Apache Commons Math Version 2.0 RELEASE NOTES This is a major release. It combines bug fixes, new features and changes to existing features. Most notable among the new features are: - decomposition algorithms in the linear algebra package (LU, QR, Cholesky, SVD, eigen decomposition) which are based on the popular JAMA API (but much faster), - support for sparse matrices and vectors, - support for any field-based matrix (Complex, Fraction ...), - support for genetic algorithms - several new optimization algorithms (Dantzig's simplex for linear constrained problems, conjugate gradient, Brent) - support for curve fitting with special cases for harmonic and polynomial functions - support for state derivative in ODE step handlers - new multistep integrators (Adams-Bashforth and Adams-Moulton) with variable stepsize - regression algorithms - rank transformations - Mersenne twister pseudo random number generator This release is NOT source and binary compatible with earlier versions of Commons Math. Starting with version 2.0 of the library, the minimal version of the Java platform required to compile and use commons-math is Java 5. Users are encouraged to upgrade to this version, as in addition to new features, this release includes numerous bug fixes. Users of Commons Math 1.0-1.2 should recompile their code against the 2.0 jar. Most of the compilation errors users will encounter after the switch will be due to classes moved due to package reorganization. These errors are simply solved by adjusting the import statements in users code. Users can ask for help with migration or any other problem related to commons math by sending a message to the apache commons users mailing list: user@commons.apache.org. SUMMARY OF CHANGES New features: o Added curve fitting with a general case and two specific cases (polynomial and harmonic). o Added a way to limit the number of functions evaluations in optimizers (the number of iterations could already be limited) Thanks to Gilles Sadowski. o Added support for rank transformations. o Added an implementation of the Mersenne twister pseudo random number generator from Makoto Matsumoto and Takuji Nishimura o Added support for any type of field in linear algebra (FielxMatrix, FieldVector, FieldLUDecomposition) o The RealMatrixImpl implementation classes has been renamed Array2DRowRealMatrix to reflect its specificities and for consistency with the new implementations. The previous name is still available but is deprecated o Added a block-based storage type for dense matrices improving speed for large dimensions o Added AggregateSummaryStatistics class to support aggregation of SummaryStatistics. Thanks to John Bollinger. o Added general Field and FieldElement interfaces to allow generic algorithms to operate on fields. The library already provides several implementations: Complex, Fraction, BigFraction and BigReal o Added a SparseRealVector class that implements a sparse vector for the RealVector interface. o Added a getCovariance method to singular value decomposition Thanks to Dimitri Pourbaix. o Added method to walk matrix entries with or without changing them in the visitor design pattern sense. Three different orders can be used, row by row, column by column or optimized order according to internal storage. Optimized order should be preferred when no specific order is needed, because it will be more cache efficient. o Added an int/double hash map (OpenIntToDoubleHashMap) with much smaller memory overhead than standard java.util.Map (open addressing and no boxing). Thanks to Ismael Juma. o Support for one dimensional vectors has been added to the linear algebra package with a RealVector interface, a RealVectorImpl default implementation using a single double array to store elements and a RealVectorFormat for input/output. Thanks to Andreas Rieger. o New ODE integrators have been added: the explicit Adams-Bashforth and implicit Adams-Moulton multistep methods. As the implementations of these methods are based on Nordsieck vector rather than a traditional array of previous steps, they both have been improved to handle adaptive stepsize. These methods provide the same rich features has the existing ones: continuous output, step handlers, discrete events, G-stop ... o All ODE integrators now support setting a maximal number of evaluations of differential equations function. If this number is exceeded, an exception will be thrown during integration. This can be used to prevent infinite loops if for example error control or discrete events create a really large number of extremely small steps. o All step interpolators for ODE integrators now provide interpolation for both the state and its time derivatives. The interpolated derivatives are the exact derivatives of the interpolated state, thus preserving consistency. The general step handlers hence do not need to call the derivation function anymore. The fixed step handlers also get the time derivative of the state as an additional argument along with the state when they are called. o Switching functions can now throw dedicated SwitchException from all their method. At upper call level, the various ODE integrators handle these new exceptions and wrap them into IntegratorException instances, hence the integrators methods signature did not change. o Added factory methods to create Chebyshev, Hermite, Laguerre and Legendre polynomials. o Added add, subtract, negate, multiply and toString methods to PolynomialFunction. o Added a Legendre-Gauss integrator. o Added add/subtract/multiply/divide functions with integer parameters to Fraction o Added some utility functions to compute powers with integral types (int, long, BigInteger). o Added a scalb method in MathUtils. This method is similar to the method with same name added in java.lang.Math as of Java 6. o Added several convenience methods and constants for