01b6aa7857d1b6fb836e8ead2c540cf7fd8caeb6
1270033299
Phil Steitz
Tagged 2.1 release.

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/tags/MATH_2_1@929473 13f79535-47bb-0310-9956-ffa450edef68

01b6aa7857d1b6fb836e8ead2c540cf7fd8caeb6
0039ce2ffb2d24fddfa5020d3720bbff26e450fa
1269735720
Phil Steitz
Tagged 2.1 RC3

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/tags/MATH_2_1_RC3@928309 13f79535-47bb-0310-9956-ffa450edef68

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svn:eol-style native

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Phil Steitz
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Sebastian Bazley
JIRA: MATH-360 Fix use of wrong variable in SmoothingBicubicSplineInterpolatorTest.testPreconditions()

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Oops - remove spurious bracket

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Replace deprecated issueLinkTemplate.

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Tab police

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Sebastian Bazley
Suppress unused variable warnings

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Unnecessary semi-colons

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Sebastian Bazley
Unused import

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Sebastian Bazley
Translate double-space into new-line when generating release notes

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typo

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Sebastian Bazley
Fix up project name

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Sebastian Bazley
Re-arrange description to make it easier to paste into the generated release notes
(It's also a bit easier to read in the source).

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Phil Steitz
Edited description of MATH-356.

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Phil Steitz
Checkstyle fixes, @since tags.

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Phil Steitz
Dropped trailing spaces.

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Phil Steitz
Updated to reflect recent bug fixes.

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Phil Steitz
Dropped broken report.

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1269468711
Luc Maisonobe
Fixed an error in events handling in ODE solvers. In some rare cases, events occurring close to a step start were handled without truncating the step, making them appear as is they occurred close to the step end
JIRA: MATH-358

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Add compatibility notes from changes.xml

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Sebastian Bazley
Bugzilla => JIRA; CVS => SVN

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Gilles Sadowski
Issues 356 and 357.


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Added better release description including summary of compatability breaks.

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Phil Steitz
Updated release notes, download page.

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Phil Steitz
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Prepare for 2.1 release.

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Phil Steitz
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Corrected an error in sample code.  The example did not illustrate the technique being described.

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Eliminated references to factory methods dropped in math 2.0.

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Phil Steitz
* Added density functions to remaining continuous distributions (F, T, Weibull, Cauchy).
* Deprecated HasDensity interface.
* Added density tests.
* Made Brent Solver (inverse cum) absolute accuracy configurable for all continuous distributions.

JIRA: MATH-332
JIRA: MATH-282
Thanks to Mikkel Meyer Andersen

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MATH-335 Fraction.hashCode() inconsistent with Fraction.equals()
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Issues
  https://issues.apache.org/jira/browse/MATH-348
  https://issues.apache.org/jira/browse/MATH-349



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:100644 100644 4f4985af3a1dfeb2fa053d66ad84099ba0cc00b0 7347a58087b2f8debffcbc98bee3bb3cadfb9996 M	src/main/java/org/apache/commons/math/distribution/WeibullDistributionImpl.java
:100644 100644 4d9f72a8cabc99ab7363a890dcfbd922d898134d 7d1026f901291c04daff37c4c5248251452fe3e9 M	src/main/java/org/apache/commons/math/distribution/ZipfDistribution.java
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fcabfb5a821e31e42aa15740ebc7d740e689819f
1268089052
Phil Steitz
Resolved multiple problems leading to inaccuracy and/or failure to compute Normal, ChiSquare and 
Poisson probabilities, Erf and Gamma functions.

JIRA: MATH-282
JIRA: MATH-301

Summary of changes:

* BrentSolver has been changed to expose its configured absolute accuracy. This solver is used by
  the default inverse cum implementation in AbstractContinuousDistribution and the hard-coded setting
  (1E-6) was limiting accuracy in inverse cumulative probability estimates. AbstractContinuousDistribution
  was changed to allow distributions to set this value and NormalDistributionImpl was changed to set it to
  1E-9 by default and allow users to configure it via a constructor argument.

* AbstractContinuousDistribution and AbstractIntegerDistribution inverseCumulativeProbability methods
  have been modified to check for NaN values returned by cumulativeProbability and throw MathExceptions
  when this happens.

* The criteria for choosing between the Lanczos series and continued fraction expansion when computing
  regularized gamma functions has been changed to (x >= a + 1). When using the series approximation
  (regularizedGammaP), divergence to infinity is checked and when this happens, 1 is returned.

* When scaling continued fractions to (try to) avoid divergence to infinity, the larger of a and b is
  used as a scale factor and the attempt to scale is repeated up to 5 times, using successive powers
  of the scale factor.

* The maximum number of iterations used in estimating cumulative probabilities for PoissonDistributionImpl
  has been decreased from Integer.MAX_VALUE to 10000000 and made configurable.


git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@920558 13f79535-47bb-0310-9956-ffa450edef68

fcabfb5a821e31e42aa15740ebc7d740e689819f
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:100644 100644 c92f346e6d2d7785816a01c42a9d62d4130460a7 478de19292c24845fa0533e952a76955084a6926 M	src/test/java/org/apache/commons/math/special/ErfTest.java

46af8180a7dca91b3a59d587b35ddcb56d508dc4
1268007110
Niall Kegan Pemberton
Re-generate the download pages using the new commons-build-plugin .12 (via commons-parent version 13)

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@920156 13f79535-47bb-0310-9956-ffa450edef68

46af8180a7dca91b3a59d587b35ddcb56d508dc4
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1492acad24b4b39ceda3a25ee00c66bb7b5c41e5
1268006747
Niall Kegan Pemberton
Upgrade to version 13 of commons-parent

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@920154 13f79535-47bb-0310-9956-ffa450edef68

1492acad24b4b39ceda3a25ee00c66bb7b5c41e5
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dddb89860169cc7b25d628156e9e9b2060f671aa
1268000544
Luc Maisonobe
fixed wrong subscript

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@920132 13f79535-47bb-0310-9956-ffa450edef68

dddb89860169cc7b25d628156e9e9b2060f671aa
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31811262d7bffbc68503029ee243b23d2ee2c059
1268000358
Luc Maisonobe
improved documentation of ODE package, including the new jacobians part

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@920131 13f79535-47bb-0310-9956-ffa450edef68

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2c281e086ba98e3c2dde12dda126035c2088fac6
1267959573
Luc Maisonobe
separated ODEWithJacobians from ParameterizedODE:
when jacobians are already available, there is no need to have a setParameter method

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@919963 13f79535-47bb-0310-9956-ffa450edef68

2c281e086ba98e3c2dde12dda126035c2088fac6
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:000000 100644 0000000000000000000000000000000000000000 14e279e48ba7cbcbda1ff1740428ed5cbec19f2a A	src/main/java/org/apache/commons/math/ode/jacobians/ODEWithJacobians.java
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90f8b1ac97efc2e10f58be02ce8e5a52bef7df4c
1267911222
Luc Maisonobe
suppressed a warning for unused constructor
the constructor is called only by externalization

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@919856 13f79535-47bb-0310-9956-ffa450edef68

90f8b1ac97efc2e10f58be02ce8e5a52bef7df4c
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78ad153bb7fc93721b8c3c348a3ca5c23dccd94a
1267911037
Luc Maisonobe
fixed findbugs errors

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@919855 13f79535-47bb-0310-9956-ffa450edef68

78ad153bb7fc93721b8c3c348a3ca5c23dccd94a
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c09c944f91b2c7a502e2ccdc7c8b921798ca85cb
1267908602
Luc Maisonobe
fixed javadoc errors

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@919848 13f79535-47bb-0310-9956-ffa450edef68

c09c944f91b2c7a502e2ccdc7c8b921798ca85cb
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b25bec37c059442830ee749c6653ff83e8510259
1267907935
Luc Maisonobe
added event handling to ODE integrators with jacobians

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@919844 13f79535-47bb-0310-9956-ffa450edef68

b25bec37c059442830ee749c6653ff83e8510259
:000000 100644 0000000000000000000000000000000000000000 c567e9c70449196174ab97f230d21d15962b84c3 A	src/main/java/org/apache/commons/math/ode/jacobians/EventHandlerWithJacobians.java
:100644 100644 c2ede1a674cd0998d063ff6e850796bb310638ec e21438821ab26a8c6a8b1192fba688f29595985e M	src/main/java/org/apache/commons/math/ode/jacobians/FirstOrderIntegratorWithJacobians.java
:100644 100644 9a851010020d39b8eafd6d8f9dd13f5cd535ec3f 78d1d34cc877d0c5e03adccc091af79d2a107858 M	src/test/java/org/apache/commons/math/ode/jacobians/FirstOrderIntegratorWithJacobiansTest.java

5d16b13bf54b319705e352638205a8c1c204a6cb
1267904357
Luc Maisonobe
added miscellaneous methods to get some feedback on the integration process
(step start, step size, number of evaluations ...)

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@919829 13f79535-47bb-0310-9956-ffa450edef68

5d16b13bf54b319705e352638205a8c1c204a6cb
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1161903b77703b1a6487d2f768703011ef58dcad
1267901667
Luc Maisonobe
Set up a named Wrapper inner class to map state plus jacobians into compound state
for ODE integration with added variational equations

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@919815 13f79535-47bb-0310-9956-ffa450edef68

1161903b77703b1a6487d2f768703011ef58dcad
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87ccced5653a90bbd8f05e918298e4ea24aff875
1267807150
Luc Maisonobe
improved test coverage

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@919481 13f79535-47bb-0310-9956-ffa450edef68

87ccced5653a90bbd8f05e918298e4ea24aff875
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da4756ac563ffb33a8b716f066525d15fa0fd67b
1267807082
Luc Maisonobe
fixed handling of the time-derivatives of jacobians
simplified copy and serialization

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@919480 13f79535-47bb-0310-9956-ffa450edef68

da4756ac563ffb33a8b716f066525d15fa0fd67b
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b283304b93e880d62d15fecfd31b2a37a9407ad5
1267806956
Luc Maisonobe
Fixed a problem with getInterpolatedDerivatives returning zero derivatives when
an ODE step handler is configured to not use interpolation. It now returns a
constant but non-zero value consistent with at least one point inside the step


git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@919479 13f79535-47bb-0310-9956-ffa450edef68

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389154b79c80ea7368f0cce9bbba38540a3f4580
1267736186
Luc Maisonobe
typos

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@919178 13f79535-47bb-0310-9956-ffa450edef68

389154b79c80ea7368f0cce9bbba38540a3f4580
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556c577089a0d270bb68e4da55a13cd98ecc15c8
1267735808
Luc Maisonobe
explained test rationale

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Luc Maisonobe
added package.html for ode.jacobians

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Luc Maisonobe
fixed an index error in dy/dy0 computation

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Luc Maisonobe
Simplified names of ODE with Jacobians integration classes
Added step handling for this feature

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Luc Maisonobe
Fixed too stringent interval check in Brent solver:
initial guess is now allowed to be at either interval end
JIRA: MATH-347

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Luc Maisonobe
Added a way to compute both the final state in an Initial Value Problem (IVP)
for Ordinary Differential Equations (ODE) and its derivatives with respect to
initial state and with respect to some problem parameters. This allows wrapping
ODE solvers into optimization or root finding algorithms, which in turn can be
used to solve Boundary Value Problems (BVP). There are no implementations (yet)
of BVP solvers in the library.


