Fix some javadoc issues.
Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/53ec46ba Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/53ec46ba Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/53ec46ba Branch: refs/heads/master Commit: 53ec46ba272e23c0c96ada42f26f4e70e96f3115 Parents: cdf22ce Author: Ray DeCampo <[email protected]> Authored: Sun May 7 12:35:54 2017 -0400 Committer: Ray DeCampo <[email protected]> Committed: Sun May 7 12:35:54 2017 -0400 ---------------------------------------------------------------------- .../interpolation/SplineInterpolator.java | 2 +- .../commons/math4/complex/Quaternion.java | 2 +- .../commons/math4/complex/RootsOfUnity.java | 2 +- .../java/org/apache/commons/math4/dfp/Dfp.java | 8 +- .../apache/commons/math4/dfp/package-info.java | 4 +- .../distribution/EmpiricalDistribution.java | 24 +-- .../EnumeratedIntegerDistribution.java | 2 +- .../math4/distribution/GammaDistribution.java | 1 - .../math4/distribution/ParetoDistribution.java | 1 - .../math4/distribution/PascalDistribution.java | 10 +- .../math4/distribution/ZipfDistribution.java | 1 - ...ateNormalMixtureExpectationMaximization.java | 2 +- .../math4/fitting/AbstractCurveFitter.java | 4 +- .../math4/fitting/GaussianCurveFitter.java | 2 +- .../math4/fitting/HarmonicCurveFitter.java | 2 +- .../math4/fitting/PolynomialCurveFitter.java | 2 +- .../leastsquares/AbstractEvaluation.java | 2 +- .../leastsquares/GaussNewtonOptimizer.java | 10 +- .../leastsquares/LeastSquaresAdapter.java | 2 +- .../leastsquares/LeastSquaresBuilder.java | 2 +- .../leastsquares/LeastSquaresProblem.java | 2 +- .../LevenbergMarquardtOptimizer.java | 6 +- .../fitting/leastsquares/package-info.java | 4 +- .../commons/math4/fraction/BigFraction.java | 2 - .../apache/commons/math4/fraction/Fraction.java | 2 - .../math4/genetics/GeneticAlgorithm.java | 1 - .../euclidean/threed/FieldVector3D.java | 2 +- .../geometry/euclidean/threed/Vector3D.java | 2 +- .../math4/linear/AbstractFieldMatrix.java | 2 +- .../math4/linear/Array2DRowFieldMatrix.java | 4 +- .../commons/math4/linear/BlockFieldMatrix.java | 5 +- .../commons/math4/linear/BlockRealMatrix.java | 1 - .../commons/math4/linear/ConjugateGradient.java | 7 +- .../commons/math4/linear/DiagonalMatrix.java | 4 +- .../commons/math4/linear/FieldMatrix.java | 3 +- .../commons/math4/linear/MatrixUtils.java | 2 - .../PreconditionedIterativeLinearSolver.java | 2 +- .../commons/math4/linear/RRQRDecomposition.java | 2 +- .../math4/linear/RealLinearOperator.java | 2 +- .../apache/commons/math4/linear/RealMatrix.java | 2 +- .../apache/commons/math4/linear/RealVector.java | 4 +- .../RectangularCholeskyDecomposition.java | 2 +- .../commons/math4/linear/SparseFieldMatrix.java | 2 +- .../org/apache/commons/math4/linear/SymmLQ.java | 8 +- .../ml/clustering/FuzzyKMeansClusterer.java | 4 +- .../commons/math4/ml/neuralnet/Neuron.java | 4 +- .../math4/ml/neuralnet/SquareNeighbourhood.java | 4 +- .../math4/ml/neuralnet/oned/NeuronString.java | 4 +- .../ml/neuralnet/sofm/KohonenUpdateAction.java | 6 +- .../sofm/util/ExponentialDecayFunction.java | 2 +- .../sofm/util/QuasiSigmoidDecayFunction.java | 2 +- .../ml/neuralnet/twod/NeuronSquareMesh2D.java | 6 +- .../twod/util/SmoothedDataHistogram.java | 4 +- .../commons/math4/ode/JacobianMatrices.java | 1 - .../math4/ode/MultistepFieldIntegrator.java | 10 +- .../commons/math4/ode/MultistepIntegrator.java | 10 +- .../commons/math4/ode/events/EventHandler.java | 2 +- .../math4/ode/events/FieldEventHandler.java | 2 +- .../nonstiff/AdamsBashforthFieldIntegrator.java | 29 ++- .../ode/nonstiff/AdamsBashforthIntegrator.java | 29 ++- .../ode/nonstiff/AdamsFieldIntegrator.java | 12 +- .../math4/ode/nonstiff/AdamsIntegrator.java | 12 +- .../nonstiff/AdamsMoultonFieldIntegrator.java | 29 ++- .../ode/nonstiff/AdamsMoultonIntegrator.java | 29 ++- .../AdamsNordsieckFieldTransformer.java | 43 ++-- .../ode/nonstiff/AdamsNordsieckTransformer.java | 43 ++-- .../AdaptiveStepsizeFieldIntegrator.java | 6 +- .../nonstiff/AdaptiveStepsizeIntegrator.java | 6 +- .../ClassicalRungeKuttaFieldIntegrator.java | 1 - ...lassicalRungeKuttaFieldStepInterpolator.java | 1 - .../nonstiff/ClassicalRungeKuttaIntegrator.java | 1 - .../ClassicalRungeKuttaStepInterpolator.java | 1 - .../DormandPrince54FieldIntegrator.java | 2 +- .../ode/nonstiff/DormandPrince54Integrator.java | 2 +- .../EmbeddedRungeKuttaFieldIntegrator.java | 1 - .../nonstiff/EmbeddedRungeKuttaIntegrator.java | 1 - .../nonstiff/EulerFieldStepInterpolator.java | 1 - .../ode/nonstiff/EulerStepInterpolator.java | 1 - .../math4/ode/nonstiff/GillFieldIntegrator.java | 2 +- .../ode/nonstiff/GillFieldStepInterpolator.java | 1 - .../math4/ode/nonstiff/GillIntegrator.java | 2 +- .../ode/nonstiff/GillStepInterpolator.java | 1 - .../nonstiff/GraggBulirschStoerIntegrator.java | 17 +- .../ode/nonstiff/LutherFieldIntegrator.java | 2 +- .../math4/ode/nonstiff/LutherIntegrator.java | 2 +- .../ode/nonstiff/MidpointFieldIntegrator.java | 1 - .../nonstiff/MidpointFieldStepInterpolator.java | 1 - .../math4/ode/nonstiff/MidpointIntegrator.java | 1 - .../ode/nonstiff/MidpointStepInterpolator.java | 1 - .../ode/nonstiff/RungeKuttaFieldIntegrator.java | 1 - .../ode/nonstiff/RungeKuttaIntegrator.java | 1 - .../nonstiff/ThreeEighthesFieldIntegrator.java | 1 - .../ThreeEighthesFieldStepInterpolator.java | 1 - .../ode/nonstiff/ThreeEighthesIntegrator.java | 1 - .../nonstiff/ThreeEighthesStepInterpolator.java | 1 - .../apache/commons/math4/ode/package-info.java | 15 +- .../math4/ode/sampling/FieldStepNormalizer.java | 10 +- .../math4/ode/sampling/StepNormalizer.java | 10 +- .../BaseMultiStartMultivariateOptimizer.java | 6 +- .../commons/math4/optim/ConvergenceChecker.java | 4 +- .../commons/math4/optim/InitialGuess.java | 2 +- .../commons/math4/optim/SimpleBounds.java | 2 +- .../commons/math4/optim/SimplePointChecker.java | 2 +- .../commons/math4/optim/SimpleValueChecker.java | 2 +- .../math4/optim/SimpleVectorValueChecker.java | 2 +- .../math4/optim/linear/LinearConstraint.java | 21 +- .../optim/linear/LinearObjectiveFunction.java | 5 +- .../nonlinear/scalar/LeastSquaresConverter.java | 18 +- .../MultivariateFunctionPenaltyAdapter.java | 6 +- .../NonLinearConjugateGradientOptimizer.java | 4 +- .../scalar/noderiv/AbstractSimplex.java | 4 +- .../scalar/noderiv/BOBYQAOptimizer.java | 10 +- .../scalar/noderiv/CMAESOptimizer.java | 6 +- .../scalar/noderiv/PowellOptimizer.java | 10 +- .../scalar/noderiv/SimplexOptimizer.java | 4 +- .../commons/math4/optim/package-info.java | 2 +- .../math4/optim/univariate/BrentOptimizer.java | 2 +- .../MultiStartUnivariateOptimizer.java | 4 +- .../math4/optim/univariate/SearchInterval.java | 2 +- .../SimpleUnivariateValueChecker.java | 2 +- .../apache/commons/math4/random/RngAdaptor.java | 2 +- .../apache/commons/math4/special/BesselJ.java | 7 +- .../org/apache/commons/math4/special/Erf.java | 10 +- .../apache/commons/math4/stat/Frequency.java | 2 +- .../apache/commons/math4/stat/StatUtils.java | 6 - .../stat/correlation/KendallsCorrelation.java | 6 +- .../stat/correlation/PearsonsCorrelation.java | 8 +- .../stat/descriptive/DescriptiveStatistics.java | 2 +- .../MultivariateSummaryStatistics.java | 14 +- .../stat/descriptive/SummaryStatistics.java | 16 +- .../stat/descriptive/moment/FirstMoment.java | 3 +- .../stat/descriptive/moment/GeometricMean.java | 4 +- .../math4/stat/descriptive/moment/Mean.java | 4 +- .../stat/descriptive/moment/SecondMoment.java | 2 +- .../stat/descriptive/moment/SemiVariance.java | 4 +- .../math4/stat/descriptive/moment/Variance.java | 24 +-- .../math4/stat/descriptive/package-info.java | 26 +-- .../math4/stat/descriptive/rank/Max.java | 6 +- .../math4/stat/descriptive/rank/Min.java | 6 +- .../descriptive/rank/PSquarePercentile.java | 2 +- .../math4/stat/descriptive/rank/Percentile.java | 19 +- .../math4/stat/descriptive/summary/Product.java | 4 +- .../math4/stat/descriptive/summary/Sum.java | 8 +- .../stat/descriptive/summary/SumOfLogs.java | 2 +- .../math4/stat/inference/BinomialTest.java | 2 +- .../math4/stat/inference/ChiSquareTest.java | 20 +- .../commons/math4/stat/inference/GTest.java | 26 +-- .../stat/inference/InferenceTestUtils.java | 198 ++++++++++++++++++- .../stat/inference/KolmogorovSmirnovTest.java | 40 ++-- .../math4/stat/inference/MannWhitneyUTest.java | 4 +- .../math4/stat/inference/OneWayAnova.java | 16 +- .../commons/math4/stat/inference/TTest.java | 75 ++++--- .../stat/inference/WilcoxonSignedRankTest.java | 8 +- .../interval/BinomialConfidenceInterval.java | 1 - .../math4/stat/interval/ConfidenceInterval.java | 1 - .../math4/stat/interval/IntervalUtils.java | 1 - .../math4/stat/ranking/NaturalRanking.java | 4 +- .../AbstractMultipleLinearRegression.java | 4 +- .../regression/MillerUpdatingRegression.java | 4 +- .../regression/OLSMultipleLinearRegression.java | 6 +- .../stat/regression/RegressionResults.java | 8 +- .../math4/stat/regression/SimpleRegression.java | 20 +- .../math4/transform/FastCosineTransformer.java | 2 +- .../transform/FastHadamardTransformer.java | 18 +- .../math4/transform/FastSineTransformer.java | 2 +- .../apache/commons/math4/util/Combinations.java | 4 +- .../commons/math4/util/CombinatoricsUtils.java | 9 +- .../commons/math4/util/ContinuedFraction.java | 2 - .../org/apache/commons/math4/util/FastMath.java | 28 +-- .../commons/math4/util/IntegerSequence.java | 14 +- .../apache/commons/math4/util/MathArrays.java | 42 ++-- .../apache/commons/math4/util/MathUtils.java | 6 +- .../math4/util/MultidimensionalCounter.java | 2 +- .../org/apache/commons/math4/util/Pair.java | 2 +- .../math4/util/ResizableDoubleArray.java | 2 +- ...stractLeastSquaresOptimizerAbstractTest.java | 2 +- .../leastsquares/EvaluationTestValidation.java | 14 +- ...NonLinearConjugateGradientOptimizerTest.java | 2 +- .../util/FastMathStrictComparisonTest.java | 6 +- .../userguide/sofm/ChineseRingsClassifier.java | 2 +- 180 files changed, 778 insertions(+), 667 deletions(-) ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/analysis/interpolation/SplineInterpolator.