Vector3D and Rotation. o MATH-114: Added PearsonsCorrelation class to compute correlation matrices, standard errors and p-values for correlation coefficients. Thanks to John Gant. o MATH-114: Added Covariance class to compute variance-covariance matrices in new correlation package. o MATH-136: Added Spearman's rank correlation (SpearmansCorrelation). Thanks to John Gant. o MATH-152: Added support for multi-dimensional Fourier transform. Thanks to Remi Arntzen. o MATH-177: Added a new univariate sub-package below the optimization package. Thanks to Gilles Sadowski. o MATH-178: Added support for the Zipf distribution. Thanks to Paul Cowan. o MATH-202: Added the getSwitchingFunctions and clearSwitchingFunctions to the FirstOrderIntegrator interface and all its implementations o MATH-203: Added Mauro's patch to support multiple regression. Thanks to Mauro Talevi. o MATH-212: Added support for copying statistics. Changes to stats classes include copy constructor, static copy(-,-) and instance copy() methods. Added copy() to UnivariateStatistic and StorelessUnivariateStatistic interfaces. Thanks to Jason C. HandUber. o MATH-215: Added Fast Hadamard Transform. Thanks to Bernhard Grünewaldt. o MATH-219: Added removeData methods for the SimpleRegression class. This allows to support regression calculations across a sliding window of (time-based) observations without having to recalculate for the entire window every time. Thanks to Andrew Berry. o MATH-220: Added JAMA-like interfaces for eigen/singular problems. The implementation are based on the very quick dqd/dqds algorithms and some parts of the MRRR algorithm. This leads to very fast and accurate solutions. o MATH-220: Added JAMA-like interfaces for decomposition algorithms. These interfaces decompose a matrix as a product of several other matrices with predefined properties and shapes depending on the algorithm. These algorithms allow to solve the equation A * X = B, either for an exact linear solution (LU-decomposition, Cholesky decomposition) or an exact or least-squares solution (QR-decomposition). o MATH-222: Added beta distribution. Thanks to Ted Dunning. o MATH-222: Added probability density functions computation for distributions for which it is feasible. Thanks to Ted Dunning. o MATH-229: Added a removal feature for observations in descriptive statistics. Thanks to Cyril Briquet. o MATH-230: Added support for sparse matrix. Thanks to Sujit Pal and Ismael Juma. o MATH-231: Added an abstract matrix implementation simplifying extension by users. o MATH-232: Added Frobenius matrix norm. o MATH-234: Added setter methods for rows and columns in matrices. o MATH-236: Added nth root computation for complex numbers. Thanks to Bernhard Grünewaldt. o MATH-246: Added an optimizer for constrained linear problems based on 2-phases standard simplex. Thanks to Benjamin McCann. o MATH-247: Added a MathUtils method to check equality given some error bounds. Thanks to Benjamin McCann. o MATH-251: Added a BigFraction class that does not overflow when big numerators or denominators are used. Thanks to Benjamin Croizet. o MATH-256: Added Fraction.toString() o MATH-266: Added a clustering package with an implementation of the k-means++ algorithm Thanks to Benjamin McCann. o MATH-267: Added digamma function. Thanks to Ted Dunning. o MATH-277: Added a scalar multiply to the Complex class Thanks to Mark Anderson. o MATH-278: Added robust locally weighted regression (Loess). Thanks to Eugene Kirpichov. o MATH-279: Added a check for too few rows with respect to the number of predictors in linear regression Thanks to Michael Bjorkegren. Fixed Bugs: o Fixed an infinite loop encountered in some backward integration cases for ODE solvers. Thanks to Pascal Parraud. o Fixed inconsistencies in the naming scheme for static fields in Vector3D and Rotation with respect to the overall library. o MATH-177: Redesigned the optimization framework for a simpler yet more powerful API. Added non-linear conjugate gradient optimizer. o MATH-193: Javadoc and style fixes. Thanks to Michael Heuer and Sebb. o MATH-198: Added an error detection for missing imaginary character while parsing complex string Thanks to Frederick Salardi. o MATH-199: Detect numerical problems in Q.R decomposition for Levenberg-Marquardt estimator and report them appropriately Thanks to Mick. o MATH-200: Fixed several crashes in getCovariances() and guessParametersErrors() in AbstractEstimator when some parameters are bound. The methods now explicitly give result only about unbound parameters. Thanks to Plamen Petrov. o MATH-201: Fixed truncation error in t-test classes for large t values. Thanks to Peter Wyngaard. o MATH-204: Added root checks for the endpoints. Thanks to Mick. o MATH-205: Fixed formula in fast cosine transformer javadoc comments. Thanks to Roman Werpachowski. o MATH-207: Added Genetic Algorithm implementation. Thanks to David Stefka. o MATH-209: Fixed dimension error on output vector for the operate method in RealMatrixImpl and BigMatrixImpl classes. Thanks to Thomas Chust. o MATH-210: Changed return type for FirstOrderIntegrator.getSwitchingFunctions() to a collection of SwitchingFunction instances. This better suits the intended use of the method and fixes a visibility error since the previous return type referenced the package private SwitchState class. o MATH-213: Changed return type for FirstOrderIntegrator.integrate() to double in order to retrieve exact stop time. This allows to handle properly integration interruption due to an EventHandler instance asking to stop the integration when its associated event is triggered. The state was already set to the current state at interruption time, but it was difficult to get the corresponding time (it involved setting a step handler monitoring the last step specially). o MATH-214: Replaced size adjustment of all steps of fixed