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Luc Maisonobe
updated an exclusion filter for findbugs after recent changes in eigen decomposition

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Luc Maisonobe
fixed a checkstyle warning concerning extra parentheses

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Luc Maisonobe
fixed variables declaration order to match checkstyle rules

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Luc Maisonobe
removed tab

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Luc Maisonobe
fixed javadoc

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Phil Steitz
Removed trailing spaces.

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Phil Steitz
Removed trailing spaces.

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Luc Maisonobe
removed personal webpages URL

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Luc Maisonobe
added a test that was used some time ago while looking at MATH-341

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Luc Maisonobe
removed a compilation warning about unused variable

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Luc Maisonobe
removed unreachable code
JIRA: MATH-343

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Luc Maisonobe
Fixed wrong return values when enpoints are roots in Brent solver with a user provided initial guess
JIRA: MATH-344

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Luc Maisonobe
Fixed a missing bracketing check of initial interval in Brent solver
JIRA: MATH-343

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Dimitri Pourbaix
MATH-432 fixed

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Phil Steitz
Added test utility inadvertently omitted from r910264. JIRA: MATH-323.

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Dimitri Pourbaix
Dummy tests removed after revision 910475

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Dimitri Pourbaix
MATH-333 fixed

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Phil Steitz
Added SemiVariance. JIRA: MATH-323. Reported and patched by Larry Diamond.

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Phil Steitz
Eliminated trailing spaces.

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1265746056
Luc Maisonobe
Added a warning in the getCoefficients method documentation for
PolynomialFunctionLagrangeForm. Computation may be ill-conditioned
so this method should be used with care.
JIRA: MATH-341


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1265231994
Luc Maisonobe
Fixed an error in BigFraction multiplication for large numerators that don't fit in a primitive int.

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@906251 13f79535-47bb-0310-9956-ffa450edef68

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098d6d5d487dc4fc3b11107f9f5e204b73b19378
1264784908
Luc Maisonobe
fixed a spurious exception in EigenDecompositionImpl when a 3x3 block had two identical eigenvalues

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@904561 13f79535-47bb-0310-9956-ffa450edef68

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01bc6a7b664af64cc7c74abc5a96a8809880a7d8
1264707751
Luc Maisonobe
added min/max getters for real vectors
For compatibility reasons, these methods have been put in the topmost abstract class but not in the interface yet. It could be pushed to the interface when next major version will be released.
JIRA: MATH-334

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@904231 13f79535-47bb-0310-9956-ffa450edef68

01bc6a7b664af64cc7c74abc5a96a8809880a7d8
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d06e7b7c8e646ff489a5dfba47dfcb283a194e9b
1264690915
Luc Maisonobe
Fixed automatic step initialization in embedded Runge-Kutta integrators.
The relative tolerance setting was never used, only the absolute tolerance was used.
JIRA: MATH-338


git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@904112 13f79535-47bb-0310-9956-ffa450edef68

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034b4d68157defc3199f618fdd2d3a487306dbc2
1264543033
Luc Maisonobe
removed unused import

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@903446 13f79535-47bb-0310-9956-ffa450edef68

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1264542980
Luc Maisonobe
typos

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@903442 13f79535-47bb-0310-9956-ffa450edef68

af4ee07f71b8e44477d947fcd628f5ed759c2c70
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8acd07911a2831d86842ed1fff10ce26c5f41264
1264542839
Luc Maisonobe
added Eugene Kirpichov's patch to ignore zero weights in Loess interpolation
JIRA: MATH-296

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@903440 13f79535-47bb-0310-9956-ffa450edef68

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0fb163458b263830d282bd6c6787ea7c8725a5ac
1264501692
Phil Steitz
Disabled testNextPoissonConsistency pending resolution of MATH-282.

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a3b45ceffede0bc816d095e161ed2ebe43628816
1264474380
Sebastian Bazley
Document why OK to suppress unchecked warning
Move tag as close as possible to site of warning

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d25a5b451c5543e058c718da9f36fd9ab766a432
1264471662
Sebastian Bazley
Document why OK to suppress unchecked warning

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@903047 13f79535-47bb-0310-9956-ffa450edef68

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1264471646
Sebastian Bazley
Document why OK to suppress unchecked warning
Move tag as close as possible to site of warning

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@903046 13f79535-47bb-0310-9956-ffa450edef68

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09e3ca2bbf929b26cb5e84b5fa80fd2a7089416f
1264471209
Sebastian Bazley
Document why OK to suppress unchecked warning

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@903044 13f79535-47bb-0310-9956-ffa450edef68

09e3ca2bbf929b26cb5e84b5fa80fd2a7089416f
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79522bbb5869778ec805ee001710eccc6a4d2ca0
1264446557
Sebastian Bazley
Fix typo in copy() code

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@902934 13f79535-47bb-0310-9956-ffa450edef68

79522bbb5869778ec805ee001710eccc6a4d2ca0
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e14f74a96a85dc67b8f430746b01449c4b0f100c
1264446300
Sebastian Bazley
Does not make sense for count variable to be public

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@902931 13f79535-47bb-0310-9956-ffa450edef68

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f3f90a33c91ec902362a86a0a0f431cfe626764c
1264446272
Sebastian Bazley
Make private static fields final

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@902930 13f79535-47bb-0310-9956-ffa450edef68

f3f90a33c91ec902362a86a0a0f431cfe626764c
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3cf54d27bd6d6f51d31d363543e0cab9513b4a73
1264446236
Sebastian Bazley
Document field thread-safety

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@902929 13f79535-47bb-0310-9956-ffa450edef68

3cf54d27bd6d6f51d31d363543e0cab9513b4a73
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5d1db75c0eb4e6cdb28d3a64017ebd60ae79e2d0
1264446206
Sebastian Bazley
Make private constant final

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@902928 13f79535-47bb-0310-9956-ffa450edef68

5d1db75c0eb4e6cdb28d3a64017ebd60ae79e2d0
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aecfd52634ddc7a1ccc0ad68477ef96415a860b5
1264185678
Sebastian Bazley
Fix may be null warnings

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@902216 13f79535-47bb-0310-9956-ffa450edef68

aecfd52634ddc7a1ccc0ad68477ef96415a860b5
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01e82da7f9b3caab2e82206e366aa883c5c3cfd1
1264185655
Sebastian Bazley
FIx deprecation warnings

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@902215 13f79535-47bb-0310-9956-ffa450edef68

01e82da7f9b3caab2e82206e366aa883c5c3cfd1
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ff0352df4a4f8c2a1480f3d6f877beb909bcc025
1264185628
Sebastian Bazley
Javadoc fixes

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ff0352df4a4f8c2a1480f3d6f877beb909bcc025
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3081ee1490074bb3ecf276137c6dc8836da8775e
1264184861
Sebastian Bazley
Fix missing @Override and @Deprecated annotations

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@902203 13f79535-47bb-0310-9956-ffa450edef68

3081ee1490074bb3ecf276137c6dc8836da8775e
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380b8f9c992064e961950cbe90f1c93d958d98c3
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Sebastian Bazley
Remove suite() methods

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@902201 13f79535-47bb-0310-9956-ffa450edef68

380b8f9c992064e961950cbe90f1c93d958d98c3
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de335323ecca89e16666bd1be2da92967c3c4009
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Sebastian Bazley
Unused import

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Sebastian Bazley
Ignore lib/

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Sebastian Bazley
Synch. with test cases listed in pom.xml

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@902089 13f79535-47bb-0310-9956-ffa450edef68

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fixed link typo

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@900457 13f79535-47bb-0310-9956-ffa450edef68

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aab15d03dfa62169c0c1c7c24639b0ac3f4a8ae6
1263832278
Luc Maisonobe
improved javadoc

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aab15d03dfa62169c0c1c7c24639b0ac3f4a8ae6
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523df0c13719150b1397a6094f410274bfaf1475
1263672077
Phil Steitz
Fixed regression in Frequency.getPct(Object) introduced in 2.0. Cumulative
percent was being returned for Object arguments in place of percent.

JIRA: MATH-329
Reported by Will Wu

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@900016 13f79535-47bb-0310-9956-ffa450edef68

523df0c13719150b1397a6094f410274bfaf1475
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39e2ad8af8fdedac51144158061cb31e7863c3a1
1262281936
Luc Maisonobe
Singular Value Decomposition now computes either the compact SVD (using only positive singular values) or truncated SVD (using a user-specified maximal number of singular values).
Fixed Singular Value Decomposition solving of singular systems.
JIRA: MATH-320, MATH-321


git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@894908 13f79535-47bb-0310-9956-ffa450edef68

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d607614a8827a1a5fab587b6e692601d5673833e
1262215600
Phil Steitz
Updated to reflect recent commits.

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@894738 13f79535-47bb-0310-9956-ffa450edef68

d607614a8827a1a5fab587b6e692601d5673833e
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e62bb3b7a7a3bbf0f2139a5d111c05f2f09d3221
1262215021
Luc Maisonobe
changed SVD to compute either compact SVD (using only positive singular values)
or truncated SVD (using only singular values up to a user-specified max number)
started fix of SVD solver that did not compute a least square solution
the fix is not complete yet as it seems the solution does not really gives the
smallest possible residuals. See for example the commented out parts of
testMath320A in SingularValueSolverTest.
JIRA: MATH-320

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@894735 13f79535-47bb-0310-9956-ffa450edef68

e62bb3b7a7a3bbf0f2139a5d111c05f2f09d3221
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0fd871ca2c7b94bde0237cdf2f688460a05c1895
1262214203
Phil Steitz
Added gcd(long, long), lcm(long, long) methods. JIRA: MATH-239.

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@894730 13f79535-47bb-0310-9956-ffa450edef68

0fd871ca2c7b94bde0237cdf2f688460a05c1895
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Phil Steitz
Added @since tags for new methods. JIRA: MATH-287

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3962779401061b95c64e3a73c02ce608f36b4ece
1262136460
Phil Steitz
Deprecated addValue(Integer). JIRA: MATH-260.

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@894529 13f79535-47bb-0310-9956-ffa450edef68

3962779401061b95c64e3a73c02ce608f36b4ece
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47c5f8a397f83650d1f3b590bdfbaa2b00758e5b
1262135012
Phil Steitz
Changed weighted variance computational formula to use Chan-Golub method (consistent with unweighted version).

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@894528 13f79535-47bb-0310-9956-ffa450edef68

47c5f8a397f83650d1f3b590bdfbaa2b00758e5b
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59cfef1afb36913df921966dbf2dd8ad0545425a
1262116957
Phil Steitz
Fixed type from r894472. JIRA: MATH-287

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@894474 13f79535-47bb-0310-9956-ffa450edef68

59cfef1afb36913df921966dbf2dd8ad0545425a
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44492acc710f898ea50257275adf3064f1025fff
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Phil Steitz
Added WeightedEvaluation interface and added evaluate(values, weights) to weighted statistics implementations. JIRA: MATH-287.

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@894472 13f79535-47bb-0310-9956-ffa450edef68

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1262098898
Phil Steitz
Fixed contributor alpha sort.