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/analysis/interpolation/SplineInterpolator.java b/src/main/java/org/apache/commons/math4/analysis/interpolation/SplineInterpolator.java index 77dc7b1..9515dde 100644 --- a/src/main/java/org/apache/commons/math4/analysis/interpolation/SplineInterpolator.java +++ b/src/main/java/org/apache/commons/math4/analysis/interpolation/SplineInterpolator.java @@ -42,7 +42,7 @@ import org.apache.commons.math4.util.MathArrays; * corresponding y value.</li> * <li>Adjacent polynomials are equal through two derivatives at the knot points (i.e., adjacent polynomials * "match up" at the knot points, as do their first and second derivatives).</li> - * </ol></p> + * </ol> * <p> * The cubic spline interpolation algorithm implemented is as described in R.L. Burden, J.D. Faires, * <u>Numerical Analysis</u>, 4th Ed., 1989, PWS-Kent, ISBN 0-53491-585-X, pp 126-131. http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/complex/Quaternion.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/complex/Quaternion.java b/src/main/java/org/apache/commons/math4/complex/Quaternion.java index 0394d18..f5f22cc 100644 --- a/src/main/java/org/apache/commons/math4/complex/Quaternion.java +++ b/src/main/java/org/apache/commons/math4/complex/Quaternion.java @@ -29,7 +29,7 @@ import org.apache.commons.numbers.core.Precision; /** * This class implements <a href="http://mathworld.wolfram.com/Quaternion.html";> * quaternions</a> (Hamilton's hypercomplex numbers). - * <br/> + * <br> * Instance of this class are guaranteed to be immutable. * * @since 3.1 http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/complex/RootsOfUnity.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/complex/RootsOfUnity.java b/src/main/java/org/apache/commons/math4/complex/RootsOfUnity.java index 80fcb4b..9d4079e 100644 --- a/src/main/java/org/apache/commons/math4/complex/RootsOfUnity.java +++ b/src/main/java/org/apache/commons/math4/complex/RootsOfUnity.java @@ -107,7 +107,7 @@ public class RootsOfUnity implements Serializable { * <ul> * <li>{@code abs(n)} is always the number of roots of unity.</li> * <li>If {@code n > 0}, then the roots are stored in counter-clockwise order.</li> - * <li>If {@code n < 0}, then the roots are stored in clockwise order.</p> + * <li>If {@code n < 0}, then the roots are stored in clockwise order. * </ul> * * @param n the (signed) number of roots of unity to be computed http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/dfp/Dfp.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/dfp/Dfp.java b/src/main/java/org/apache/commons/math4/dfp/Dfp.java index 4c02ac0..22f2868 100644 --- a/src/main/java/org/apache/commons/math4/dfp/Dfp.java +++ b/src/main/java/org/apache/commons/math4/dfp/Dfp.java @@ -39,7 +39,7 @@ import org.apache.commons.math4.util.FastMath; * algebraic operation</li> * <li>Comply with IEEE 854-1987 as much as possible. * (See IEEE 854-1987 notes below)</li> - * </ol></p> + * </ol> * * <p>Trade offs: * <ol> @@ -48,15 +48,15 @@ import org.apache.commons.math4.util.FastMath; * <li>Digits are bigger, so rounding is a greater loss. So, if you * really need 12 decimal digits, better use 4 base 10000 digits * there can be one partially filled.</li> - * </ol></p> + * </ol> * * <p>Numbers are represented in the following form: * <pre> - * n = sign × mant × (radix)<sup>exp</sup>;</p> + * n = sign × mant × (radix)<sup>exp</sup>; * </pre> * where sign is ±1, mantissa represents a fractional number between * zero and one. mant[0] is the least significant digit. - * exp is in the range of -32767 to 32768</p> + * exp is in the range of -32767 to 32768 * * <p>IEEE 854-1987 Notes and differences</p> * http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/dfp/package-info.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/dfp/package-info.java b/src/main/java/org/apache/commons/math4/dfp/package-info.java index 4013231..7ad965a 100644 --- a/src/main/java/org/apache/commons/math4/dfp/package-info.java +++ b/src/main/java/org/apache/commons/math4/dfp/package-info.java @@ -31,7 +31,7 @@ * algebraic operation</li> * <li>Comply with IEEE 854-1987 as much as possible. * (See IEEE 854-1987 notes below)</li> - * </ol></p> + * </ol> * * <p>Trade offs: * <ol> @@ -40,7 +40,7 @@ * <li>Digits are bigger, so rounding is a greater loss. So, if you * really need 12 decimal digits, better use 4 base 10000 digits * there can be one partially filled.</li> - * </ol></p> + * </ol> * * <p>Numbers are represented in the following form: * <pre> http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/distribution/EmpiricalDistribution.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/distribution/EmpiricalDistribution.java b/src/main/java/org/apache/commons/math4/distribution/EmpiricalDistribution.java index 755d97e..567c7c2 100644 --- a/src/main/java/org/apache/commons/math4/distribution/EmpiricalDistribution.java +++ b/src/main/java/org/apache/commons/math4/distribution/EmpiricalDistribution.java @@ -76,7 +76,7 @@ import org.apache.commons.math4.util.MathUtils; * <li>Generate a uniformly distributed value in (0,1) </li> * <li>Select the subinterval to which the value belongs. * <li>Generate a random Gaussian value with mean = mean of the associated - * bin and std dev = std dev of associated bin.</li></ol></p> + * bin and std dev = std dev of associated bin.</li></ol> * * <p>EmpiricalDistribution implements the {@link RealDistribution} interface * as follows. Given x within the range of values in the dataset, let B @@ -94,7 +94,7 @@ import org.apache.commons.math4.util.MathUtils; * by 10. </li> *<li>The input file <i>must</i> be a plain text file containing one valid numeric * entry per line.</li> - * </ul></p> + * </ul> * */ public class EmpiricalDistribution extends AbstractRealDistribution { @@ -434,7 +434,7 @@ public class EmpiricalDistribution extends AbstractRealDistribution { /** * <p>Returns a fresh copy of the array of upper bounds for the bins. - * Bins are: <br/> + * Bins are: <br> * [min,upperBounds[0]],(upperBounds[0],upperBounds[1]],..., * (upperBounds[binCount-2], upperBounds[binCount-1] = max].</p> * @@ -508,7 +508,7 @@ public class EmpiricalDistribution extends AbstractRealDistribution { * <li>Compute K(B) = the mass of B with respect to the within-bin kernel (i.e., the * integral of the kernel density over B).</li> * <li>Return k(x) * P(B) / K(B), where k is the within-bin kernel density - * and P(B) is the mass of B.</li></ol></p> + * and P(B) is the mass of B.</li></ol> * @since 3.1 */ @Override @@ -569,16 +569,16 @@ public class EmpiricalDistribution extends AbstractRealDistribution { * <li>Find the smallest i such that the sum of the masses of the bins * through i is at least p.</li> * <li> - * Let K be the within-bin kernel distribution for bin i.</br> - * Let K(B) be the mass of B under K. <br/> + * Let K be the within-bin kernel distribution for bin i.<br> + * Let K(B) be the mass of B under K. <br> * Let K(B-) be K evaluated at the lower endpoint of B (the combined - * mass of the bins below B under K).<br/> - * Let P(B) be the probability of bin i.<br/> - * Let P(B-) be the sum of the bin masses below bin i. <br/> - * Let pCrit = p - P(B-)<br/> - * <li>Return the inverse of K evaluated at <br/> + * mass of the bins below B under K).<br> + * Let P(B) be the probability of bin i.<br> + * Let P(B-) be the sum of the bin masses below bin i. <br> + * Let pCrit = p - P(B-)<br> + * <li>Return the inverse of K evaluated at <br> * K(B-) + pCrit * K(B) / P(B) </li> - * </ol></p> + * </ol> * * @since 3.1 */ http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/distribution/EnumeratedIntegerDistribution.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/distribution/EnumeratedIntegerDistribution.java b/src/main/java/org/apache/commons/math4/distribution/EnumeratedIntegerDistribution.java index f507a53..25ef0f2 100644 --- a/src/main/java/org/apache/commons/math4/distribution/EnumeratedIntegerDistribution.java +++ b/src/main/java/org/apache/commons/math4/distribution/EnumeratedIntegerDistribution.java @@ -34,7 +34,7 @@ import org.apache.commons.math4.util.Pair; * <p>Implementation of an integer-valued {@link EnumeratedDistribution}.</p> * * <p>Values with zero-probability are allowed but they do not extend the - * support.<br/> + * support.<br> * Duplicate values are allowed. Probabilities of duplicate values are combined * when computing cumulative probabilities and statistics.</p> * http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/distribution/GammaDistribution.