis/DifferentiableMultivariateFunction.html">
+
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/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/math4/optimization/direct/PowellOptimizer.html">
+ The <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/optimization/direct/PowellOptimizer.html">
PowellOptimizer</a> provides an optimization method for
non-differentiable functions.
</p>
</subsection>
diff --git a/src/site/xdoc/userguide/overview.xml
b/src/site/xdoc/userguide/overview.xml
index b1ea29278..d20705391 100644
--- a/src/site/xdoc/userguide/overview.xml
+++ b/src/site/xdoc/userguide/overview.xml
@@ -105,9 +105,9 @@
<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/math4/exception/MathIllegalArgumentException.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/exception/MathIllegalArgumentException.html">
MathIllegalArgumentException</a> or
- <a
href="../apidocs/org/apache/commons/math4/exception/MathIllegalStateException.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/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.
@@ -119,7 +119,7 @@
<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/math4/exception/NullArgumentException.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/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>.
diff --git a/src/site/xdoc/userguide/random.xml
b/src/site/xdoc/userguide/random.xml
index 5c3558e29..a95e5cbda 100644
--- a/src/site/xdoc/userguide/random.xml
+++ b/src/site/xdoc/userguide/random.xml
@@ -30,7 +30,7 @@
<subsection name="2.1 Overview"
href="overview">
<p>
- Utilities in package <a
href="../apidocs/org/apache/commons/math4/legacy/random/package-summary.html">
+ Utilities in package <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/random/package-summary.html">
o.a.c.m.legacy.random</a> often uses an underlying "source of
randomness": A pseudo-random
number generator (PRNG) that produces sequences of numbers that are
uniformly distributed
within their range.
@@ -48,7 +48,7 @@
</p>
<p>
When the components are correlated however, generating them is more
difficult.
- The <a
href="../apidocs/org/apache/commons/math4/legacy/random/CorrelatedVectorFactory.html">
+ The <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/random/CorrelatedVectorFactory.html">
CorrelatedVectorFactory</a> class provides this service.
In this case, a complete covariance matrix must be provided (instead of a
simple standard deviations vector) gathering both the variance and the
@@ -114,9 +114,9 @@ RealMatrix covariance = MatrixUtils.createRealMatrix(cov);
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/math4/legacy/random/SobolSequenceGenerator.html">
+ <li><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/random/SobolSequenceGenerator.html">
Sobol sequence</a> (pre-configured up to dimension 1000)</li>
- <li><a
href="../apidocs/org/apache/commons/math4/legacy/random/HaltonSequenceGenerator.html">
+ <li><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/random/HaltonSequenceGenerator.html">
Halton sequence</a> (pre-configured up to dimension 40)</li>
</ul>
diff --git a/src/site/xdoc/userguide/stat.xml b/src/site/xdoc/userguide/stat.xml
index 2824c0366..61ced6c56 100644
--- a/src/site/xdoc/userguide/stat.xml
+++ b/src/site/xdoc/userguide/stat.xml
@@ -61,12 +61,12 @@
</p>
<p>
The top level interface is
- <a
href="../apidocs/org/apache/commons/math4/stat/descriptive/UnivariateStatistic.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/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/math4/stat/descriptive/StorelessUnivariateStatistic.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/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
@@ -75,9 +75,9 @@
</p>
<p>
Abstract implementations of the top level interfaces are provided in
- <a
href="../apidocs/org/apache/commons/math4/stat/descriptive/AbstractUnivariateStatistic.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/stat/descriptive/AbstractUnivariateStatistic.html">
AbstractUnivariateStatistic</a> and
- <a
href="../apidocs/org/apache/commons/math4/stat/descriptive/AbstractStorelessUnivariateStatistic.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/stat/descriptive/AbstractStorelessUnivariateStatistic.html">
AbstractStorelessUnivariateStatistic</a> respectively.
</p>
<p>
@@ -87,9 +87,9 @@
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/math4/stat/descriptive/DescriptiveStatistics.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/stat/descriptive/DescriptiveStatistics.html">
DescriptiveStatistics</a> and
- <a
href="../apidocs/org/apache/commons/math4/stat/descriptive/SummaryStatistics.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/stat/descriptive/SummaryStatistics.html">
SummaryStatistics.</a>
</p>
<p>
@@ -107,18 +107,18 @@
<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/math4/stat/descriptive/DescriptiveStatistics.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/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/math4/stat/descriptive/SummaryStatistics.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/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/math4/stat/descriptive/AggregateSummaryStatistics.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/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.