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1262089498
Luc Maisonobe
fixed a wrong implementation of the Linf vector norm
JIRA: MATH-326

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@894367 13f79535-47bb-0310-9956-ffa450edef68

d6555de715889237b7be11639d164e7098862003
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1262014203
Luc Maisonobe
fixed checkstyle warnings

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0263d1f5e0f736ed86b49fe40358bf5446ad6940
1262013803
Luc Maisonobe
improved test coverage (now somewhere between 99% and 100%)

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@894186 13f79535-47bb-0310-9956-ffa450edef68

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1262013660
Luc Maisonobe
fixed a few remaining unnecessary copy
added more constructors

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@894185 13f79535-47bb-0310-9956-ffa450edef68

8404231006b9d6670dabf742d99a5df48a9b1c34
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340af239a361695d8c9c2b7009de45f12c17bead
1261947981
Luc Maisonobe
fixed a forgotten replacement of divide method
JIRA: MATH-307

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340af239a361695d8c9c2b7009de45f12c17bead
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dc3d8e687d1678fc9557bc8ed85104ebaac96c41
1261944188
Luc Maisonobe
adding rounding mode and scale as per 1.2
JIRA: MATH-307

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@894107 13f79535-47bb-0310-9956-ffa450edef68

dc3d8e687d1678fc9557bc8ed85104ebaac96c41
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8ea4ff364c2d5961fb6afc2c18ee40c25b5f06c3
1261939696
Luc Maisonobe
removed support for non-zero default values in OpenMapRealVector
JIRA: MATH-312

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@894093 13f79535-47bb-0310-9956-ffa450edef68

8ea4ff364c2d5961fb6afc2c18ee40c25b5f06c3
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c44b2009e01632c51980c22d05340c769cbf34c9
1261935217
Luc Maisonobe
added tests showing that issues MATH-303 and MATH-304 are both invalid.
Jira: MATH-303, MATH-304

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@894083 13f79535-47bb-0310-9956-ffa450edef68

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a9ececc5b2cea19b433fde33f45ccd05634afbce
1261510210
Luc Maisonobe
Fixed a convergence discrepancy with respect to theory in Gragg-Bulirsch-Stoer integrator.
JIRA: MATH-324


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663b0539f6b7fd2a68c9af5337acddf4f3a9e478
1260999853
Luc Maisonobe
Fixed a wrong dimension check in SVD solver
thanks to Dimitri for identifying and solving this

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@891436 13f79535-47bb-0310-9956-ffa450edef68

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b704ce8686d77cd8c2b28374a40ee42d806be563
1260759220
William Barker
Add an optimized dotProduct to OpenMapRealVector.
Slightly modified from contribution by Jake Mannix.
JIRA: MATH-317


git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@890159 13f79535-47bb-0310-9956-ffa450edef68

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dd7c8dfb0a53aae71716d23b411efbfc934fa2d0
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William Barker
Removing the mapTo* metheds from OpenMapRealVector, and use the base class methods instead

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@890023 13f79535-47bb-0310-9956-ffa450edef68

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136132c0e8a4ac69ad12adf445dd35895784b36f
1260659732
Luc Maisonobe
added composition features for real functions
JIRA: MATH-313

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@890002 13f79535-47bb-0310-9956-ffa450edef68

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7f94e8515fa43bae5ff044d11dd7ef340d8fd9f6
1260659461
Luc Maisonobe
fixed checkstyle errors

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@889999 13f79535-47bb-0310-9956-ffa450edef68

7f94e8515fa43bae5ff044d11dd7ef340d8fd9f6
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4ae6314f2ae3a3bbb7c121be60c244e8d36a4424
1260513500
William Barker
Initial fixes to the iterators.

This fixes the default sparseIterator problem where a RealVector only contains zero elements, and add a sparseIterator to the OpenMapRealVector.

Still TODO:
1) add unit tests
2) remove *mapTo and *mapToSelf from OpenMapRealVector
3) fix javadocs
4) remove support for non-zero default values in OpenMapRealVector 


git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@889516 13f79535-47bb-0310-9956-ffa450edef68

4ae6314f2ae3a3bbb7c121be60c244e8d36a4424
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26ca02d94e85f6e6b8c9db96c0411b901d6c89fc
1260399371
Luc Maisonobe
Added mapping and iteration methods to vectors.
Provided a default implementation for the numerous simple methods in the RealVectorInterface.


git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@889008 13f79535-47bb-0310-9956-ffa450edef68

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9b6224b2d4c5c34e349d582dc105daec48411659
1260398964
Luc Maisonobe
added UnivariateRealFunction type implementations of the java.lang.Math methods

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@889007 13f79535-47bb-0310-9956-ffa450edef68

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1ceccd4179c044af7197f30adaa85b33fb11a56e
1260398796
Luc Maisonobe
removed trailing whitespace

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1260326220
Sebastian Bazley
Unnecessary casts

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1260326188
Sebastian Bazley
Unnecessary ;

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1260326051
Sebastian Bazley
Tab police

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e0da30042a3e9ab15f359aeb4e321d7e508db07c
1260325802
Sebastian Bazley
Unnecessary casts; tab police

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@888680 13f79535-47bb-0310-9956-ffa450edef68

e0da30042a3e9ab15f359aeb4e321d7e508db07c
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b3ed2415fc58b34667d99f077bae6c8e38b7aced
1260140695
Luc Maisonobe
Fixed an error in handling of very close events during ODE integration
JIRA: MATH-322

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@887794 13f79535-47bb-0310-9956-ffa450edef68

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cc7e3e7fe46844f068c622cf439ef4b654d971ec
1259531616
Luc Maisonobe
Prevent NaN to occur for singular matrices
Numerical inaccuracies in the underlying eigendecomposition could induce
very small negative eigenvalues, so the square root produced NaNs. The
eigenvalues really cannot be negative, so it is safe to replace the negative
ones by 0.
There are remaining problems with singular matrices:
 - the singular vectors also contain NaNs
 - the solver does not really work in least square sense and
   complain about singular matrices
JIRA: MATH-320 

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@885279 13f79535-47bb-0310-9956-ffa450edef68

cc7e3e7fe46844f068c622cf439ef4b654d971ec
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bd345d954b85ef8eb3867c5044f933e34df0c124
1259531271
Luc Maisonobe
replaced duplicated strings by a single static string in many classes
this will later allow enabling the MultipleStringLiterals rule in checkstyle
(there are many other duplicated strings, so this cannot be enabled yet, I'll
do another pass on it later on)

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@885278 13f79535-47bb-0310-9956-ffa450edef68

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9ca7fb78ef078e05e164cab0ad742c6ae49374ae
1259529710
Luc Maisonobe
fixed some NaN appearing in eigenvectors when null pivots occurred in dstqds or dqds algorithms
this is a partial fix for MATH-297 but not a complete one as for example computing the
eigendecomposition if identity leads to three times the same vector ...
JIRA: MATH-297

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@885268 13f79535-47bb-0310-9956-ffa450edef68

9ca7fb78ef078e05e164cab0ad742c6ae49374ae
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788953ec424f23e2e26b3eb09edffc2cd44c3687
1259364436
Luc Maisonobe
removed an unneeded constant

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@885049 13f79535-47bb-0310-9956-ffa450edef68

788953ec424f23e2e26b3eb09edffc2cd44c3687
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1e8de82657aba6bbe9129b94d78832c93e4072a4
1259364252
Luc Maisonobe
added a test with a singular matrix
updated class to Junit4

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@885048 13f79535-47bb-0310-9956-ffa450edef68

1e8de82657aba6bbe9129b94d78832c93e4072a4
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138baec1c778c2ea1dc1a6efe6d5e76a3b072b1d
1259358338
Phil Steitz
Fixed an overflow error in MathUtils.distance that was causing KMeansPlusPlusClusterer to fail with a NullPointerException when
component distances between points exceeded Integer.MAXVALUE.
JIRA: MATH-305
Reported by Erik van Ingen

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@885027 13f79535-47bb-0310-9956-ffa450edef68

138baec1c778c2ea1dc1a6efe6d5e76a3b072b1d
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ca1ca9250b99dd49434468aa5530eb00b2f0680d
1259355904
Phil Steitz
Added toString.

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@885013 13f79535-47bb-0310-9956-ffa450edef68

ca1ca9250b99dd49434468aa5530eb00b2f0680d
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5835bcd27f6d3d1ce163d1c33309bdd5b0b86e33
1259355814
Phil Steitz
Fixed test case for number of generations evolved.

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@885009 13f79535-47bb-0310-9956-ffa450edef68

5835bcd27f6d3d1ce163d1c33309bdd5b0b86e33
:100644 100644 32af2c4773f8709949aeb3298fc5d9a893f5224c 365d654cbe3809904307495ead7aa2ef6b598993 M	src/test/java/org/apache/commons/math/genetics/GeneticAlgorithmTestBinary.java

6e242983eec762a3ecf24824633550e09287e9bb
1258919454
Phil Steitz
Added generationsEvolved property to GeneticAlgorithm to track the number
of generations evolved by the evolve() method before reaching the StoppingCondition.
JIRA: MATH-315
Reported and patched by Mikkel Meyer Andersen

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@883132 13f79535-47bb-0310-9956-ffa450edef68

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Phil Steitz
Added test includes to cover tests with nonstandard names in genetics package.

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Luc Maisonobe
fixed yet another eigen decomposition bug identified, debugged and fixed by Dimitri!
Many thanks to him.

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Luc Maisonobe
Fixed an index computation error in eigen decomposition.
Once again, kudos to Dimitri for debugging this.
JIRA: MATH-318

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Luc Maisonobe
fixed an ArrayIndexOutOfBoundsException
Kudos to Dimitri who debugged this mess of fortran/java array indices translation
JIRA: MATH-308

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Phil Steitz
Fixed parameter test in RandomDataImpl#nextExponential. JIRA: MATH-309.

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Luc Maisonobe
fixed findbugs false positive

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Luc Maisonobe
fixed checkstyle errors

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Luc Maisonobe
changed TWO_PI visibility to public

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Brent Worden
MATH-311.  Changed probability calculations for Binomial, Poisson, and Hypergeometric distributions to use Catherine Loader's saddle point approximations

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Phil Steitz
Removed dead code, improved test coverage.  Dead code pointed out in JIRA: MATH-306. Thanks to Joerg Huber.

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Niall Kegan Pemberton
Update to commons-parent-12

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Phil Steitz
Javadoc only.  Dropped 'now defunct' from JAMA attribution.

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William Barker
documenting change

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William Barker
Fix for possible zero divide on an indefinite matrix

Fix for: MATH-297


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Luc Maisonobe
fixed typo

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Luc Maisonobe
replaced custom linear solve computation by use of the linear package features

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Luc Maisonobe
tighten checkstyle rules: declaring multiple variables in one statement is now forbidden

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Luc Maisonobe
fixed a checkstyle warning

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Luc Maisonobe
removed a Math.min computation that could be avoided
improved javadoc 

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Luc Maisonobe
improved array structure in Romberg integrator
since the integrator uses only two rows at a time, we allocate only two arrays and reuse them

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@824822 13f79535-47bb-0310-9956-ffa450edef68

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53939623daf2c4e194eae3d51afbfbf3ff3cb812
1255444227
Luc Maisonobe
tightened checkstyle rules
catching top level exceptions (Exception, Throwable and RuntimeException) is now forbidden

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@824783 13f79535-47bb-0310-9956-ffa450edef68

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Luc Maisonobe
fixed checkstyle warnings

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@824760 13f79535-47bb-0310-9956-ffa450edef68

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e91dec76a00e05c451496bdcc7029a626ac684d7
1255313046
Phil Steitz
Implemented alternative algorithm for generating poisson deviates when the mean is large. JIRA: MATH-294.

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@824214 13f79535-47bb-0310-9956-ffa450edef68

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Phil Steitz
Added (disabled) test case demonstrating MATH-282 impact on poisson distribution for large means.