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/distribution/GammaDistribution.java b/src/main/java/org/apache/commons/math4/distribution/GammaDistribution.java index db6feb6..1f9d5ee 100644 --- a/src/main/java/org/apache/commons/math4/distribution/GammaDistribution.java +++ b/src/main/java/org/apache/commons/math4/distribution/GammaDistribution.java @@ -375,7 +375,6 @@ public class GammaDistribution extends AbstractRealDistribution { * </blockquote> * </li> * </ul> - * </p> */ @Override public RealDistribution.Sampler createSampler(final UniformRandomProvider rng) { http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/distribution/ParetoDistribution.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/distribution/ParetoDistribution.java b/src/main/java/org/apache/commons/math4/distribution/ParetoDistribution.java index 10fbaad..b4bff1c 100644 --- a/src/main/java/org/apache/commons/math4/distribution/ParetoDistribution.java +++ b/src/main/java/org/apache/commons/math4/distribution/ParetoDistribution.java @@ -33,7 +33,6 @@ import org.apache.commons.rng.sampling.distribution.InverseTransformParetoSample * <pre> * α * k^α / x^(α + 1) * </pre> - * <p> * <ul> * <li>{@code k} is the <em>scale</em> parameter: this is the minimum possible value of {@code X},</li> * <li>{@code α} is the <em>shape</em> parameter: this is the Pareto index</li> http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/distribution/PascalDistribution.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/distribution/PascalDistribution.java b/src/main/java/org/apache/commons/math4/distribution/PascalDistribution.java index b8f2464..1394e30 100644 --- a/src/main/java/org/apache/commons/math4/distribution/PascalDistribution.java +++ b/src/main/java/org/apache/commons/math4/distribution/PascalDistribution.java @@ -40,14 +40,14 @@ import org.apache.commons.math4.util.FastMath; * </p> * <p> * For a random variable {@code X} whose values are distributed according to this - * distribution, the probability mass function is given by<br/> - * {@code P(X = k) = C(k + r - 1, r - 1) * p^r * (1 - p)^k,}<br/> + * distribution, the probability mass function is given by<br> + * {@code P(X = k) = C(k + r - 1, r - 1) * p^r * (1 - p)^k,}<br> * where {@code r} is the number of successes, {@code p} is the probability of * success, and {@code X} is the total number of failures. {@code C(n, k)} is * the binomial coefficient ({@code n} choose {@code k}). The mean and variance - * of {@code X} are<br/> - * {@code E(X) = (1 - p) * r / p, var(X) = (1 - p) * r / p^2.}<br/> - * Finally, the cumulative distribution function is given by<br/> + * of {@code X} are<br> + * {@code E(X) = (1 - p) * r / p, var(X) = (1 - p) * r / p^2.}<br> + * Finally, the cumulative distribution function is given by<br> * {@code P(X <= k) = I(p, r, k + 1)}, * where I is the regularized incomplete Beta function. * </p> http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/distribution/ZipfDistribution.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/distribution/ZipfDistribution.java b/src/main/java/org/apache/commons/math4/distribution/ZipfDistribution.java index 69e7674..9f77bf7 100644 --- a/src/main/java/org/apache/commons/math4/distribution/ZipfDistribution.java +++ b/src/main/java/org/apache/commons/math4/distribution/ZipfDistribution.java @@ -35,7 +35,6 @@ import org.apache.commons.rng.sampling.distribution.RejectionInversionZipfSample * </pre> * {@code H(N,s)} is the normalizing constant * which corresponds to the generalized harmonic number of order N of s. - * <p> * <ul> * <li>{@code N} is the number of elements</li> * <li>{@code s} is the exponent</li> http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/distribution/fitting/MultivariateNormalMixtureExpectationMaximization.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/distribution/fitting/MultivariateNormalMixtureExpectationMaximization.java b/src/main/java/org/apache/commons/math4/distribution/fitting/MultivariateNormalMixtureExpectationMaximization.java index 20cbfc2..499a3df 100644 --- a/src/main/java/org/apache/commons/math4/distribution/fitting/MultivariateNormalMixtureExpectationMaximization.java +++ b/src/main/java/org/apache/commons/math4/distribution/fitting/MultivariateNormalMixtureExpectationMaximization.java @@ -37,7 +37,7 @@ import org.apache.commons.math4.util.MathArrays; import org.apache.commons.math4.util.Pair; /** - * Expectation-Maximization</a> algorithm for fitting the parameters of + * Expectation-Maximization algorithm for fitting the parameters of * multivariate normal mixture model distributions. * * This implementation is pure original code based on <a http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/fitting/AbstractCurveFitter.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/fitting/AbstractCurveFitter.java b/src/main/java/org/apache/commons/math4/fitting/AbstractCurveFitter.java index 06527f5..32aebc7 100644 --- a/src/main/java/org/apache/commons/math4/fitting/AbstractCurveFitter.java +++ b/src/main/java/org/apache/commons/math4/fitting/AbstractCurveFitter.java @@ -30,12 +30,12 @@ import org.apache.commons.math4.fitting.leastsquares.LevenbergMarquardtOptimizer * real functions <code>y = f(p<sub>i</sub>;x)</code>, where {@code x} is * the independent variable and the <code>p<sub>i</sub></code> are the * <em>parameters</em>. - * <br/> + * <br> * A fitter will find the optimal values of the parameters by * <em>fitting</em> the curve so it remains very close to a set of * {@code N} observed points <code>(x<sub>k</sub>, y<sub>k</sub>)</code>, * {@code 0 <= k < N}. - * <br/> + * <br> * An algorithm usually performs the fit by finding the parameter * values that minimizes the objective function * <pre><code> http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/fitting/GaussianCurveFitter.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/fitting/GaussianCurveFitter.java b/src/main/java/org/apache/commons/math4/fitting/GaussianCurveFitter.java index 3c5f14a..711fc1d 100644 --- a/src/main/java/org/apache/commons/math4/fitting/GaussianCurveFitter.java +++ b/src/main/java/org/apache/commons/math4/fitting/GaussianCurveFitter.java @@ -38,7 +38,7 @@ import org.apache.commons.math4.util.FastMath; * Fits points to a {@link * org.apache.commons.math4.analysis.function.Gaussian.Parametric Gaussian} * function. - * <br/> + * <br> * The {@link #withStartPoint(double[]) initial guess values} must be passed * in the following order: * <ul> http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/fitting/HarmonicCurveFitter.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/fitting/HarmonicCurveFitter.java b/src/main/java/org/apache/commons/math4/fitting/HarmonicCurveFitter.java index fbd643f..a487781 100644 --- a/src/main/java/org/apache/commons/math4/fitting/HarmonicCurveFitter.java +++ b/src/main/java/org/apache/commons/math4/fitting/HarmonicCurveFitter.java @@ -34,7 +34,7 @@ import org.apache.commons.math4.util.FastMath; * Fits points to a {@link * org.apache.commons.math4.analysis.function.HarmonicOscillator.Parametric harmonic oscillator} * function. - * <br/> + * <br> * The {@link #withStartPoint(double[]) initial guess values} must be passed * in the following order: * <ul> http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/fitting/PolynomialCurveFitter.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/fitting/PolynomialCurveFitter.java b/src/main/java/org/apache/commons/math4/fitting/PolynomialCurveFitter.java index 30d86a9..6704c16 100644 --- a/src/main/java/org/apache/commons/math4/fitting/PolynomialCurveFitter.java +++ b/src/main/java/org/apache/commons/math4/fitting/PolynomialCurveFitter.java @@ -28,7 +28,7 @@ import org.apache.commons.math4.linear.DiagonalMatrix; * Fits points to a {@link * org.apache.commons.math4.analysis.polynomials.PolynomialFunction.Parametric polynomial} * function. - * <br/> + * <br> * The size of the {@link #withStartPoint(double[]) initial guess} array defines the * degree of the polynomial to be fitted. * They must be sorted in increasing order of the polynomial's degree. http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/fitting/leastsquares/AbstractEvaluation.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/fitting/leastsquares/AbstractEvaluation.java b/src/main/java/org/apache/commons/math4/fitting/leastsquares/AbstractEvaluation.java index 4dedbe5..bc4f23b 100644 --- a/src/main/java/org/apache/commons/math4/fitting/leastsquares/AbstractEvaluation.java +++ b/src/main/java/org/apache/commons/math4/fitting/leastsquares/AbstractEvaluation.java @@ -27,7 +27,7 @@ import org.apache.commons.math4.util.FastMath; /** * An implementation of {@link Evaluation} that is designed for extension. All of the * methods implemented here use the methods that are left unimplemented. - * <p/> + * <p> * TODO cache results? * * @since 3.3 http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/fitting/leastsquares/GaussNewtonOptimizer.