@@ -132,19 +132,19 @@
<p>
Neither <code>DescriptiveStatistics</code> nor
<code>SummaryStatistics</code>
is thread-safe.
- <a
href="../apidocs/org/apache/commons/math4/stat/descriptive/SynchronizedDescriptiveStatistics.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/stat/descriptive/SynchronizedDescriptiveStatistics.html">
SynchronizedDescriptiveStatistics</a> and
- <a
href="../apidocs/org/apache/commons/math4/stat/descriptive/SynchronizedSummaryStatistics.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/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/math4/stat/descriptive/SynchronizedMultiVariateSummaryStatistics.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/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/math4/stat/StatUtils.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/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/math4/stat/descriptive/AggregateSummaryStatistics.html#createContributingStatistics()">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/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/math4/stat/descriptive/AggregateSummaryStatistics.html#aggregate(java.util.Collection)">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/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/math4/stat/Frequency.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/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/math4/stat/regression/SimpleRegression.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/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/math4/stat/regression/SimpleRegression.html#SimpleRegression(boolean)">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/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/math4/stat/regression/OLSMultipleLinearRegression.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/stat/regression/OLSMultipleLinearRegression.html">
OLSMultipleLinearRegression</a> and
- <a
href="../apidocs/org/apache/commons/math4/stat/regression/GLSMultipleLinearRegression.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/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/math4/stat/regression/OLSMultipleLinearRegression.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/stat/regression/OLSMultipleLinearRegression.html">
OLSMultipleLinearRegression</a> provides Ordinary Least Squares
Regression, and
- <a
href="../apidocs/org/apache/commons/math4/stat/regression/GLSMultipleLinearRegression.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/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/math4/stat/regression/AbstractMultipleLinearRegression.html#newSampleData(double[],
int, int)">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/stat/regression/AbstractMultipleLinearRegression.html#newSampleData(double[],
int, int)">
AbstractMultipleLinearRegression#newSampleData(double[],int,int)</a>,
- <a
href="../apidocs/org/apache/commons/math4/stat/regression/OLSMultipleLinearRegression.html#newSampleData(double[],
double[][])">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/stat/regression/OLSMultipleLinearRegression.html#newSampleData(double[],
double[][])">
OLSMultipleLinearRegression#newSampleData(double[], double[][])</a>
and
- <a
href="../apidocs/org/apache/commons/math4/stat/regression/GLSMultipleLinearRegression.html#newSampleData(double[],
double[][], double[][])">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/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/math4/stat/ranking/package-summary.html">
+ The <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/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">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/stat/ranking/RankingAlgorithm.html">
RankingAlgorithm</a> defines the interface for ranking.
- <a
href="../apidocs/org/apache/commons/math4/stat/ranking/NaturalRanking.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/stat/ranking/NaturalRanking.html">
NaturalRanking</a> provides an implementation that has two
configuration options.