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@824183 13f79535-47bb-0310-9956-ffa450edef68

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Luc Maisonobe
delay message build until really needed
this allows not wasting time dealing with resources, strings and formatting when the exception is discarded and its message not used
thanks to Gilles for the suggestion

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@822850 13f79535-47bb-0310-9956-ffa450edef68

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Luc Maisonobe
fixed javadoc typo

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@822454 13f79535-47bb-0310-9956-ffa450edef68

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Luc Maisonobe
fixed missing throw

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@822429 13f79535-47bb-0310-9956-ffa450edef68

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Phil Steitz
Dump expected/observed bin counts on poisson consistency test failure.

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@822205 13f79535-47bb-0310-9956-ffa450edef68

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Luc Maisonobe
added multidimensional interpolation using the microsphere algorithm.
JIRA: MATH-300

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@821626 13f79535-47bb-0310-9956-ffa450edef68

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Phil Steitz
Added goodness of fit test for poisson deviates.

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@819492 13f79535-47bb-0310-9956-ffa450edef68

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Luc Maisonobe
fixed checkstyle warning on missing javadoc

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@818943 13f79535-47bb-0310-9956-ffa450edef68

4812d094678a68b01a68d459523fb79a5c2f3da6
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ba97018855851acc627871d5660054a3d1bba8c0
1253903614
Luc Maisonobe
fixed wrong results in Loess interpolator
also added a way to set weights for smoothing
JIRA: MATH-296

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@818942 13f79535-47bb-0310-9956-ffa450edef68

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Phil Steitz
Commit change inadvertenly omitted from r817128.  JIRA: MATH-298

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@817132 13f79535-47bb-0310-9956-ffa450edef68

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14c336d5881b97740fc8656aca514c8ca49204ea
1253496653
Phil Steitz
Fixed implementation of EmpiricalDistributionImpl#getUpperBounds to match interface
contract.  Added getGeneratorUpperBounds method to EmpiricalDistributionImpl providing previous behavior.

Jira: Math-298

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@817128 13f79535-47bb-0310-9956-ffa450edef68

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Luc Maisonobe
cleaned up tests wrt Junit 4

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@816654 13f79535-47bb-0310-9956-ffa450edef68

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be4cd671b1bfe2df0df6a8f7484e041c90123677
1252570828
Luc Maisonobe
Fixed a OutOfBoundException in simplex solver when some constraints are tight
JIRA: MATH-293

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@813301 13f79535-47bb-0310-9956-ffa450edef68

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Luc Maisonobe
renamed a test after a change in the tested class

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@813296 13f79535-47bb-0310-9956-ffa450edef68

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Luc Maisonobe
applied Andrea's patch to improve test
JIRA: MATH-286

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@812921 13f79535-47bb-0310-9956-ffa450edef68

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1252491075
Sebastian Bazley
MATH-292 TestUtils.assertRelativelyEquals() generates misleading error on failure

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@812871 13f79535-47bb-0310-9956-ffa450edef68

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b05f8dca124e43a35f9d61f26aa776a423cf67e4
1252486083
Luc Maisonobe
applied Benjamin's patch from 2009-09-08
warning: I had to update the expected matrix in SimplexTableauTest.testdiscardArtificialVariables

JIRA: MATH-286

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@812831 13f79535-47bb-0310-9956-ffa450edef68

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71b31811964d5dc9387a53235e3f70616944de99
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Luc Maisonobe
added Benjamin's patch from 2009-09-07
JIRA: MATH-286

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@812390 13f79535-47bb-0310-9956-ffa450edef68

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Sebastian Bazley
Clarify test failure messages

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Sebastian Bazley
Clarify parse test messages

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@811897 13f79535-47bb-0310-9956-ffa450edef68

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Luc Maisonobe
removed unnecessary parentheses

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292e891aab4d737a83ebf786c02bf4003ae0442d
1252251170
Luc Maisonobe
use standard declaration order rules

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@811827 13f79535-47bb-0310-9956-ffa450edef68

292e891aab4d737a83ebf786c02bf4003ae0442d
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e837f7cf8601e0cd68bd946a650f4937e4d44ff6
1252229768
Luc Maisonobe
tighten rules for public/private/abstract/final/... modifiers

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@811786 13f79535-47bb-0310-9956-ffa450edef68

e837f7cf8601e0cd68bd946a650f4937e4d44ff6
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fd5e4bf4e2efc81c9d3b1d6ad125ef034705d0ed
1252227418
Luc Maisonobe
added checkstyle rule to forbid @authors
authors should be listed in the pom file

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@811783 13f79535-47bb-0310-9956-ffa450edef68

fd5e4bf4e2efc81c9d3b1d6ad125ef034705d0ed
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39e7aea40d277ff141cc2ddae7634cd84ded97d9
1252226339
Luc Maisonobe
fixed checkstyle errors about utility classes constructors

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@811780 13f79535-47bb-0310-9956-ffa450edef68

39e7aea40d277ff141cc2ddae7634cd84ded97d9
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337e3fd44c2bbca922fee27daacb572940e6b74b
1252174310
Phil Steitz
Added check for System.out.println stmts in code.

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@811691 13f79535-47bb-0310-9956-ffa450edef68

337e3fd44c2bbca922fee27daacb572940e6b74b
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Phil Steitz
Added check for newline at end of file.

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@811690 13f79535-47bb-0310-9956-ffa450edef68

811d7faab4db68c10ad319ff3333610f8e894569
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Phil Steitz
Removed trailing spaces.

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@811685 13f79535-47bb-0310-9956-ffa450edef68

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6d7818c21e9c784f650bbd912dd6cd9d50ada7a6
1252057494
Luc Maisonobe
fixed misleading number formats in error messages for adaptive stepsize integrators
JIRA: MATH-291

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@811328 13f79535-47bb-0310-9956-ffa450edef68

6d7818c21e9c784f650bbd912dd6cd9d50ada7a6
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e200df3ca7ae2b6ec88c561f07e03876dc9c53fe
1251839675
Luc Maisonobe
replaced a catch for Exception by a catch for NumberFormatException

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@810243 13f79535-47bb-0310-9956-ffa450edef68

e200df3ca7ae2b6ec88c561f07e03876dc9c53fe
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62d4e335d011ce9a1ce5f3ac4fc3a75d7e4ff540
1251839078
Luc Maisonobe
removed unused imports

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@810239 13f79535-47bb-0310-9956-ffa450edef68

62d4e335d011ce9a1ce5f3ac4fc3a75d7e4ff540
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d6beaeaa9c53aa4e6ae128a856e68a9eeb1cadb8
1251838979
Luc Maisonobe
tighten checkstyle rules for hidden fields

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@810238 13f79535-47bb-0310-9956-ffa450edef68

d6beaeaa9c53aa4e6ae128a856e68a9eeb1cadb8
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4dea9e48953a39645038a5aaa296b3124cf610d5
1251835522
Luc Maisonobe
handle an impossible case consistently with other parts of the library

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@810206 13f79535-47bb-0310-9956-ffa450edef68

4dea9e48953a39645038a5aaa296b3124cf610d5
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a0943be0de0b41c646328b38a9a728c39f21002b
1251834466
Luc Maisonobe
tighten rules for constants naming conventions

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@810196 13f79535-47bb-0310-9956-ffa450edef68

a0943be0de0b41c646328b38a9a728c39f21002b
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966160f1d5520d1d807fb69568df26dac0b00a0d
1251832370
Luc Maisonobe
tighten checkstyle rules for switch statements

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@810179 13f79535-47bb-0310-9956-ffa450edef68

966160f1d5520d1d807fb69568df26dac0b00a0d
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89dfffaf228076eeca444bfd87baccd9a35c2999
1251831799
Luc Maisonobe
Added a check for utility class constructor which must be private to prevent instantiation

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@810173 13f79535-47bb-0310-9956-ffa450edef68

89dfffaf228076eeca444bfd87baccd9a35c2999
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d30c941b7f5dbd59bd62557cd115af6d82026776
1251752355
Luc Maisonobe
tighten checkstyle rules for import statements

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@809744 13f79535-47bb-0310-9956-ffa450edef68

d30c941b7f5dbd59bd62557cd115af6d82026776
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3dc75f4f69b53b0dedf96c73d1442acfbe894890
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Luc Maisonobe
added missing javadoc parameter

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@809725 13f79535-47bb-0310-9956-ffa450edef68

3dc75f4f69b53b0dedf96c73d1442acfbe894890
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900592f22b9a1c0b12334b1a78902699d7a75c8b
1251683769
Phil Steitz
Added first batch of weighted statistics
  * mean
  * sum
  * product
  * variance
JIRA: MATH-287
Thanks to Matthew Rowles

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@809448 13f79535-47bb-0310-9956-ffa450edef68

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96287d3103a142a4200e4027876a62939a3e322c
1251660089
Luc Maisonobe
translated new messages and added variable part in format

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@809404 13f79535-47bb-0310-9956-ffa450edef68

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3ef8840567a01c76b3c8536a8e21b367e83aa652
1251655816
Phil Steitz
Added normalizeArray method to MathUtils.

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3ef8840567a01c76b3c8536a8e21b367e83aa652
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1251655396
Phil Steitz
Refer to simplex solver in issues related to this component.

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e1ceab4efdf4eb55133d91ba5abf9407eaa2a16b
1251360403
Luc Maisonobe
removed unused import

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e1ceab4efdf4eb55133d91ba5abf9407eaa2a16b
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8a1a9165920bb3d1223a79f12bb898724846953b
1251360301
Luc Maisonobe
added tests for both the <= and the >= versions of the constraints
one leads to 0 as a solution, the other one leads to no feasible solution
JIRA: MATH-290

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@808312 13f79535-47bb-0310-9956-ffa450edef68

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31aad6494d0e9f8cc41ea1f716fcfdea1e13bca0
1251359871
Luc Maisonobe
removed an unused argument in a private method
JIRA: MATH-289

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31aad6494d0e9f8cc41ea1f716fcfdea1e13bca0
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1251276882
Luc Maisonobe
fixed weird spacing as per last patch from Ben

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327124cf4ca07f9e733ccc06f7432b50e149ea9c
1251276207
Luc Maisonobe
fixed an error with negative constraints and unfeasible solution
JIRA: MATH-290

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@807923 13f79535-47bb-0310-9956-ffa450edef68

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4ece1884cc408e15c8f1db9010fec5cac43937b9
1251223633
Luc Maisonobe
fixed an error induced by zero entries in simplex solver
JIRA: MATH-288

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f36be8e8b7371fb8814456b6c095866aa802de78
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Luc Maisonobe
fixed an error leading the simplex solver to compute the right solution but return another one
JIRA: MATH-286

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1250423414
Sebastian Bazley
Typo

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1250391152
Phil Steitz
Removed reference to maven 1 build.

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Phil Steitz
restored development reports.

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abc35fa9eb58b09dbb2ad317853a7a59a70f4e3e
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Phil Steitz
Fixed broken link, dropped reference to deprecated package.

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317793eeff84dc9b260301adbe4aa8f5c79f703a
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Luc Maisonobe
Prevent infinite loops in multi-directional direct optimization method when the start point is exactly at the optimal point
JIRA: MATH-283

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Phil Steitz
Updated to reflect 2.0 release.