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/fitting/leastsquares/GaussNewtonOptimizer.java b/src/main/java/org/apache/commons/math4/fitting/leastsquares/GaussNewtonOptimizer.java index 637382c..24589ab 100644 --- a/src/main/java/org/apache/commons/math4/fitting/leastsquares/GaussNewtonOptimizer.java +++ b/src/main/java/org/apache/commons/math4/fitting/leastsquares/GaussNewtonOptimizer.java @@ -56,7 +56,7 @@ public class GaussNewtonOptimizer implements LeastSquaresOptimizer { * using the {@link LUDecomposition}. * * <p> Theoretically this method takes mn<sup>2</sup>/2 operations to compute the - * normal matrix and n<sup>3</sup>/3 operations (m > n) to solve the system using + * normal matrix and n<sup>3</sup>/3 operations (m > n) to solve the system using * the LU decomposition. </p> */ LU { @@ -81,7 +81,7 @@ public class GaussNewtonOptimizer implements LeastSquaresOptimizer { * QRDecomposition}. * * <p> Theoretically this method takes mn<sup>2</sup> - n<sup>3</sup>/3 operations - * (m > n) and has better numerical accuracy than any method that forms the normal + * (m > n) and has better numerical accuracy than any method that forms the normal * equations. </p> */ QR { @@ -102,7 +102,7 @@ public class GaussNewtonOptimizer implements LeastSquaresOptimizer { * using the {@link CholeskyDecomposition}. * * <p> Theoretically this method takes mn<sup>2</sup>/2 operations to compute the - * normal matrix and n<sup>3</sup>/6 operations (m > n) to solve the system using + * normal matrix and n<sup>3</sup>/6 operations (m > n) to solve the system using * the Cholesky decomposition. </p> */ CHOLESKY { @@ -143,7 +143,7 @@ public class GaussNewtonOptimizer implements LeastSquaresOptimizer { /** * Solve the linear least squares problem Jx=r. * - * @param jacobian the Jacobian matrix, J. the number of rows >= the number or + * @param jacobian the Jacobian matrix, J. the number of rows >= the number or * columns. * @param residuals the computed residuals, r. * @return the solution x, to the linear least squares problem Jx=r. @@ -166,7 +166,7 @@ public class GaussNewtonOptimizer implements LeastSquaresOptimizer { /** * Creates a Gauss Newton optimizer. - * <p/> + * <p> * The default for the algorithm is to solve the normal equations using QR * decomposition. */ http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/fitting/leastsquares/LeastSquaresAdapter.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/fitting/leastsquares/LeastSquaresAdapter.java b/src/main/java/org/apache/commons/math4/fitting/leastsquares/LeastSquaresAdapter.java index 1aff778..94e6a90 100644 --- a/src/main/java/org/apache/commons/math4/fitting/leastsquares/LeastSquaresAdapter.java +++ b/src/main/java/org/apache/commons/math4/fitting/leastsquares/LeastSquaresAdapter.java @@ -58,7 +58,7 @@ public class LeastSquaresAdapter implements LeastSquaresProblem { } /** {@inheritDoc} - * @param point*/ + */ @Override public Evaluation evaluate(final RealVector point) { return problem.evaluate(point); http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/fitting/leastsquares/LeastSquaresBuilder.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/fitting/leastsquares/LeastSquaresBuilder.java b/src/main/java/org/apache/commons/math4/fitting/leastsquares/LeastSquaresBuilder.java index 5f6beae..9117e59 100644 --- a/src/main/java/org/apache/commons/math4/fitting/leastsquares/LeastSquaresBuilder.java +++ b/src/main/java/org/apache/commons/math4/fitting/leastsquares/LeastSquaresBuilder.java @@ -112,7 +112,7 @@ public class LeastSquaresBuilder { /** * Configure the convergence checker. - * <p/> + * <p> * This function is an overloaded version of {@link #checker(ConvergenceChecker)}. * * @param newChecker the convergence checker. http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/fitting/leastsquares/LeastSquaresProblem.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/fitting/leastsquares/LeastSquaresProblem.java b/src/main/java/org/apache/commons/math4/fitting/leastsquares/LeastSquaresProblem.java index 353c925..6283c9f 100644 --- a/src/main/java/org/apache/commons/math4/fitting/leastsquares/LeastSquaresProblem.java +++ b/src/main/java/org/apache/commons/math4/fitting/leastsquares/LeastSquaresProblem.java @@ -80,7 +80,7 @@ public interface LeastSquaresProblem extends OptimizationProblem<LeastSquaresPro public interface Evaluation { /** - * Get the covariance matrix of the optimized parameters. <br/> Note that this + * Get the covariance matrix of the optimized parameters. <br> Note that this * operation involves the inversion of the <code>J<sup>T</sup>J</code> matrix, * where {@code J} is the Jacobian matrix. The {@code threshold} parameter is a * way for the caller to specify that the result of this computation should be http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/fitting/leastsquares/LevenbergMarquardtOptimizer.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/fitting/leastsquares/LevenbergMarquardtOptimizer.java b/src/main/java/org/apache/commons/math4/fitting/leastsquares/LevenbergMarquardtOptimizer.java index 9e256d1..1cf0c58 100644 --- a/src/main/java/org/apache/commons/math4/fitting/leastsquares/LevenbergMarquardtOptimizer.java +++ b/src/main/java/org/apache/commons/math4/fitting/leastsquares/LevenbergMarquardtOptimizer.java @@ -55,9 +55,9 @@ import org.apache.commons.numbers.core.Precision; * </ul> * The redistribution policy for MINPACK is available <a * href="http://www.netlib.org/minpack/disclaimer";>here</a>, for convenience, it - * is reproduced below.</p> + * is reproduced below. * - * <table border="0" width="80%" cellpadding="10" align="center" bgcolor="#E0E0E0"> + * <table style="text-align: center; background-color: #E0E0E0" border="0" width="80%" cellpadding="10" summary="MINPACK redistribution policy"> * <tr><td> * Minpack Copyright Notice (1999) University of Chicago. * All rights reserved @@ -102,7 +102,7 @@ import org.apache.commons.numbers.core.Precision; * (INCLUDING NEGLIGENCE OR STRICT LIABILITY), OR OTHERWISE, * EVEN IF ANY OF SAID PARTIES HAS BEEN WARNED OF THE * POSSIBILITY OF SUCH LOSS OR DAMAGES.</strong></li> - * <ol></td></tr> + * </ol></td></tr> * </table> * * @since 3.3 http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/fitting/leastsquares/package-info.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/fitting/leastsquares/package-info.java b/src/main/java/org/apache/commons/math4/fitting/leastsquares/package-info.java index b565376..45b3dc2 100644 --- a/src/main/java/org/apache/commons/math4/fitting/leastsquares/package-info.java +++ b/src/main/java/org/apache/commons/math4/fitting/leastsquares/package-info.java @@ -23,13 +23,13 @@ * <em>cost</em> or <em>χ<sup>2</sup></em>) between model and * observations. * - * <br/> + * <br> * Algorithms in this category need access to a <em>problem</em> * (represented by a {@link org.apache.commons.math4.fitting.leastsquares.LeastSquaresProblem * LeastSquaresProblem}). * Such a model predicts a set of values which the algorithm tries to match * with a set of given set of observed values. - * <br/> + * <br> * The problem can be created progressively using a {@link * org.apache.commons.math4.fitting.leastsquares.LeastSquaresBuilder builder} or it can * be created at once using a {@link org.apache.commons.math4.fitting.leastsquares.LeastSquaresFactory http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/fraction/BigFraction.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/fraction/BigFraction.java b/src/main/java/org/apache/commons/math4/fraction/BigFraction.java index a3da8c0..851c472 100644 --- a/src/main/java/org/apache/commons/math4/fraction/BigFraction.java +++ b/src/main/java/org/apache/commons/math4/fraction/BigFraction.java @@ -212,7 +212,6 @@ public class BigFraction * <li><a href="http://mathworld.wolfram.com/ContinuedFraction.html";> * Continued Fraction</a> equations (11) and (22)-(26)</li> * </ul> - * </p> * * @param value * the double value to convert to a fraction. @@ -345,7 +344,6 @@ public class BigFraction * <li><a href="http://mathworld.wolfram.com/ContinuedFraction.html";> * Continued Fraction</a> equations (11) and (22)-(26)</li> * </ul> - * </p> * * @param value * the double value to convert to a fraction. http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/fraction/Fraction.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/fraction/Fraction.java b/src/main/java/org/apache/commons/math4/fraction/Fraction.java index 834573c..d410000 100644 --- a/src/main/java/org/apache/commons/math4/fraction/Fraction.java +++ b/src/main/java/org/apache/commons/math4/fraction/Fraction.java @@ -109,7 +109,6 @@ public class Fraction * <li><a href="http://mathworld.wolfram.com/ContinuedFraction.html";> * Continued Fraction</a> equations (11) and (22)-(26)</li> * </ul> - * </p> * @param value the double value to convert to a fraction. * @param epsilon maximum error allowed. The resulting fraction is within * {@code epsilon} of {@code value}, in absolute terms. @@ -131,7 +130,6 @@ public class Fraction * <li><a href="http://mathworld.wolfram.com/ContinuedFraction.html";> * Continued Fraction</a> equations (11) and (22)-(26)</li> * </ul> - * </p> * @param value the double value to convert to a fraction. * @param maxDenominator The maximum allowed value for denominator * @throws FractionConversionException if the continued fraction failed to http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/genetics/GeneticAlgorithm.