Update userguide.

Some links are still broken (due to the refactoring).
apache · Apr 5, 2024 · ffcdf39 · ffcdf39
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diff --git a/src/site/xdoc/userguide/analysis.xml b/src/site/xdoc/userguide/analysis.xml
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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>