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fixed an error in RealMatrix javadoc
JIRA: MATH-281

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d6a438e931412713e99624cf9ed74470f1040184
1249137025
Luc Maisonobe
moved main java directory for compliance with maven standard directory layout

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@799870 13f79535-47bb-0310-9956-ffa450edef68

d6a438e931412713e99624cf9ed74470f1040184
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Luc Maisonobe
moved assembly directory for compliance with maven standard directory layout

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Luc Maisonobe
cleaned more subversion properties

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Luc Maisonobe
added a protection against infinite loops that occur with some JVM (Sun before 1.4, JRockit, ...)

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Luc Maisonobe
fixed properties

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Luc Maisonobe
added forgotten Apache header

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Phil Steitz
Reverted trunk version back during release vote.

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Phil Steitz
Prepare (again) for 2.0 release.

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Phil Steitz
Added description for 2.0 release.

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Phil Steitz
Change trunk version back during release vote.

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Phil Steitz
Prepare for 2.0 release

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Phil Steitz
Fixed typo and one missed s/used/translated

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Phil Steitz
Put copyright notices in NOTICE.txt, clean up LICENSE.txt (mostly s/used/translated)

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Luc Maisonobe
added references to the classes that are derived works of existing products
in the NOTICE and LICENSE files

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Luc Maisonobe
improved introduction of derived works original licenses as per Phil's suggestion

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Luc Maisonobe
fixed copyright year

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Phil Steitz
Updated menu to include 2.0 javadoc.

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Phil Steitz
Disabled development reports for release.

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Luc Maisonobe
moves subcomponents licenses and disclaimers from NOTICE to LICENSE file,
as required by Apache release policy
http://www.apache.org/dev/release.html#distributing-code-under-several-licenses

thanks to sebb for identifying the issue and providing a pointer to the right way to handle this

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Phil Steitz
fixed typo

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Phil Steitz
Minor edits.

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Phil Steitz
Updated download page for 2.0 release.

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Phil Steitz
Dropped maven 1 release notes jsl.

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Phil Steitz
Prepare for 2.0-RC1.

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Phil Steitz
Dropped unenlightening reference.

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Phil Steitz
Fixed javadoc link.

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Phil Steitz
Dropped reference to non-existent method.

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Luc Maisonobe
removed a print

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Luc Maisonobe
removed a print

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Luc Maisonobe
improved test coverage

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Luc Maisonobe
improved test coverage

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Luc Maisonobe
improved test coverage

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Luc Maisonobe
improved test coverage

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Luc Maisonobe
removed unused function

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Luc Maisonobe
added tests for recent changes
improved coverage

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Luc Maisonobe
make sure at least one run in the multistart univariate optimizer uses the complete search domain

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Luc Maisonobe
fixed an error in multistart univariate optimizer:
the optima found were sorted according to the independant variable x,
not according to the function value y

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Luc Maisonobe
limited accuracy of numbers in string comparisons

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Luc Maisonobe
improved test coverage

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Luc Maisonobe
the new base class does not call setSeed,
defensive programming against too early calls to setSeed are not useful anymore

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Luc Maisonobe
removed a javadoc paragraph that is not true anymore

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Luc Maisonobe
improved test coverage

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Luc Maisonobe
fixed javadoc

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Luc Maisonobe
added an implementation of the Mersenne twister pseudo random number generator
the implementation comes from Mantissa and was a translation of the 2002 version
in C by the algorithm authors, which was published under a BSD license

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Luc Maisonobe
added a base class for bits streams based modern pseudo random generators

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Luc Maisonobe
added new seeding methods for random generators
this will allow implementing some modern and efficient generators
that require a lots of bits for seeding in the form of complete integer arrays

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Luc Maisonobe
fixed an index error triggering ArrayIndexOutOfBoundException for an add after a clear
if size has grown

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Luc Maisonobe
added tests for the synchronized version of multivariate summary statistics

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Luc Maisonobe
delegate creation of tested class to a factory so that the derived class
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SynchronizedDescriptiveStatistics

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Luc Maisonobe
checked serialization of TransformerMap and added a test for it

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Luc Maisonobe
checked serialization of EuclideanIntegerPoint and added a tests suite for the class

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Luc Maisonobe
optimizers should not be serializable

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Luc Maisonobe
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Luc Maisonobe
removed automatically generated TODO comment

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Luc Maisonobe
convergence checkers should not be serializable

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Luc Maisonobe
checked serialization of BigReal and added a tests suite for the class

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Luc Maisonobe
handle serialization of BigRealField (which is a singleton) properly and test it

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Luc Maisonobe
handle serialization of ComplexField (which is a singleton) properly and test it

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Luc Maisonobe
handle serialization of FractionField (which is a singleton) properly and test it

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Luc Maisonobe
handle serialization of BigFractionField (which is a singleton) properly and test it

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Luc Maisonobe
removed TODO item: the solvers tests are quite different, an abstract test class seems overkill here

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Luc Maisonobe
added test for Fraction serialization

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Luc Maisonobe
added test for BigFraction serialization

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Luc Maisonobe
added new tests for multistart optimizers

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Luc Maisonobe
changing multistart behaviour to rely on search domain boundary rather than on start point
the only implementation of the raw minimizer ignores the start point so the multistart optimizer always found the same point before the change

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Luc Maisonobe
updated plugins to latest version
(except cobertura for now because version 2.3 triggers a strange error in MathUtils)

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Luc Maisonobe
moved velocity template to a default directory where the maven-changes-plugin look for it

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Luc Maisonobe
fixed an error identified by findbugs

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Luc Maisonobe
fixed an exclusion rule after an API change some time ago

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Luc Maisonobe
removed obsolete files

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Luc Maisonobe
added Apache header to some files that didn't have it

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Luc Maisonobe
fixed typo

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Luc Maisonobe
first attempt at release notes for 2.0

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Luc Maisonobe
fixed a change entry after several layer of changes have occurred
to avoid confusing users

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Phil Steitz
Added release notes velocity template.

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1247941296
Luc Maisonobe
Changed the default max growth factor for multistep methods using Nordsieck representation.
The previous value (10.0) was far too big and lead to numerical instability at high orders
because the last component of the Nordsieck vector, which has a low accuracy, could be
multiplied by 10^k which was ... huge.

These integrators are at least usable now!

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1247756942
Luc Maisonobe
Changed the return type of the various interpolation algorithms to the
specific implementation of UnivariateRealFunction each one uses
(thanks to Gilles for reporting the problem and providing the patch)


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Phil Steitz
Added AggregateSummaryStatistics.

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Phil Steitz
Fixed types.

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1247100812
Phil Steitz
Cleanup / complete AggregateSummaryStatistics implementation
 * Fully synchronized access to aggregating SummaryStatistics instance
 * Exposed all SummaryStatistics stats
 * Improved test coverage
 * Improved javadoc
JIRA: MATH-224

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Phil Steitz
Made long conversion conistent. Improved test coverage. JIRA: MATH-224.

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Luc Maisonobe
added a test case and documentation for the new contract about roots bracketing in univariate real solvers (roots exactly at endpoints are now accepted)
JIRA: MATH-280

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Luc Maisonobe
fixed a bracketing issue due to inconsistent checks
JIRA: MATH-280

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Luc Maisonobe
added an exclusion rule for a false positive from findbugs concerning a desired and documented feature

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Luc Maisonobe
removed compilation/findbugs warnings about type safety
the changes include API changes (replacing Object by Comparable<?>).
The class itself is still not generic as this would prevent mixing types which is a desired feature here that is checked in the unit tests
JIRA: MATH-261

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1246951070
Luc Maisonobe
fixed missing @return tag

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Luc Maisonobe
removed tabs

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Luc Maisonobe
removed tabs

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Phil Steitz
Added static direct aggregation method to AggregateSummaryStatistics.  JIRA: MATH-224.

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Phil Steitz
Exposed second moment.

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Phil Steitz
Fixed alpha sort of developers.

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Luc Maisonobe
compute state variation avoiding cancellation in a critical subtraction to preserve accuracy

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Luc Maisonobe
javadoc

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Luc Maisonobe
Added a check for too few data in linear regression
JIRA: MATH-279

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Luc Maisonobe
added scalar multiply to the Complex class
JIRA: MATH-277

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Luc Maisonobe
fixed package documentation that still referenced mantissa

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Luc Maisonobe
fixed javadoc

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Luc Maisonobe
optimized matrix update loop

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Luc Maisonobe
fixed another set of warnings identified by recent findbugs versions

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Luc Maisonobe
removed import

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Luc Maisonobe
fixed another set of warnings identified by recent findbugs versions

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Phil Steitz
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Added GA.

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Phil Steitz
Fixed broken javadoc links.

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Phil Steitz
Fixed incorrect javadoc link.

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Luc Maisonobe
fixed a serialization error introduced by yesterday changes
(sorry for the noise)

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Luc Maisonobe
fixed typo

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Luc Maisonobe
simplified and reorganized slightly the Adams integrators class hierarchy
this will allow a future BDF integrator development for stiff problems

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Luc Maisonobe
changed Nordsieck transformer to an Adams-specific Nordsieck transformer
the transformer associated with BDF integrator will be quite different

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Luc Maisonobe
improve both numerical accuracy and speed by using optimized loops
in reversed row order (i.e. from higher orders to lower orders) directly
on matrix data.

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Luc Maisonobe
be more precise on return type, we really return a Array2DRowRealMatrix,
so tell it in case some callers can use this information for optimization
(which is the case for Nordsieck transformers, they will be able to use
customized loops on matrix data for the sake of numerical accuracy)

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Luc Maisonobe
moved test problems one package up, to prepare their reuse for stiff integrators

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Luc Maisonobe
added Dimitri to contributors

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Luc Maisonobe
Added a getCovariance method to singular value decomposition

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Luc Maisonobe
added a missing @Override

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8418371b03d8afb1a74636ebe988e00d7fd805b1
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1245724550
William Barker
Add test cases for Serialization of subclasses of Complex

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Luc Maisonobe
fixed TWO_FIFTH value in both Fraction and BigFraction

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1245673237
Luc Maisonobe
fixed a forgotten adjustment of integrator setting
the first integer parameter semantics have changed and the test
was not updated to reflect this, thus leading to test failure

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@787215 13f79535-47bb-0310-9956-ffa450edef68

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1245630369
William Barker
Yes, sebb is correct.  After running tests, readResolve needs to be visible to subclasses to be used.  Since Complex is clearly designed to be subclassed, changing the visiblity.


git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@787118 13f79535-47bb-0310-9956-ffa450edef68

e9b7a1fe39cd1ba0bc3537186c5074623f5d4bbc
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Phil Steitz
Made protected fields private.  JIRA: MATH-207.

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1245604047
Luc Maisonobe
fixed Adams-Bashforth order for error control (it is k, not k+1)

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Luc Maisonobe
removed the current point from count in multistep integrators
updated documentation since now Adams-Bashforth and Adams-Moulton
are adaptive stepsize integrators

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@787050 13f79535-47bb-0310-9956-ffa450edef68

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Phil Steitz
Added Spearman's correlation.

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314c516318fae1abcecdcac6acdd65e026eda5ef
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William Barker
Restore Serializable to PolynomialFunction

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@786936 13f79535-47bb-0310-9956-ffa450edef68

8cc888a8f66dc7132b97745339b64a9f840bf057
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Phil Steitz
Added ranking subsection.

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4569ccaebb061b2e2ad9224308f53f825e7cfa68
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1e42e6b3f535d945eae79689e90f6e9d656b0837
1245541067
William Barker
Remove Serializable from some tranient analitics classes.