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/genetics/GeneticAlgorithm.java b/src/main/java/org/apache/commons/math4/genetics/GeneticAlgorithm.java index e4fcf4c..5dd2be2 100644 --- a/src/main/java/org/apache/commons/math4/genetics/GeneticAlgorithm.java +++ b/src/main/java/org/apache/commons/math4/genetics/GeneticAlgorithm.java @@ -125,7 +125,6 @@ public class GeneticAlgorithm { /** * Evolve the given population into the next generation. - * <p> * <ol> * <li>Get nextGeneration population to fill from <code>current</code> * generation, using its nextGeneration method</li> http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/geometry/euclidean/threed/FieldVector3D.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/geometry/euclidean/threed/FieldVector3D.java b/src/main/java/org/apache/commons/math4/geometry/euclidean/threed/FieldVector3D.java index bec2d74..4f04edf 100644 --- a/src/main/java/org/apache/commons/math4/geometry/euclidean/threed/FieldVector3D.java +++ b/src/main/java/org/apache/commons/math4/geometry/euclidean/threed/FieldVector3D.java @@ -538,7 +538,7 @@ public class FieldVector3D<T extends RealFieldElement<T>> implements Serializabl * Vector3D k = u.normalize(); * Vector3D i = k.orthogonal(); * Vector3D j = Vector3D.crossProduct(k, i); - * </code></pre></p> + * </code></pre> * @return a new normalized vector orthogonal to the instance * @exception MathArithmeticException if the norm of the instance is null */ http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/geometry/euclidean/threed/Vector3D.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/geometry/euclidean/threed/Vector3D.java b/src/main/java/org/apache/commons/math4/geometry/euclidean/threed/Vector3D.java index 7e43245..1d00387 100644 --- a/src/main/java/org/apache/commons/math4/geometry/euclidean/threed/Vector3D.java +++ b/src/main/java/org/apache/commons/math4/geometry/euclidean/threed/Vector3D.java @@ -323,7 +323,7 @@ public class Vector3D implements Serializable, Vector<Euclidean3D> { * Vector3D k = u.normalize(); * Vector3D i = k.orthogonal(); * Vector3D j = Vector3D.crossProduct(k, i); - * </code></pre></p> + * </code></pre> * @return a new normalized vector orthogonal to the instance * @exception MathArithmeticException if the norm of the instance is null */ http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/linear/AbstractFieldMatrix.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/linear/AbstractFieldMatrix.java b/src/main/java/org/apache/commons/math4/linear/AbstractFieldMatrix.java index a182e49..c2f3b18 100644 --- a/src/main/java/org/apache/commons/math4/linear/AbstractFieldMatrix.java +++ b/src/main/java/org/apache/commons/math4/linear/AbstractFieldMatrix.java @@ -61,7 +61,7 @@ public abstract class AbstractFieldMatrix<T extends FieldElement<T>> } /** - * Create a new FieldMatrix<T> with the supplied row and column dimensions. + * Create a new {@code FieldMatrix<T>} with the supplied row and column dimensions. * * @param field Field to which the elements belong. * @param rowDimension Number of rows in the new matrix. http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/linear/Array2DRowFieldMatrix.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/linear/Array2DRowFieldMatrix.java b/src/main/java/org/apache/commons/math4/linear/Array2DRowFieldMatrix.java index 7a70931..f49f888 100644 --- a/src/main/java/org/apache/commons/math4/linear/Array2DRowFieldMatrix.java +++ b/src/main/java/org/apache/commons/math4/linear/Array2DRowFieldMatrix.java @@ -33,11 +33,11 @@ import org.apache.commons.math4.util.MathArrays; import org.apache.commons.math4.util.MathUtils; /** - * Implementation of FieldMatrix<T> using a {@link FieldElement}[][] array to store entries. + * Implementation of {@code FieldMatrix<T>} using a {@link FieldElement}[][] array to store entries. * <p> * As specified in the {@link FieldMatrix} interface, matrix element indexing * is 0-based -- e.g., <code>getEntry(0, 0)</code> - * returns the element in the first row, first column of the matrix.</li></ul> + * returns the element in the first row, first column of the matrix. * </p> * * @param <T> the type of the field elements http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/linear/BlockFieldMatrix.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/linear/BlockFieldMatrix.java b/src/main/java/org/apache/commons/math4/linear/BlockFieldMatrix.java index 74c6fe8..03417a3 100644 --- a/src/main/java/org/apache/commons/math4/linear/BlockFieldMatrix.java +++ b/src/main/java/org/apache/commons/math4/linear/BlockFieldMatrix.java @@ -115,9 +115,8 @@ public class BlockFieldMatrix<T extends FieldElement<T>> extends AbstractFieldMa * Create a new dense matrix copying entries from raw layout data. * <p>The input array <em>must</em> already be in raw layout.</p> * <p>Calling this constructor is equivalent to call: - * <pre>matrix = new BlockFieldMatrix<T>(getField(), rawData.length, rawData[0].length, - * toBlocksLayout(rawData), false);</pre> - * </p> + * {@code matrix = new BlockFieldMatrix<T>(getField(), rawData.length, rawData[0].length, + * toBlocksLayout(rawData), false);} * * @param rawData Data for the new matrix, in raw layout. * @throws DimensionMismatchException if the {@code blockData} shape is http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/linear/BlockRealMatrix.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/linear/BlockRealMatrix.java b/src/main/java/org/apache/commons/math4/linear/BlockRealMatrix.java index 7554007..20192ad 100644 --- a/src/main/java/org/apache/commons/math4/linear/BlockRealMatrix.java +++ b/src/main/java/org/apache/commons/math4/linear/BlockRealMatrix.java @@ -112,7 +112,6 @@ public class BlockRealMatrix extends AbstractRealMatrix implements Serializable * <p>Calling this constructor is equivalent to call: * <pre>matrix = new BlockRealMatrix(rawData.length, rawData[0].length, * toBlocksLayout(rawData), false);</pre> - * </p> * * @param rawData data for new matrix, in raw layout * @throws DimensionMismatchException if the shape of {@code blockData} is http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/linear/ConjugateGradient.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/linear/ConjugateGradient.java b/src/main/java/org/apache/commons/math4/linear/ConjugateGradient.java index de831ff..3681a7d 100644 --- a/src/main/java/org/apache/commons/math4/linear/ConjugateGradient.java +++ b/src/main/java/org/apache/commons/math4/linear/ConjugateGradient.java @@ -53,9 +53,9 @@ import org.apache.commons.math4.util.IterationManager; * <ul> * <li>key {@code "operator"} points to the offending linear operator, say L,</li> * <li>key {@code "vector"} points to the offending vector, say x, such that - * x<sup>T</sup> · L · x < 0.</li> + * x<sup>T</sup> · L · x < 0.</li> * </ul> - * </p> + * * <h3>References</h3> * <dl> * <dt><a id="BARR1994">Barret et al. (1994)</a></dt> @@ -64,8 +64,7 @@ import org.apache.commons.math4.util.IterationManager; * <a href="http://www.netlib.org/linalg/html_templates/Templates.html";><em> * Templates for the Solution of Linear Systems: Building Blocks for Iterative * Methods</em></a>, SIAM</dd> - * <dt><a id="STRA2002">Strakos and Tichy (2002) - * <dt> + * <dt><a id="STRA2002">Strakos and Tichy (2002)</a></dt> * <dd>Z. Strakos and P. Tichy, <a * href="http://etna.mcs.kent.edu/vol.13.2002/pp56-80.dir/pp56-80.pdf";> * <em>On error estimation in the conjugate gradient method and why it works http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/linear/DiagonalMatrix.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/linear/DiagonalMatrix.java b/src/main/java/org/apache/commons/math4/linear/DiagonalMatrix.java index 1b35204..d850529 100644 --- a/src/main/java/org/apache/commons/math4/linear/DiagonalMatrix.java +++ b/src/main/java/org/apache/commons/math4/linear/DiagonalMatrix.java @@ -54,7 +54,7 @@ public class DiagonalMatrix extends AbstractRealMatrix /** * Creates a matrix using the input array as the underlying data. - * <br/> + * <br> * The input array is copied, not referenced. * * @param d Data for the new matrix. @@ -65,7 +65,7 @@ public class DiagonalMatrix extends AbstractRealMatrix /** * Creates a matrix using the input array as the underlying data. - * <br/> + * <br> * If an array is created specially in order to be embedded in a * this instance and not used directly, the {@code copyArray} may be * set to {@code false}. http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/linear/FieldMatrix.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/linear/FieldMatrix.java b/src/main/java/org/apache/commons/math4/linear/FieldMatrix.java index 7cab1d2..16f529a 100644 --- a/src/main/java/org/apache/commons/math4/linear/FieldMatrix.java +++ b/src/main/java/org/apache/commons/math4/linear/FieldMatrix.java @@ -45,7 +45,7 @@ public interface FieldMatrix<T extends FieldElement<T>> extends AnyMatrix { Field<T> getField(); /** - * Create a new FieldMatrix<T> of the same type as the instance with + * Create a new {@code FieldMatrix<T>} of the same type as the instance with * the supplied row and column dimensions. * * @param rowDimension the number of rows in the new matrix @@ -238,7 +238,6 @@ public interface FieldMatrix<T extends FieldElement<T>> extends AnyMatrix { * 9 5 6 2 * </pre> * - * </p> * * @param subMatrix Array containing the submatrix replacement data. * @param row Row coordinate of the top-left element to be replaced. http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/linear/MatrixUtils.