steps Runge-Kutta integrators by a truncation of the last step only. o MATH-216: Improved fast Fourier transform efficiency. Thanks to Cyril Briquet. o MATH-221: Changed the Complex.equals() method so that it considers +0 and -0 are equal, as required by IEEE-754 standard. Thanks to Dieter Roth. o MATH-223: Greatly improved QR-decomposition speed using transposed matrices internally. Thanks to John Mulcahy. o MATH-226: Fixed an error in CorrelatedRandomVectorGenerator leading to a component of the generated vector being constant. Thanks to Stuart Siegel. o MATH-227: Fixed F distribution inverse CDF computation for small denominator degrees of freedom. Thanks to Joerg Henning. o MATH-238: Fixed an error in gcd computation for large values. Thanks to Christian Semrau. o MATH-240: Fixed error in factorial computation for 17 <= n <= 20. Thanks to Christian Semrau. o MATH-241: Fixed error in binomial coefficient computation. Thanks to Christian Semrau. o MATH-243: Fixed an error in computing gcd and lcm for some extreme values at integer range boundaries. Thanks to Christian Semrau. o MATH-248: Greatly improved multiplication speed for sparse matrices o MATH-252: Fixed a comparison error when two different fractions evaluate to the same double due to limited precision. o MATH-253: Fixed threading issues with MathException and MathRuntimeException Thanks to Sebb. o MATH-254: Fixed threading issues with UnivariateRealSolverUtils factory Thanks to Sebb. o MATH-255: Reduced visibility of MessagesResources_fr.contents field to private Thanks to Sebb. o MATH-257: Fixed inconsistent access to multidimensional array in FastFourierTransformer Thanks to Sebb. o MATH-263: Added getNorm1, getNormInf, distance1 and distanceInf to the Vector3D class o MATH-264: Added an utility equality method between double numbers using tolerance in ulps (Units in Last Position) Thanks to Gilles Sadowski. o MATH-265: Added distance1, distance and distanceInf utility methods for double and int arrays in MathUtils Thanks to Benjamin McCann. o MATH-272: Fixed a problem when setting some variables (several variables were set instead of only one) Thanks to Benjamin McCann. o MATH-273: Fixed a wrong check for basic variables Thanks to Benjamin McCann. o MATH-274: Fixed detection of not positive definite matrices in Cholesky decomposition o MATH-280: The behavior of the bracket method in UnivariateRealSolverUtils has been changed to return successfully when a tentative bracketing interval has a root exactly at one of its end points. Previously, such intervals triggered an exception. o MATH-281: Fixed an error in RealMatrix javadoc Changes: o Changed the return type of the various interpolation algorithms to the specific implementation of UnivariateRealFunction each one uses Thanks to Gilles Sadowski. o Completed internationalization of all error messages o Integration algorithms now can have both relative and absolute accuracy settings. o The analysis package has been reorganized with several sub-packages. o The ODE integrators now support several step handlers at once, instead of just one. This is more consistent with event handlers management. The setStepHandler method has therefore been replaced by addStephandler, the getStepHandler method has been replaced by getStepHandlers which returns a Collection and a clearStepHandlers method has been added. o Events handlers in the ODE package now also provide the switching function variation (increasing/decreasing) when an event occurs o Clarified the ODE package by breaking in into several sub-packages and renaming classes (SwitchingFunctions/EventHandler, SwitchingFunctionsHandler/CombinedEventsManager) o The FirstOrderDifferentialEquations, FirstOrderIntegrator and FixedStepHandler interfaces now extends Serializable, allowing integrators, problems and handlers to be embedded into users Serializable classes. o Replaced public no argument constructors with IDENTITY or ZERO static instances for immutable classes Vector3D and Rotation. o Greatly improved RealMatrixImpl and BigMatrixImpl performances, both in terms of speed and in terms of temporary memory footprint. o Starting with version 2.0 of the library, the minimal version of the Java platform required to compile and use commons-math is Java 5. This version is widely deployed now on many systems. It brings new important features for specific mathematical developments, for example new functions (log10, cbrt, ulp, signum, cosh, sinh, tanh, hypot, expm1, log1p), autoboxing, MathContext or RoundingMode. It also brings important features for general development, for example enums, generics or annotations. o Removed deprecated features. This includes the following changes. Factory-based instantiation replaced by setter injection in 1.2 in several classes have been removed. Protected fields in matrices implementations have been declared final and private. Identity factory methods moved to MatrixUtils class have been removed. Complex utilities methods that have been superseded by Complex instance methods have been removed. o MATH-189: Changed FractionFormat to extend NumberFormat. o MATH-217: Changed OLS regression implementation added in MATH-203 to use QR decomposition to solve the normal equations. o MATH-218: The root solvers and the integrators now take the function to solve as a parameter to the solve/integrate methods, thus allowing to reuse the same solver/integrator for different functions. o MATH-242: Forced symmetry in binomialCoefficientLog and added test cases for MathUtils. Thanks to Christian Semrau. o MATH-276: Optimized Complex isNaN(), isInfinite() by moving computation to constructor. Thanks to Mark Anderson. For complete information on commons-math, including instructions on how to submit bug reports, patches, or suggestions for improvement, see the commons-math website: http://commons.apache.org/math/