Let me know if I've nuked ur favorite one, and I can put it back


git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@786927 13f79535-47bb-0310-9956-ffa450edef68

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9d3a3ad3e670e8b90e17d68506ec9faf77f1743c
1245536256
Sebastian Bazley
Fix thread-safety issues
- code failed to use synch. read
- code could potentially use two different random Generators if another thread changed it

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@786918 13f79535-47bb-0310-9956-ffa450edef68

9d3a3ad3e670e8b90e17d68506ec9faf77f1743c
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081dc3307d21519b4f81411c1e5774ad215c88e5
1245533732
Phil Steitz
Made aggregation threadsafe.

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Luc Maisonobe
removed old maven 1 stuff

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@786900 13f79535-47bb-0310-9956-ffa450edef68

3fcf1beb934a0046db58f7a3c1ce9ac39a5885ee
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336af060a29beebb600be28ad5a1b092e4a026cd
1245525824
Luc Maisonobe
adding missing Apache header

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@786890 13f79535-47bb-0310-9956-ffa450edef68

336af060a29beebb600be28ad5a1b092e4a026cd
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363228bf3f5c300bcddc2feeb98175212ca860dc
1245524815
Luc Maisonobe
documented Adams-Bashforth and Adams-Moulton ODE integrators

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@786885 13f79535-47bb-0310-9956-ffa450edef68

363228bf3f5c300bcddc2feeb98175212ca860dc
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9c2f4a988cabb6136c755dedcbd3091d729dda83
1245524250
Luc Maisonobe
fixed a warning about a mission serializeVersionUID.
However, should this really be serializable at all ?

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@786883 13f79535-47bb-0310-9956-ffa450edef68

9c2f4a988cabb6136c755dedcbd3091d729dda83
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37fb4b50920133ce8f60b239713af64df48554fd
1245523988
Luc Maisonobe
removed lots of serialization in ODE
the only classes/interfaces for which serialization is really important in this package are the step interpolators. The reason for that is that the ContinuousOutputModel is explicitly serializable and contains step interpolators. This allows users to perform integration of any complex model and to save the result of the integration for all integration range by serializing a ContinuousOutputModel instance. This feature is a major one.

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@786881 13f79535-47bb-0310-9956-ffa450edef68

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2109b5b38444ecd6dbdad6cff1da2a4de59714e3
1245521852
Luc Maisonobe
removed serialization for multistart optimizers

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@786878 13f79535-47bb-0310-9956-ffa450edef68

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a04a035c49bf2bcb34c41a5a7a16195084e4b852
1245521754
Luc Maisonobe
changed the Adams-Bashforth and Adams-Moulton multistep integrators to adaptive stepsize.
this was made possible thanks to the Nordsieck representation of integration state

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@786877 13f79535-47bb-0310-9956-ffa450edef68

a04a035c49bf2bcb34c41a5a7a16195084e4b852
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ca2b746e226170f2c25c8ce944a08cbbffa61142
1245521604
Luc Maisonobe
completely changed integration start phase: now the starter integrator for
multistep methods do not advance time anymore, it is interrupted at first step
end and the interpolator is used to reconstruct Nordsieck vector information at
integration start. Then the normal multistep integrators does start also exactly
at integration start and is responsible for all time advancing stuff, including
step handlers and events handlers management.

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@786875 13f79535-47bb-0310-9956-ffa450edef68

ca2b746e226170f2c25c8ce944a08cbbffa61142
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ce8aff1a7c90e91c207fe0d99732958d3f765365
1245521356
Luc Maisonobe
simplified arrays allocation and copying

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@786874 13f79535-47bb-0310-9956-ffa450edef68

ce8aff1a7c90e91c207fe0d99732958d3f765365
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361239ca3bcd578bfc3d176657516428ce6e3027
1245505409
Luc Maisonobe
error messages for Loess interpolation

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b80bab2dc0ffe93b3fe705b4f695cc3982a66735
1245505376
Luc Maisonobe
added Loess interpolator, applying Eugene Kirpichov's patch
JIRA: MATH-278

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@786819 13f79535-47bb-0310-9956-ffa450edef68

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f6b2283957c59ba7d50cc41f90c822b8b9fe90f1
1245504708
Luc Maisonobe
fixed checkstyle errors

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f6b2283957c59ba7d50cc41f90c822b8b9fe90f1
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cf9d715a5877d7e622f867ac090fa7dc34f3f835
1245466818
William Barker
Change Complex to use readResolve instead of introspection

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b0a49dae2ea76425f731dbaf9469868fda1aa9e7
1245415081
Luc Maisonobe
added back findbugs exclusion rules for a deprecated class that is still there under its old name

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8fd1834813ca42fa107b783fd57672f4f5bc9091
1245414976
Luc Maisonobe
merged curve fitting from mantissa into commons-math

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2f65d00640bf4ba57dd24f390c489b131480cc2f
1245414816
Luc Maisonobe
added internal error generation for defensive programming

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@786478 13f79535-47bb-0310-9956-ffa450edef68

2f65d00640bf4ba57dd24f390c489b131480cc2f
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cb6ba883140a043fdbbb4599cf72c116802a42b7
1245413041
Luc Maisonobe
added new tests

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@786467 13f79535-47bb-0310-9956-ffa450edef68

cb6ba883140a043fdbbb4599cf72c116802a42b7
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c92a3d9eee0701aae4e62d6678815c0eb03f5a11
1245412994
Luc Maisonobe
added protection against infinite loops by setting a maximal number of evaluations
(some classes were forgotten in the first pass to fix this problem)

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@786466 13f79535-47bb-0310-9956-ffa450edef68

c92a3d9eee0701aae4e62d6678815c0eb03f5a11
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5c1e4e54c9ddb6942febde798e0e06f73af71544
1245381988
William Barker
Change the Complex isNaN and isInfinite fields to be transient

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@786359 13f79535-47bb-0310-9956-ffa450edef68

5c1e4e54c9ddb6942febde798e0e06f73af71544
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d6d2b673595e33fa906ab9e90dcf36d480f3895d
1245236440
Phil Steitz
Optimized isNaN, isInfinite.  Jira: MATH-2276.  Contributed by Mark Anderson.

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@785552 13f79535-47bb-0310-9956-ffa450edef68

d6d2b673595e33fa906ab9e90dcf36d480f3895d
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7695a8c9162520d0d8770bbab6d6088c9a4cd657
1245211355
William Barker
More Serialization changes, mostly for ode and friends.

Unfortunately, had to leave some abstract base classes as Serializable, since they had no senible default construters.  But left them with meaningless UIDs, to break anyone that doesn't override it.

Of course, if anyone has a better patch, I'm happy to implement it.  At this point, the serialization changes for [math] should be almost done.


git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@785473 13f79535-47bb-0310-9956-ffa450edef68

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602e3fec32294ab720a30c11b743cd04140f3ff7
1245006272
Phil Steitz
Added Genetic Algorithm implementation.
JIRA: MATH-207
Contributed by David Stefka

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@784604 13f79535-47bb-0310-9956-ffa450edef68

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62bed05b1491a68d1416392e3e4cb2665f995010
1244723742
Luc Maisonobe
removed remaining references to DenseXxx{Matrix/Vector}

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@783741 13f79535-47bb-0310-9956-ffa450edef68

62bed05b1491a68d1416392e3e4cb2665f995010
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dbae4b01341d9d72e52d1e07a15d5023deca3d92
1244710442
Luc Maisonobe
renamed RealMatrixImpl, RealVectorImpl, FieldMatrixImpl and FieldVectorImpl
into Array2DRowRealMatrix, ArrayRealVector, Array2DRowFieldMatrix and ArrayFieldVector
as suggested by Sam in http://markmail.org/message/hh37ivxpzaoapekj

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@783702 13f79535-47bb-0310-9956-ffa450edef68

dbae4b01341d9d72e52d1e07a15d5023deca3d92
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3325ab51b3a0037ddd7dad8ab2269edcabad8fa0
1244707565
Luc Maisonobe
switch the matrix type built by factory methods depending on the dimension

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@783680 13f79535-47bb-0310-9956-ffa450edef68

3325ab51b3a0037ddd7dad8ab2269edcabad8fa0
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22f406556284019a8d5eb2dfcce01f2feef947ae
1244707524
Luc Maisonobe
renamed Dense{Real/Field}Matrix into Block{Real/Field}Matrix
as suggested by Phil in http://markmail.org/message/iibgiz4bsv6hjjvh

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@783678 13f79535-47bb-0310-9956-ffa450edef68

22f406556284019a8d5eb2dfcce01f2feef947ae
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9494baedb5ca3346ce6817f5bf03c73918f91d8b
1244670273
Luc Maisonobe
prevent too small (sometimes exactly 0) steps to occur
when an event is within convergence tolerance to the step end

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@783529 13f79535-47bb-0310-9956-ffa450edef68

9494baedb5ca3346ce6817f5bf03c73918f91d8b
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8dad16f5e74feaaa5bf36afb1f2d384848247318
1244667509
Luc Maisonobe
fixed a forgotten field in copy constructor

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@783516 13f79535-47bb-0310-9956-ffa450edef68

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1244576635
Luc Maisonobe
fixed checkstyle errors

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Luc Maisonobe
added support for max number of evaluations to ODE integrators

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Luc Maisonobe
removed unneeded import

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@783044 13f79535-47bb-0310-9956-ffa450edef68

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1244561695
Luc Maisonobe
removed unneeded import


git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@783041 13f79535-47bb-0310-9956-ffa450edef68

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4eb810e816aac9329ae05715a8ebb8aa7c400031
1244409858
William Barker
Serialization changes for optimization.

Still need to add junit test, but for this it doesn't look like a blocker.


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1244402375
Luc Maisonobe
changed again the Adams-Bashforth and Adams-Moulton integrators
they now both use Nordsieck representation
this is the first really usable implementation, it still integrates only with fixed stepsize,
but thanks to Nordsieck representation they will be improved to adaptive stepsize soon

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@782442 13f79535-47bb-0310-9956-ffa450edef68

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1244402114
Luc Maisonobe
removed step interpolator prototype

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1244401997
Luc Maisonobe
added serialization test
changed tests to Junit 4

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1244401938
Luc Maisonobe
improved max errors computations: previously, NaN values induces the error update to be skipped, thus leading to artificially good results

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Luc Maisonobe
updated step interpolators implementations tests to latest interface changes

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Luc Maisonobe
updated step interpolators implementations to latest interface changes

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daf025e7eb5c951a08eb630af00210ee2c5238db
1244401477
Luc Maisonobe
added a lazy evaluation for step interpolators
moved the possible exceptions from setInterpolatedTime (which now does almost nothing) to getInterpolatedState and getInterpolatedDerivatives (which now do the evaluations)
renamed an internal function to make sure people overriding it don't forget to set the derivatives


git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@782431 13f79535-47bb-0310-9956-ffa450edef68

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Luc Maisonobe
removed a print

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Luc Maisonobe
fixed detection of not positive definite matrices
JIRA: MATH-274

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@781845 13f79535-47bb-0310-9956-ffa450edef68

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1244019968
Luc Maisonobe
Fixed a wrong check for basic variables
JIRA: MATH-273

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d0c52c49b7efa5367b154443bba9910cb19e6419
1243976534
Luc Maisonobe
fixed javadoc link

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@781167 13f79535-47bb-0310-9956-ffa450edef68

d0c52c49b7efa5367b154443bba9910cb19e6419
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08a57af7ffc839086ce9ec351ad911fcfe547017
1243975605
Luc Maisonobe
removed unneeded import statement