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/linear/MatrixUtils.java b/src/main/java/org/apache/commons/math4/linear/MatrixUtils.java index cb71b37..1f97a5e 100644 --- a/src/main/java/org/apache/commons/math4/linear/MatrixUtils.java +++ b/src/main/java/org/apache/commons/math4/linear/MatrixUtils.java @@ -746,7 +746,6 @@ public class MatrixUtils { * * } * </code></pre> - * </p> * * @param vector real vector to serialize * @param oos stream where the real vector should be written @@ -847,7 +846,6 @@ public class MatrixUtils { * * } * </code></pre> - * </p> * * @param matrix real matrix to serialize * @param oos stream where the real matrix should be written http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/linear/PreconditionedIterativeLinearSolver.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/linear/PreconditionedIterativeLinearSolver.java b/src/main/java/org/apache/commons/math4/linear/PreconditionedIterativeLinearSolver.java index 4110a0c..a02c891 100644 --- a/src/main/java/org/apache/commons/math4/linear/PreconditionedIterativeLinearSolver.java +++ b/src/main/java/org/apache/commons/math4/linear/PreconditionedIterativeLinearSolver.java @@ -39,7 +39,7 @@ import org.apache.commons.math4.util.MathUtils; * while matrix-vector products of the type M · y remain comparatively * easy to compute. In this library, M (not M<sup>-1</sup>!) is called the * <em>preconditionner</em>. - * </p> + * * <p> * Concrete implementations of this abstract class must be provided with the * preconditioner M, as a {@link RealLinearOperator}. http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/linear/RRQRDecomposition.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/linear/RRQRDecomposition.java b/src/main/java/org/apache/commons/math4/linear/RRQRDecomposition.java index f85b22e..9f41ea6 100644 --- a/src/main/java/org/apache/commons/math4/linear/RRQRDecomposition.java +++ b/src/main/java/org/apache/commons/math4/linear/RRQRDecomposition.java @@ -152,7 +152,7 @@ public class RRQRDecomposition extends QRDecomposition { * bottom right submatrices. When a large fall in norm is seen, * the rank is returned. The drop is computed as:</p> * <pre> - * (thisNorm/lastNorm) * rNorm < dropThreshold + * (thisNorm/lastNorm) * rNorm < dropThreshold * </pre> * <p> * where thisNorm is the Frobenius norm of the current submatrix, http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/linear/RealLinearOperator.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/linear/RealLinearOperator.java b/src/main/java/org/apache/commons/math4/linear/RealLinearOperator.java index 06ff43c..5ad4421 100644 --- a/src/main/java/org/apache/commons/math4/linear/RealLinearOperator.java +++ b/src/main/java/org/apache/commons/math4/linear/RealLinearOperator.java @@ -35,7 +35,7 @@ import org.apache.commons.math4.exception.DimensionMismatchException; * supply a subroutine for computing y (and perhaps z) given x, which permits * full exploitation of the sparsity or other special structure of A. * </blockquote> - * <br/> + * <br> * * <dl> * <dt><a name="BARR1994">Barret et al. (1994)</a></dt> http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/linear/RealMatrix.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/linear/RealMatrix.java b/src/main/java/org/apache/commons/math4/linear/RealMatrix.java index 1cafe3e..c41d839 100644 --- a/src/main/java/org/apache/commons/math4/linear/RealMatrix.java +++ b/src/main/java/org/apache/commons/math4/linear/RealMatrix.java @@ -244,7 +244,7 @@ public interface RealMatrix extends AnyMatrix { * 1 2 3 4 * 5 3 4 8 * 9 5 6 2 - * </pre></p> + * </pre> * * @param subMatrix array containing the submatrix replacement data * @param row row coordinate of the top, left element to be replaced http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/linear/RealVector.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/linear/RealVector.java b/src/main/java/org/apache/commons/math4/linear/RealVector.java index 545a521..f4fa843 100644 --- a/src/main/java/org/apache/commons/math4/linear/RealVector.java +++ b/src/main/java/org/apache/commons/math4/linear/RealVector.java @@ -803,12 +803,12 @@ public abstract class RealVector { /** * Acts as if it is implemented as: - * <pre> + * {@code * Entry e = null; * for(Iterator<Entry> it = iterator(); it.hasNext(); e = it.next()) { * e.setValue(function.value(e.getValue())); * } - * </pre> + * } * Entries of this vector are modified in-place by this method. * * @param function Function to apply to each entry. http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/linear/RectangularCholeskyDecomposition.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/linear/RectangularCholeskyDecomposition.java b/src/main/java/org/apache/commons/math4/linear/RectangularCholeskyDecomposition.java index b32a5da..16e446f 100644 --- a/src/main/java/org/apache/commons/math4/linear/RectangularCholeskyDecomposition.java +++ b/src/main/java/org/apache/commons/math4/linear/RectangularCholeskyDecomposition.java @@ -30,7 +30,7 @@ import org.apache.commons.math4.util.FastMath; * of the traditional triangular shape) and there is a threshold to ignore * small diagonal elements. This is used for example to generate {@link * org.apache.commons.math4.random.CorrelatedRandomVectorGenerator correlated - * random n-dimensions vectors} in a p-dimension subspace (p < n). + * random n-dimensions vectors} in a p-dimension subspace (p < n). * In other words, it allows generating random vectors from a covariance * matrix that is only positive semidefinite, and not positive definite.</p> * <p>Rectangular Cholesky decomposition is <em>not</em> suited for solving http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/linear/SparseFieldMatrix.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/linear/SparseFieldMatrix.java b/src/main/java/org/apache/commons/math4/linear/SparseFieldMatrix.java index 70d5999..a3ae81d 100644 --- a/src/main/java/org/apache/commons/math4/linear/SparseFieldMatrix.java +++ b/src/main/java/org/apache/commons/math4/linear/SparseFieldMatrix.java @@ -55,7 +55,7 @@ public class SparseFieldMatrix<T extends FieldElement<T>> extends AbstractFieldM } /** - * Create a new SparseFieldMatrix<T> with the supplied row and column + * Create a new {@code SparseFieldMatrix<T>} with the supplied row and column * dimensions. * * @param field Field to which the elements belong. http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/linear/SymmLQ.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/linear/SymmLQ.java b/src/main/java/org/apache/commons/math4/linear/SymmLQ.java index ef52904..0e92aa7 100644 --- a/src/main/java/org/apache/commons/math4/linear/SymmLQ.java +++ b/src/main/java/org/apache/commons/math4/linear/SymmLQ.java @@ -113,7 +113,7 @@ import org.apache.commons.math4.util.MathUtils; * initial phase. If x<sub>0</sub> is known to be a good approximation to x, one * should compute r<sub>0</sub> = b - A · x, solve A · dx = r0, * and set x = x<sub>0</sub> + dx. - * </p> + * * <h3><a id="context">Exception context</a></h3> * <p> * Besides standard {@link DimensionMismatchException}, this class might throw @@ -127,7 +127,7 @@ import org.apache.commons.math4.util.MathUtils; * that x<sup>T</sup> · L · y ≠ y<sup>T</sup> · L * · x (within a certain accuracy).</li> * </ul> - * </p> + * * <p> * {@link NonPositiveDefiniteOperatorException} might also be thrown in case the * preconditioner is not positive definite. The relevant keys to the @@ -136,9 +136,9 @@ import org.apache.commons.math4.util.MathUtils; * <li>key {@code "operator"}, which points to the offending linear operator, * say L,</li> * <li>key {@code "vector"}, which points to the offending vector, say x, such - * that x<sup>T</sup> · L · x < 0.</li> + * that x<sup>T</sup> · L · x < 0.</li> * </ul> - * </p> + * * <h3>References</h3> * <dl> * <dt><a id="PAIG1975">Paige and Saunders (1975)</a></dt> http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/ml/clustering/FuzzyKMeansClusterer.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/ml/clustering/FuzzyKMeansClusterer.java b/src/main/java/org/apache/commons/math4/ml/clustering/FuzzyKMeansClusterer.java index ee3d590..a214107 100644 --- a/src/main/java/org/apache/commons/math4/ml/clustering/FuzzyKMeansClusterer.java +++ b/src/main/java/org/apache/commons/math4/ml/clustering/FuzzyKMeansClusterer.java @@ -43,9 +43,9 @@ import org.apache.commons.math4.util.MathUtils; * to the cluster j. * <p> * The algorithm then tries to minimize the objective function: - * <pre> + * <div style="white-space: pre"><code> * J = ∑<sub>i=1..C</sub>∑<sub>k=1..N</sub> u<sub>ik</sub><sup>m</sup>d<sub>ik</sub><sup>2</sup> - * </pre> + * </code></div> * with d<sub>ik</sub> being the distance between data point i and the cluster center k. * <p> * The algorithm requires two parameters: http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/ml/neuralnet/Neuron.