<ul>
- <li><a
href="../apidocs/org/apache/commons/math4/stat/ranking/TiesStrategy.html">
+ <li><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/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/math4/stat/ranking/NaNStrategy.html">
+ <li><a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/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/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>
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/stat/ranking/NaturalRanking.html">
+ NaturalRanking</a> for more examples and <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/stat/ranking/TiesStrategy.html">
+ TiesStrategy</a> and <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/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/math4/stat/correlation/package-summary.html">
+ The <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/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/math4/stat/correlation/Covariance.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/stat/correlation/Covariance.html">
Covariance</a> computes covariances,
- <a
href="../apidocs/org/apache/commons/math4/stat/correlation/PearsonsCorrelation.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/stat/correlation/PearsonsCorrelation.html">
PearsonsCorrelation</a> provides Pearson's Product-Moment
correlation coefficients,
- <a
href="../apidocs/org/apache/commons/math4/stat/correlation/SpearmansCorrelation.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/stat/correlation/SpearmansCorrelation.html">
SpearmansCorrelation</a> computes Spearman's rank correlation and
- <a
href="../apidocs/org/apache/commons/math4/stat/correlation/KendallsCorrelation.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/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/math4/stat/correlation/PearsonsCorrelation.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/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/math4/stat/correlation/SpearmansCorrelation.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/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/math4/stat/ranking/NaturalRanking.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/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/math4/stat/correlation/KendallsCorrelation.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/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>
@@ -818,7 +818,7 @@ new KendallsCorrelation().correlation(x, y)
</subsection>
<subsection name="1.8 Statistical tests">
<p>
- The <a href="../apidocs/org/apache/commons/math4/stat/inference/">
+ The <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/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>,
@@ -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/math4/stat/inference/TTest.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/stat/inference/TTest.html">
TTest</a>,
- <a
href="../apidocs/org/apache/commons/math4/stat/inference/ChiSquareTest.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/stat/inference/ChiSquareTest.html">
ChiSquareTest</a>,
- <a
href="../apidocs/org/apache/commons/math4/stat/inference/GTest.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/stat/inference/GTest.html">
GTest</a>,
- <a
href="../apidocs/org/apache/commons/math4/stat/inference/OneWayAnova.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/stat/inference/OneWayAnova.html">
OneWayAnova</a>,
- <a
href="../apidocs/org/apache/commons/math4/stat/inference/MannWhitneyUTest.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/stat/inference/MannWhitneyUTest.html">
MannWhitneyUTest</a>,
- <a
href="../apidocs/org/apache/commons/math4/stat/inference/WilcoxonSignedRankTest.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/stat/inference/WilcoxonSignedRankTest.html">
WilcoxonSignedRankTest</a>,
- <a
href="../apidocs/org/apache/commons/math4/stat/inference/BinomialTest.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/stat/inference/BinomialTest.html">
BinomialTest</a> and
- <a
href="../apidocs/org/apache/commons/math4/stat/inference/KolmogorovSmirnovTest.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/stat/inference/KolmogorovSmirnovTest.html">
KolmogorovSmirnovTest</a>.
- The <a
href="../apidocs/org/apache/commons/math4/stat/inference/TestUtils.html">
+ The <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/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
@@ -936,7 +936,7 @@ 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/math4/stat/descriptive/StatisticalSummary.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/stat/descriptive/StatisticalSummary.html">
StatisticalSummary</a> to a fixed value:
<source>
double[] observed ={1d, 2d, 3d};
diff --git a/src/site/xdoc/userguide/utilities.xml
b/src/site/xdoc/userguide/utilities.xml
index f72ac0270..6b90e8a7b 100644
--- a/src/site/xdoc/userguide/utilities.xml
+++ b/src/site/xdoc/userguide/utilities.xml
@@ -29,7 +29,7 @@
<subsection name="6.1 Overview" href="overview">
<p>
- The <a
href="../apidocs/org/apache/commons/math4/util/package-summary.html">
+ The <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/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.
@@ -42,7 +42,7 @@
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/math4/util/DoubleArray.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/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
@@ -50,7 +50,7 @@
in the list.
</p>
<p>
- The <a
href="../apidocs/org/apache/commons/math4/util/ResizableDoubleArray.html">
+ The <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/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
@@ -64,7 +64,7 @@
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/math4/util/ResizableDoubleArray.html">
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/util/ResizableDoubleArray.html">
ResizableDoubleArray</a>
for details.
</p>
@@ -72,7 +72,7 @@
<subsection name="6.3 int/double hash map" href="int_double_hash_map">
<p>
- The <a
href="../apidocs/org/apache/commons/math4/util/OpenIntToDoubleHashMap.html">
+ The <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/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
@@ -83,7 +83,7 @@
<subsection name="6.4 Continued Fractions" href="continued_fractions">
<p>
- The <a
href="../apidocs/org/apache/commons/math4/util/ContinuedFraction.html">
+ The <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/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
@@ -147,7 +147,7 @@
<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/math4/util/ArithmeticUtils.html">ArithmeticUtils</a>
+ <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/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,
@@ -233,7 +233,7 @@
</subsection>
<subsection name="6.7 Miscellaneous" href="miscellaneous">
- The <a
href="../apidocs/org/apache/commons/math4/util/MultidimensionalCounter.html">
+ The <a
href="../commons-math-docs/apidocs/org/apache/commons/math4/legacy/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.