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@781160 13f79535-47bb-0310-9956-ffa450edef68

08a57af7ffc839086ce9ec351ad911fcfe547017
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a12bab734ec9c6853f6be584430425389406f0ef
1243975553
Luc Maisonobe
reenabled tests
removed a development test that was committed by error

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@781159 13f79535-47bb-0310-9956-ffa450edef68

a12bab734ec9c6853f6be584430425389406f0ef
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63c5ec9834b0aac3e2ad8187bbbc94046c1fe95b
1243975439
Luc Maisonobe
fixed event handling during multistep restart phase,
the interpolator used for regular integration and the interpolator used during restart went out of sync

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@781158 13f79535-47bb-0310-9956-ffa450edef68

63c5ec9834b0aac3e2ad8187bbbc94046c1fe95b
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4e6ce1508bb1a9e9f6b1809ea1dbb3ed075b2b42
1243975335
Luc Maisonobe
fixed corner cases when events occur right at integration start
(which in fact always happen when a resetting event forces a restart just after the event has occurred)

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@781157 13f79535-47bb-0310-9956-ffa450edef68

4e6ce1508bb1a9e9f6b1809ea1dbb3ed075b2b42
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3c384f846f49ba673a9805c8d03d6a2156770a70
1243975181
Luc Maisonobe
fixed an infinite loop error that occurred when an event that reset the state occurs exactly at multistep initialisation start

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@781156 13f79535-47bb-0310-9956-ffa450edef68

3c384f846f49ba673a9805c8d03d6a2156770a70
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24a6a2692e942969f5c39bd88d3d12ac0f0bf0d9
1243971450
Luc Maisonobe
Fixed a problem when setting some variables (several variables were set instead of only one)
JIRA: MATH-272

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@781135 13f79535-47bb-0310-9956-ffa450edef68

24a6a2692e942969f5c39bd88d3d12ac0f0bf0d9
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1b48dbabe18ca22396bd737df73e241cfdf8c0c5
1243968803
Luc Maisonobe
merged the decomposition package back to the linear package.
This will allow later improvements as decomposition algorithms
will be able to see implementation details when more efficient
matrices implementations (for example based on blas) are added

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@781122 13f79535-47bb-0310-9956-ffa450edef68

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0832bf9bacfa9d8fc6cb3b9d0ee82756a7bca5ad
1243933586
Luc Maisonobe
fixed serialization problems

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@780976 13f79535-47bb-0310-9956-ffa450edef68

0832bf9bacfa9d8fc6cb3b9d0ee82756a7bca5ad
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62199a35c1e2b5ad445b631c5edec327e0c38686
1243933537
Luc Maisonobe
removed unneeded import statements

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@780975 13f79535-47bb-0310-9956-ffa450edef68

62199a35c1e2b5ad445b631c5edec327e0c38686
:100644 100644 52bd6394c657de9d6852fbd8e2c480b516e25d4c c5e14299da67a8c4da78d7d75f7078d957a3f755 M	src/java/org/apache/commons/math/optimization/linear/LinearOptimizer.java
:100644 100644 1aa58049065fc52b1d39558a980480773511853d 842c83fdb70afea0a8ddd2b93527181898ba9289 M	src/java/org/apache/commons/math/random/RandomData.java
:100644 100644 bff6400aa58bd547a8567eefa817958eb61c9c9e 8060c24d522319a7433874cda4a0a375fe6d8246 M	src/java/org/apache/commons/math/random/RandomGenerator.java
:100644 100644 933fc68d19ed7c4e48395f4271948cfbac0aecb0 9cad871572f699f96195f1fd90e3acd48205a560 M	src/java/org/apache/commons/math/random/RandomVectorGenerator.java
:100644 100644 607d2fb6fc695ba578a02fe6207eb62bf6bbdaad 10c5377748e0ca8af7f612341cbd0619d63ac3e1 M	src/java/org/apache/commons/math/special/Gamma.java

b2e4c7c1b81d8b54ad6dcd589c0d730c764fad08
1243933411
Luc Maisonobe
added utility methods to help serialize/deserialize classes that
have RealVector/RealMatrix fields (possibly final) since the
top level interfaces are not serializable anymore

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@780974 13f79535-47bb-0310-9956-ffa450edef68

b2e4c7c1b81d8b54ad6dcd589c0d730c764fad08
:100644 100644 a1c510193d9d14e9f2fafa6f053fba866716eb97 ac1215746f733988c5dd8aa052188be73358d9bd M	src/java/org/apache/commons/math/linear/MatrixUtils.java

7d10ae8a324878c35983eb2d81d9e943bf3844ed
1243933283
Luc Maisonobe
fixed javadoc copy/paste error

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@780973 13f79535-47bb-0310-9956-ffa450edef68

7d10ae8a324878c35983eb2d81d9e943bf3844ed
:100644 100644 1464af2db3e36eab7c33f85ead810ce24cbc4287 b40334005d2a7b22ad391de2b18845adbf31339e M	src/java/org/apache/commons/math/linear/RealVectorImpl.java

efabab28b83811b92fb2c858226b04b42bab21e6
1243917552
William Barker
More serialization changes.

Not clear what I should do with RandomAdaptor.  So I've let it remained broken (no public no-opt construtor, but Serializable).

Feel free to -1 anything that I've stripped Serializable from and you care about, but I think I've been pretty conservative.


git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@780933 13f79535-47bb-0310-9956-ffa450edef68

efabab28b83811b92fb2c858226b04b42bab21e6
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:100644 100644 b933e00a642a5f2a1224fe1f230b5945f0dee0fe 52bd6394c657de9d6852fbd8e2c480b516e25d4c M	src/java/org/apache/commons/math/optimization/linear/LinearOptimizer.java
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:100644 100644 e54b8388eb817eed59801e349106500312c34b16 b96264583e5b916fa1f85cd830491b375a2a396f M	src/test/org/apache/commons/math/random/RandomAdaptorTest.java
:100644 100644 0cf9053f3fc5135bc4f7d4c4d2caae6fd7031217 6d674210a6cfd60f381e95b959b6a470c4e51331 M	src/test/org/apache/commons/math/random/RandomDataTest.java
:100644 100644 7417060baa3ed22b9253f38d286350a611b8e78f b70e7911f66e9bafd7848995356456ee6b5afecc M	src/test/org/apache/commons/math/random/TestRandomGenerator.java
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06941303608fe910b65022681b904dfe57bef09f
1243869055
Luc Maisonobe
fixed javadoc warnings

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@780674 13f79535-47bb-0310-9956-ffa450edef68

06941303608fe910b65022681b904dfe57bef09f
:100644 100644 3016a486706fd1091a427e2c08f76629edae4829 eae0f3f5a73cb683c4b2051b4e67d1ae83f0f88a M	src/java/org/apache/commons/math/MathException.java
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:100644 100644 78116f2939e7307f936e18e53a9639597b50298d c2179384b834fed134612a1d515dd0727324f59f M	src/java/org/apache/commons/math/optimization/MultiStartDifferentiableMultivariateRealOptimizer.java
:100644 100644 5cf31056c2f82f9c8b3bf044cad3bef3bb3930cd 2a45f37ab9870edec5dd8fdcfb9e104ead69e265 M	src/java/org/apache/commons/math/optimization/MultiStartDifferentiableMultivariateVectorialOptimizer.java
:100644 100644 167a527dcb84d36a5a058caddb9a31dae4d89d11 b9133b0b9a749159977c166ada9b6018807c345f M	src/java/org/apache/commons/math/optimization/MultiStartUnivariateRealOptimizer.java
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:100644 100644 fe1970db108316e01551bb7a5ece62909eda0bd3 44908b87189dc3008f01e6cd12bb12012bf0e0bc M	src/java/org/apache/commons/math/optimization/general/GaussNewtonOptimizer.java
:100644 100644 b38e967f7959ba79ea80ad7c9ffbeaacb5dc816a 0dc76ed3d42aee446c6b8cb57f3b1c23db367530 M	src/java/org/apache/commons/math/optimization/general/NonLinearConjugateGradientOptimizer.java
:100644 100644 52b2b9daabc923e42b759bffb8db348c39aeb2df b933e00a642a5f2a1224fe1f230b5945f0dee0fe M	src/java/org/apache/commons/math/optimization/linear/LinearOptimizer.java
:100644 100644 8618e3743bb79e58e0ef0203385f456172f2e3ce 79325f02ffe4618bb831f1720c473ed90337ebe5 M	src/java/org/apache/commons/math/util/DefaultTransformer.java

b9f4e914df109dedee24e7b5674d6cfdee170ff9
1243862659
Luc Maisonobe
fixed javadoc

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@780645 13f79535-47bb-0310-9956-ffa450edef68

b9f4e914df109dedee24e7b5674d6cfdee170ff9
:100644 100644 0578aac10ba2eb3b1090c87736592b4146b48521 79c3de0a54e948297d1dd7b056bdc120db20fd91 M	src/java/org/apache/commons/math/linear/SparseFieldMatrix.java
:100644 100644 fb678cd0db726cf060d2216b6510ff6ac91a81dc e8213c54fbb7400529e28f0c0ec434ad17a33029 M	src/java/org/apache/commons/math/linear/SparseFieldVector.java
:100644 100644 c6f926000318e49e030fd68b0bbba5e7097d07e2 bc5f826a6f4929a87ec5a6de9750bb834ae2d612 M	src/java/org/apache/commons/math/stat/Frequency.java
:100644 100644 fd13fa9bff6df5f881aacb6e33e1ef96eb42fdc3 da25a736cd66e47370718c733f1fc987fc8e91ce M	src/java/org/apache/commons/math/stat/descriptive/moment/VectorialCovariance.java
:100644 100644 9293e67a564b4b9c22f1a254b4583181481aae85 eaf73edf0a1b22dcb3b355e96c495dece3358e38 M	src/java/org/apache/commons/math/stat/descriptive/moment/VectorialMean.java

0aab32b17cdece9ea5e318caf0d2c62f12d66e91
1243862597
Luc Maisonobe
remove impossible serialization
(function is no more serializable)

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@780644 13f79535-47bb-0310-9956-ffa450edef68

0aab32b17cdece9ea5e318caf0d2c62f12d66e91
:100644 100644 7c00b3634c864d6c4ed6ef27126d9ed008c714e9 561ac88801f7ac02ae157f33fc0e3bcb100df449 M	src/java/org/apache/commons/math/optimization/LeastSquaresConverter.java

218b803548add3b94961a85f14cd14135333194d
1243862463
Luc Maisonobe
updated filter after replacement of MultistepStepInterpolator by NordsieckStepInterpolator

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@780643 13f79535-47bb-0310-9956-ffa450edef68

218b803548add3b94961a85f14cd14135333194d
:100644 100644 6651be6db6881ea90a9cb62d1cf62932ac60fb3f 226827e07b3ce8db884910b452f82da6a8f18724 M	findbugs-exclude-filter.xml

2d48981a85c36bb55ea963394d57edb8e044ead1
1243860512
Luc Maisonobe
removed unneeded import statements

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@780637 13f79535-47bb-0310-9956-ffa450edef68