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/ml/neuralnet/Neuron.java b/src/main/java/org/apache/commons/math4/ml/neuralnet/Neuron.java index 409e553..6e58760 100644 --- a/src/main/java/org/apache/commons/math4/ml/neuralnet/Neuron.java +++ b/src/main/java/org/apache/commons/math4/ml/neuralnet/Neuron.java @@ -51,7 +51,7 @@ public class Neuron implements Serializable { * Creates a neuron. * The size of the feature set is fixed to the length of the given * argument. - * <br/> + * <br> * Constructor is package-private: Neurons must be * {@link Network#createNeuron(double[]) created} by the network * instance to which they will belong. @@ -113,7 +113,7 @@ public class Neuron implements Serializable { /** * Tries to atomically update the neuron's features. * Update will be performed only if the expected values match the - * current values.<br/> + * current values.<br> * In effect, when concurrent threads call this method, the state * could be modified by one, so that it does not correspond to the * the state assumed by another. http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/ml/neuralnet/SquareNeighbourhood.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/ml/neuralnet/SquareNeighbourhood.java b/src/main/java/org/apache/commons/math4/ml/neuralnet/SquareNeighbourhood.java index 4f2c175..3600ee5 100644 --- a/src/main/java/org/apache/commons/math4/ml/neuralnet/SquareNeighbourhood.java +++ b/src/main/java/org/apache/commons/math4/ml/neuralnet/SquareNeighbourhood.java @@ -24,13 +24,13 @@ package org.apache.commons.math4.ml.neuralnet; */ public enum SquareNeighbourhood { /** - * <a href="http://en.wikipedia.org/wiki/Von_Neumann_neighborhood"; + * <a href="http://en.wikipedia.org/wiki/Von_Neumann_neighborhood";> * Von Neumann neighbourhood</a>: in two dimensions, each (internal) * neuron has four neighbours. */ VON_NEUMANN, /** - * <a href="http://en.wikipedia.org/wiki/Moore_neighborhood"; + * <a href="http://en.wikipedia.org/wiki/Moore_neighborhood";> * Moore neighbourhood</a>: in two dimensions, each (internal) * neuron has eight neighbours. */ http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/ml/neuralnet/oned/NeuronString.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/ml/neuralnet/oned/NeuronString.java b/src/main/java/org/apache/commons/math4/ml/neuralnet/oned/NeuronString.java index ba454ca..864b62a 100644 --- a/src/main/java/org/apache/commons/math4/ml/neuralnet/oned/NeuronString.java +++ b/src/main/java/org/apache/commons/math4/ml/neuralnet/oned/NeuronString.java @@ -83,11 +83,11 @@ public class NeuronString implements Serializable { * Creates a one-dimensional network: * Each neuron not located on the border of the mesh has two * neurons linked to it. - * <br/> + * <br> * The links are bi-directional. * Neurons created successively are neighbours (i.e. there are * links between them). - * <br/> + * <br> * The topology of the network can also be a circle (if the * dimension is wrapped). * http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/ml/neuralnet/sofm/KohonenUpdateAction.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/ml/neuralnet/sofm/KohonenUpdateAction.java b/src/main/java/org/apache/commons/math4/ml/neuralnet/sofm/KohonenUpdateAction.java index 1c49d06..691fd90 100644 --- a/src/main/java/org/apache/commons/math4/ml/neuralnet/sofm/KohonenUpdateAction.java +++ b/src/main/java/org/apache/commons/math4/ml/neuralnet/sofm/KohonenUpdateAction.java @@ -32,7 +32,7 @@ import org.apache.commons.math4.ml.neuralnet.UpdateAction; /** * Update formula for <a href="http://en.wikipedia.org/wiki/Kohonen";> * Kohonen's Self-Organizing Map</a>. - * <br/> + * <br> * The {@link #update(Network,double[]) update} method modifies the * features {@code w} of the "winning" neuron and its neighbours * according to the following rule: @@ -46,12 +46,12 @@ import org.apache.commons.math4.ml.neuralnet.UpdateAction; * <li>{@code d} is the number of links to traverse in order to reach * the neuron from the winning neuron.</li> * </ul> - * <br/> + * <br> * This class is thread-safe as long as the arguments passed to the * {@link #KohonenUpdateAction(DistanceMeasure,LearningFactorFunction, * NeighbourhoodSizeFunction) constructor} are instances of thread-safe * classes. - * <br/> + * <br> * Each call to the {@link #update(Network,double[]) update} method * will increment the internal counter used to compute the current * values for http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/ml/neuralnet/sofm/util/ExponentialDecayFunction.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/ml/neuralnet/sofm/util/ExponentialDecayFunction.java b/src/main/java/org/apache/commons/math4/ml/neuralnet/sofm/util/ExponentialDecayFunction.java index d914bf1..c1321ea 100644 --- a/src/main/java/org/apache/commons/math4/ml/neuralnet/sofm/util/ExponentialDecayFunction.java +++ b/src/main/java/org/apache/commons/math4/ml/neuralnet/sofm/util/ExponentialDecayFunction.java @@ -24,7 +24,7 @@ import org.apache.commons.math4.util.FastMath; /** * Exponential decay function: <code>a e<sup>-x / b</sup></code>, * where {@code x} is the (integer) independent variable. - * <br/> + * <br> * Class is immutable. * * @since 3.3 http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/ml/neuralnet/sofm/util/QuasiSigmoidDecayFunction.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/ml/neuralnet/sofm/util/QuasiSigmoidDecayFunction.java b/src/main/java/org/apache/commons/math4/ml/neuralnet/sofm/util/QuasiSigmoidDecayFunction.java index 4abef6f..e71a9bf 100644 --- a/src/main/java/org/apache/commons/math4/ml/neuralnet/sofm/util/QuasiSigmoidDecayFunction.java +++ b/src/main/java/org/apache/commons/math4/ml/neuralnet/sofm/util/QuasiSigmoidDecayFunction.java @@ -23,7 +23,7 @@ import org.apache.commons.math4.exception.NumberIsTooLargeException; /** * Decay function whose shape is similar to a sigmoid. - * <br/> + * <br> * Class is immutable. * * @since 3.3 http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/ml/neuralnet/twod/NeuronSquareMesh2D.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/ml/neuralnet/twod/NeuronSquareMesh2D.java b/src/main/java/org/apache/commons/math4/ml/neuralnet/twod/NeuronSquareMesh2D.java index e42491d..3a5a126 100644 --- a/src/main/java/org/apache/commons/math4/ml/neuralnet/twod/NeuronSquareMesh2D.java +++ b/src/main/java/org/apache/commons/math4/ml/neuralnet/twod/NeuronSquareMesh2D.java @@ -34,7 +34,7 @@ import org.apache.commons.math4.ml.neuralnet.SquareNeighbourhood; /** * Neural network with the topology of a two-dimensional surface. * Each neuron defines one surface element. - * <br/> + * <br> * This network is primarily intended to represent a * <a href="http://en.wikipedia.org/wiki/Kohonen";> * Self Organizing Feature Map</a>. @@ -141,9 +141,9 @@ public class NeuronSquareMesh2D * Creates a two-dimensional network composed of square cells: * Each neuron not located on the border of the mesh has four * neurons linked to it. - * <br/> + * <br> * The links are bi-directional. - * <br/> + * <br> * The topology of the network can also be a cylinder (if one * of the dimensions is wrapped) or a torus (if both dimensions * are wrapped). http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/ml/neuralnet/twod/util/SmoothedDataHistogram.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/ml/neuralnet/twod/util/SmoothedDataHistogram.java b/src/main/java/org/apache/commons/math4/ml/neuralnet/twod/util/SmoothedDataHistogram.java index 6db74d9..1327055 100644 --- a/src/main/java/org/apache/commons/math4/ml/neuralnet/twod/util/SmoothedDataHistogram.java +++ b/src/main/java/org/apache/commons/math4/ml/neuralnet/twod/util/SmoothedDataHistogram.java @@ -26,11 +26,11 @@ import org.apache.commons.math4.exception.NumberIsTooSmallException; /** * Visualization of high-dimensional data projection on a 2D-map. * The method is described in - * <quote> + * <blockquote> * <em>Using Smoothed Data Histograms for Cluster Visualization in Self-Organizing Maps</em> * <br> * by Elias Pampalk, Andreas Rauber and Dieter Merkl. - * </quote> + * </blockquote> * @since 3.6 */ public class SmoothedDataHistogram implements MapDataVisualization { http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/ode/JacobianMatrices.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/ode/JacobianMatrices.java b/src/main/java/org/apache/commons/math4/ode/JacobianMatrices.java index 2efed92..175d060 100644 --- a/src/main/java/org/apache/commons/math4/ode/JacobianMatrices.java +++ b/src/main/java/org/apache/commons/math4/ode/JacobianMatrices.java @@ -43,7 +43,6 @@ import org.apache.commons.math4.exception.util.LocalizedFormats; * <li>a {@link ParameterJacobianProvider}</li> * <li>a {@link ParameterizedODE}</li> * </ul> - * </p> * * @see ExpandableStatefulODE * @see FirstOrderDifferentialEquations http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/ode/MultistepFieldIntegrator.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/ode/MultistepFieldIntegrator.java b/src/main/java/org/apache/commons/math4/ode/MultistepFieldIntegrator.java index edd65e2..a5e21b6 100644 --- a/src/main/java/org/apache/commons/math4/ode/MultistepFieldIntegrator.java +++ b/src/main/java/org/apache/commons/math4/ode/MultistepFieldIntegrator.java @@ -38,20 +38,20 @@ import org.apache.commons.math4.util.MathUtils; * This class is the base class for multistep integrators for Ordinary * Differential Equations. * <p>We define scaled derivatives s<sub>i</sub>(n) at step n as: - * <pre> + * <div style="white-space: pre"><code> * s<sub>1</sub>(n) = h y'<sub>n</sub> for first derivative * s<sub>2</sub>(n) = h<sup>2</sup>/2 y''<sub>n</sub> for second derivative * s<sub>3</sub>(n) = h<sup>3</sup>/6 y'''<sub>n</sub> for third derivative * ... * s<sub>k</sub>(n) = h<sup>k</sup>/k! y<sup>(k)</sup><sub>n</sub> for k<sup>th</sup> derivative - * </pre></p> + * </code></div> * <p>Rather than storing several previous steps separately, this implementation uses * the Nordsieck vector with higher degrees scaled derivatives all taken at the same * step (y<sub>n</sub>, s<sub>1</sub>(n) and r<sub>n</sub>) where r<sub>n</sub> is defined as: - * <pre> + * <div style="white-space: pre"><code> * r<sub>n</sub> = [ s<sub>2</sub>(n), s<sub>3</sub>(n) ... s<sub>k</sub>(n) ]<sup>T</sup> - * </pre> - * (we omit the k index in the notation for clarity)</p> + * </code></div> + * (we omit the k index in the notation for clarity) * <p> * Multistep integrators with Nordsieck representation are highly sensitive to * large step changes because when the step is multiplied by factor a, the http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/ode/MultistepIntegrator.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/ode/MultistepIntegrator.java b/src/main/java/org/apache/commons/math4/ode/MultistepIntegrator.java index 354db49..14736ef 100644 --- a/src/main/java/org/apache/commons/math4/ode/MultistepIntegrator.java +++ b/src/main/java/org/apache/commons/math4/ode/MultistepIntegrator.java @@ -34,20 +34,20 @@ import org.apache.commons.math4.util.FastMath; * This class is the base class for multistep integrators for Ordinary * Differential Equations. * <p>We define scaled derivatives s<sub>i</sub>(n) at step n as: - * <pre> + * <div style="white-space: pre"><code> * s<sub>1</sub>(n) = h y'<sub>n</sub> for first derivative * s<sub>2</sub>(n) = h<sup>2</sup>/2 y''<sub>n</sub> for second derivative * s<sub>3</sub>(n) = h<sup>3</sup>/6 y'''<sub>n</sub> for third derivative * ... * s<sub>k</sub>(n) = h<sup>k</sup>/k! y<sup>(k)</sup><sub>n</sub> for k<sup>th</sup> derivative - * </pre></p> + * </code></div> * <p>Rather than storing several previous steps separately, this implementation uses * the Nordsieck vector with higher degrees scaled derivatives all taken at the same * step (y<sub>n</sub>, s<sub>1</sub>(n) and r<sub>n</sub>) where r<sub>n</sub> is defined as: - * <pre> + * <div style="white-space: pre"><code> * r<sub>n</sub> = [ s<sub>2</sub>(n), s<sub>3</sub>(n) ... s<sub>k</sub>(n) ]<sup>T</sup> - * </pre> - * (we omit the k index in the notation for clarity)</p> + * </code></div> + * (we omit the k index in the notation for clarity) * <p> * Multistep integrators with Nordsieck representation are highly sensitive to * large step changes because when the step is multiplied by factor a, the http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/ode/events/EventHandler.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/ode/events/EventHandler.java b/src/main/java/org/apache/commons/math4/ode/events/EventHandler.java index f1900f7..1012b53 100644 --- a/src/main/java/org/apache/commons/math4/ode/events/EventHandler.java +++ b/src/main/java/org/apache/commons/math4/ode/events/EventHandler.java @@ -110,7 +110,7 @@ public interface EventHandler { * <p>Also note that the integrator expect that once an event has occurred, * the sign of the switching function at the start of the next step (i.e. * just after the event) is the opposite of the sign just before the event. - * This consistency between the steps <string>must</strong> be preserved, + * This consistency between the steps <strong>must</strong> be preserved, * otherwise {@link org.apache.commons.math4.exception.NoBracketingException * exceptions} related to root not being bracketed will occur.</p> * <p>This need for consistency is sometimes tricky to achieve. A typical http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/ode/events/FieldEventHandler.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/ode/events/FieldEventHandler.java b/src/main/java/org/apache/commons/math4/ode/events/FieldEventHandler.java index 07bae23..f22c3bd 100644 --- a/src/main/java/org/apache/commons/math4/ode/events/FieldEventHandler.java +++ b/src/main/java/org/apache/commons/math4/ode/events/FieldEventHandler.java @@ -74,7 +74,7 @@ public interface FieldEventHandler<T extends RealFieldElement<T>> { * <p>Also note that the integrator expect that once an event has occurred, * the sign of the switching function at the start of the next step (i.e. * just after the event) is the opposite of the sign just before the event. - * This consistency between the steps <string>must</strong> be preserved, + * This consistency between the steps <strong>must</strong> be preserved, * otherwise {@link org.apache.commons.math4.exception.NoBracketingException * exceptions} related to root not being bracketed will occur.</p> * <p>This need for consistency is sometimes tricky to achieve. A typical http://git-wip-us.apache.org/repos/asf/commons-math/blob/53ec46ba/src/main/java/org/apache/commons/math4/ode/nonstiff/AdamsBashforthFieldIntegrator.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/ode/nonstiff/AdamsBashforthFieldIntegrator.java b/src/main/java/org/apache/commons/math4/ode/nonstiff/AdamsBashforthFieldIntegrator.java index ebb31f0..64c2a1f 100644 --- a/src/main/java/org/apache/commons/math4/ode/nonstiff/AdamsBashforthFieldIntegrator.java +++ b/src/main/java/org/apache/commons/math4/ode/nonstiff/AdamsBashforthFieldIntegrator.java @@ -56,19 +56,19 @@ import org.apache.commons.math4.util.MathArrays; * <h3>Implementation details</h3> * * <p>We define scaled derivatives s<sub>i</sub>(n) at step n as: - * <pre> + * <div style="white-space: pre"><code> * s<sub>1</sub>(n) = h y'<sub>n</sub> for first derivative * s<sub>2</sub>(n) = h<sup>2</sup>/2 y''<sub>n</sub> for second derivative * s<sub>3</sub>(n) = h<sup>3</sup>/6 y'''<sub>n</sub> for third derivative * ... * s<sub>k</sub>(n) = h<sup>k</sup>/k! y<sup>(k)</sup><sub>n</sub> for k<sup>th</sup> derivative - * </pre></p> + * </code></div> * * <p>The definitions above use the classical representation with several previous first * derivatives. Lets define - * <pre> + * <div style="white-space: pre"><code> * q<sub>n</sub> = [ s<sub>1</sub>(n-1) s<sub>1</sub>(n-2) ... s<sub>1</sub>(n-(k-1)) ]<sup>T</sup> - * </pre> + * </code></div> * (we omit the k index in the notation for clarity). With these definitions, * Adams-Bashforth methods can be written: * <ul> @@ -77,30 +77,29 @@ import org.apache.commons.math4.util.MathArrays; * <li>k = 3: y<sub>n+1</sub> = y<sub>n</sub> + 23/12 s<sub>1</sub>(n) + [ -16/12 5/12 ] q<sub>n</sub></li> * <li>k = 4: y<sub>n+1</sub> = y<sub>n</sub> + 55/24 s<sub>1</sub>(n) + [ -59/24 37/24 -9/24 ] q<sub>n</sub></li> * <li>...</li> - * </ul></p> + * </ul> * * <p>Instead of using the classical representation with first derivatives only (y<sub>n</sub>, * s<sub>1</sub>(n) and q<sub>n</sub>), our implementation uses the Nordsieck vector with * higher degrees scaled derivatives all taken at the same step (y<sub>n</sub>, s<sub>1</sub>(n) * and r<sub>n</sub>) where r<sub>n</sub> is defined as: - * <pre> + * <div style="white-space: pre"><code> * r<sub>n</sub> = [ s<sub>2</sub>(n), s<sub>3</sub>(n) ... s<sub>k</sub>(n) ]<sup>T</sup> - * </pre> + * </code></div> * (here again we omit the k index in the notation for clarity) - * </p> * * <p>Taylor series formulas show that for any index offset i, s<sub>1</sub>(n-i) can be * computed from s<sub>1</sub>(n), s<sub>2</sub>(n) ... s<sub>k</sub>(n), the formula being exact * for degree k polynomials. - * <pre> + * <div style="white-space: pre"><code> * s<sub>1</sub>(n-i) = s<sub>1</sub>(n) + ∑<sub>j>0</sub> (j+1) (-i)<sup>j</sup> s<sub>j+1</sub>(n) - * </pre> + * </code></div> * The previous formula can be used with several values for i to compute the transform between * classical representation and Nordsieck vector. The transform between r<sub>n</sub> * and q<sub>n</sub> resulting from the Taylor series formulas above is: - * <pre> + * <div style="white-space: pre"><code> * q<sub>n</sub> = s<sub>1</sub>(n) u + P r<sub>n</sub> - * </pre> + * </code></div> * where u is the [ 1 1 ... 1 ]<sup>T</sup> vector and P is the (k-1)×(k-1) matrix built * with the (j+1) (-i)<sup>j</sup> terms with i being the row number starting from 1 and j being * the column number starting from 1: @@ -110,7 +109,7 @@ import org.apache.commons.math4.util.MathArrays; * P = [ -6 27 -108 405 ... ] * [ -8 48 -256 1280 ... ] * [ ... ] - * </pre></p> + * </pre> * * <p>Using the Nordsieck vector has several advantages: * <ul> @@ -119,7 +118,7 @@ import org.apache.commons.math4.util.MathArrays; * <li>it simplifies step changes that occur when discrete events that truncate * the step are triggered,</li> * <li>it allows to extend the methods in order to support adaptive stepsize.</li> - * </ul></p> + * </ul> * * <p>The Nordsieck vector at step n+1 is computed from the Nordsieck vector at step n as follows: * <ul> @@ -136,7 +135,7 @@ import org.apache.commons.math4.util.MathArrays; * [ ... | 0 ] * [ 0 0 ... 1 0 | 0 ] * [ 0 0 ... 0 1 | 0 ] - * </pre></p> + * </pre> * * <p>The P<sup>-1</sup>u vector and the P<sup>-1</sup> A P matrix do not depend on the state, * they only depend on k and therefore are precomputed once for all.</p>