2d48981a85c36bb55ea963394d57edb8e044ead1
:100644 100644 7c8904f15d5858dc057de58a4ec132dc409f5a70 ea6611962fafe26f6c30ebe6003449e833f340f9 M	src/java/org/apache/commons/math/stat/descriptive/AbstractStorelessUnivariateStatistic.java
:100644 100644 24f044ed4b4dbe22335e1e759af69f9f2aaf206b 93ca20ec4687238b1f9c96221044c784e0c6a40f M	src/test/org/apache/commons/math/linear/DenseFieldMatrixTest.java
:100644 100644 78e53cff4385b3f51dcebe8b886212bf3ae36e2c 20edd38d088480ac0f0ade54b9f1abfcd78780f6 M	src/test/org/apache/commons/math/linear/DenseRealMatrixTest.java
:100644 100644 6e42d7d73c6d35adab0142fb177c5e5275e3b5b7 9d7254f615f1a4b4a6de12c3ec20827137532e64 M	src/test/org/apache/commons/math/linear/FieldMatrixImplTest.java
:100644 100644 b6d57ebb3c68c731ee578ebc32d978fc7a5903e0 43197255a1ef290dddb1a050f116b17f3cb9eb4f M	src/test/org/apache/commons/math/linear/FieldVectorImplTest.java
:100644 100644 df81c2ad13df7c8867bf7d6752c0f6e60e383afd 7ea01a2ba44eb7f9d7f5980b3ea694262df40b93 M	src/test/org/apache/commons/math/linear/RealMatrixImplTest.java
:100644 100644 8db19a4264e0adca86565c3545991fee82e6c8ef 8b67f3732f6f856416a86ac8029297afbeccbe9b M	src/test/org/apache/commons/math/linear/RealVectorImplTest.java
:100644 100644 01ea247528306ebbda1c2268c242447942a3c086 ff537e7c67af032c61829402952100fc1e932456 M	src/test/org/apache/commons/math/linear/SparseRealMatrixTest.java
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3dd44176dcf2d2d5a5d4d4acbf325612744c62d7
1243817222
William Barker
Serialization changes for stats

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@780541 13f79535-47bb-0310-9956-ffa450edef68

3dd44176dcf2d2d5a5d4d4acbf325612744c62d7
:100644 100644 4cf1da5893014ef838039cfea6dba906c1cd268b c6f926000318e49e030fd68b0bbba5e7097d07e2 M	src/java/org/apache/commons/math/stat/Frequency.java
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:100644 100644 0d995ba8bb1215de49557ee6983165022ecd9022 919f330baf4d8e8e9a631034f4719862668469f4 M	src/test/org/apache/commons/math/stat/FrequencyTest.java
:100644 100644 98aef721b1cc20c3a0cf7403f867cfef7d242b60 461ce218ece14dc30a5e712f2bb11b28f17f71d5 M	src/test/org/apache/commons/math/stat/descriptive/DescriptiveStatisticsTest.java
:100644 100644 b04dc00f17db740d6394c6d24ac9f31e99e388bf 6d58f83a21a5dad76d66670ee49393bd57702922 M	src/test/org/apache/commons/math/stat/descriptive/MultivariateSummaryStatisticsTest.java
:100644 100644 59ef257faca38479932a939598b6efba4775c426 7a22ac639a215c837a5fa4c1be581db9d712ff61 M	src/test/org/apache/commons/math/stat/descriptive/StorelessUnivariateStatisticAbstractTest.java
:100644 100644 0d8228d154ef7e34b50fcbc6aef791797173f77e ed790e33ecfe0d1ff3af081d436e17100316619d M	src/test/org/apache/commons/math/stat/descriptive/moment/VectorialCovarianceTest.java
:100644 100644 a2d85206f14bfd1b9705be1fb0148cb1b3fbb8c1 7dbb57cdd2bb61def34266560f51834c5004c82b M	src/test/org/apache/commons/math/stat/descriptive/moment/VectorialMeanTest.java

8b52d99aa2ac66b04457eb5c0fa49e004d51c8b3
1243814940
William Barker
change to Java 5 compatible

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@780534 13f79535-47bb-0310-9956-ffa450edef68

8b52d99aa2ac66b04457eb5c0fa49e004d51c8b3
:100644 100644 8eb0fe99633cb01bf453ec19568e3c04a9fe478d 26224764b96de20b5c552743fa9f04c5f1c44c62 M	src/java/org/apache/commons/math/ode/nonstiff/AdamsIntegrator.java

05abccebc3e83f016f5922ac31bf78fe8faf8936
1243808298
William Barker
Clean up linear serialization tests

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@780521 13f79535-47bb-0310-9956-ffa450edef68

05abccebc3e83f016f5922ac31bf78fe8faf8936
:100644 100644 97b34b4d4db431f339920738eb46093f4c4dd132 24f044ed4b4dbe22335e1e759af69f9f2aaf206b M	src/test/org/apache/commons/math/linear/DenseFieldMatrixTest.java
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Luc Maisonobe
added an error message for Adams-Bashforth and Adams-Moulton integrators

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Luc Maisonobe
removed obsolete NordsieckTransformer

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Luc Maisonobe
removed obsolete MultiStepInterpolator

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Luc Maisonobe
removed obsolete MultiStepInterpolator

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7b54b47510f9bfaf72d1386f29bbe7a016036b95
1243807646
Luc Maisonobe
completely redesigned Adams-Bashforth and Adams-Moulton integrators
they are now provided by a single class and use the Nordsieck form
with higher derivatives at current step instead of classical form
with only first derivatives but at several steps.
The implementation is simpler for both the integrators and the step
interpolator and it allows a future enhancement with adaptive stepsize.

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Luc Maisonobe
added a step interpolator for multistep methods in Nordsieck form

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1243807277
Luc Maisonobe
updated tests to take into account serialization changes and the new
derivatives consistency check
these tests have been converted to Junit4

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1243807143
Luc Maisonobe
added a general test utility for checking derivatives consistency across all step interpolators

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1243807012
Luc Maisonobe
added a new test problem with polynomial behavior

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Luc Maisonobe
fixed serialization of step interpolators to allow processing them
before the associated integrator update their internal state
(i.e. when currentState is still null)

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1243806816
Luc Maisonobe
added a missing @since

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Luc Maisonobe
use the conversion functions from MatrixUtils

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1243708578
Luc Maisonobe
added conversion utility functions for
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  FieldMatrix<BigFraction> to RealMatrix

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1243453647
Luc Maisonobe
Added a way to retrieve the limited the number of functions evaluations in optimizers
(the limited number of iterations could already be retrieved)

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Luc Maisonobe
Added a way to limit the number of functions evaluations in optimizers
(the number of iterations could already be limited)


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1243432490
Brent Worden
corrected versioning in DOAP

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William Barker
Serializable changes to util

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William Barker
Serializable changes for linear.decomposition

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Phil Steitz
Added trigamma, javadoc fixes for digamma.  JIRA: MATH-267.  Patched by Ted Dunning.

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William Barker
Serializable changes for FieldVector and FieldMatrix

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Luc Maisonobe
removed Serializable from matrix visitors interfaces and classes
it doesn't make sense for these objects as they are intended to be transient

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Luc Maisonobe
removed obsolete imports

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Luc Maisonobe
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Luc Maisonobe
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Phil Steitz
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Phil Steitz
Added digamma function.
JIRA: MATH-267
Contributed by Ted Dunning


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4107cb54fd39d551e0074424b746137aff040faa
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Phil Steitz
Added support for Spearman's rank correlation.
JIRA: MATH-136
Thanks to John Gant


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Phil Steitz
removed duplicate assertion.

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William Barker
Serializable changes for RealMatrix

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William Barker
Serializable changes for RealVector

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Sebastian Bazley
Move Serializable from interface to implementations

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Move Serializable from interface to implementations

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Move Serializable from interface to implementations

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6c2b6d6581b5eec4a7cf72ed3efd8c07305267f3
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Sebastian Bazley
ReMove Serializable from interface
Implementations already implemented it

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a780db15fc1a59d729cd90d10a2e1731fc1f35da
1243000522
Sebastian Bazley
Move Serializable from interface [New to 2.0] to implementations (some existing)


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de8ae4a6935e52fefed269ee62dc2d92640d99fa
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Sebastian Bazley
Move Serializable from interface to implementations
[New to 2.0]

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c808a78dbb86d3aa897ea55a67620573c05105ca
1242999723
Sebastian Bazley
It's a new interface (target release 2.0, not 3.3!)

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53545a16780f04df9f24d05c294223fc384b106b
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Sebastian Bazley
Drop Serializable. 
Interface is new to 2.0, and not implemented except in test code, so no need to do anything further

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Luc Maisonobe
typo

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Sebastian Bazley
Move Serializable from interface to implementation

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William Barker
I've made SparseRealVector and SparseRealMatrix to be empty marker interfaces.

I've left OpenMapRealVector.getSparcity, since I'd like to use it for benchmarking, and it doesn't hurt anyone else now.


git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@777356 13f79535-47bb-0310-9956-ffa450edef68

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799abe1b83ccf6e75c654540120a55e84223ca46
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Luc Maisonobe
added a test for the detection of non-invertible transforms
use Junit 4 style for tests

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@777264 13f79535-47bb-0310-9956-ffa450edef68

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379ad27ea0279c786847bf763cca4f26789ac151
1242940875
Luc Maisonobe
trigger an error when the transform is not invertible

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780e02b61d84b04d6ec22d36d56505e9f0037f57
1242876283
William Barker
Changing DenseRealMatrix to return a specific type, instead of interface type.

I beleive the consensus is to leave RealMatrixImpl and RealVectorImpl alone for now (since they were in 1.2), so that's what I'm doing.


git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@776943 13f79535-47bb-0310-9956-ffa450edef68

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Brent Worden
re-enabled unit test.  changed testutils to use own assertEquals method to safely compare NaN values.

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15dc089dea404c59e1752af6ca55e1faec5bf951
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901b8a9c866f51e3496e236e63298778639e84aa
1242841707
Phil Steitz
Disabled test that fails under GUMP.

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Luc Maisonobe
improved hints for deprecated methods

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@776488 13f79535-47bb-0310-9956-ffa450edef68

0fa07f93e27089455c14068064f64e4b9284b995
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8275bfea9f0c4178ccfd4e6f285ded26a1ff899b
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Luc Maisonobe
typo

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@776410 13f79535-47bb-0310-9956-ffa450edef68

8275bfea9f0c4178ccfd4e6f285ded26a1ff899b
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Luc Maisonobe
added missing @Override

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@776409 13f79535-47bb-0310-9956-ffa450edef68

9c2b5cfda61bf290c7f5bd531d5f73fb5455a2c1
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fa13ca04770ba71ae53ee76f248ca6853272367a
1242739894
Phil Steitz
Added rank transformations.

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@776311 13f79535-47bb-0310-9956-ffa450edef68

fa13ca04770ba71ae53ee76f248ca6853272367a
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d539bb5e232d000954c995dcddc0aeccda5b5012
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Luc Maisonobe
removed unneeded import

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@776048 13f79535-47bb-0310-9956-ffa450edef68

d539bb5e232d000954c995dcddc0aeccda5b5012
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1757b973af087cf4086a3c7cc99a7525ce731617
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Luc Maisonobe
removed unneeded import

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@776045 13f79535-47bb-0310-9956-ffa450edef68

1757b973af087cf4086a3c7cc99a7525ce731617
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73d5ab1ec6d0dcffa7b4169282e656930660a9a3
1242608739
William Barker
Ok, so laking add/subtract tests now.  I'll try to add later, but checking in the existing tests so that [math] will at least build.


git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@775787 13f79535-47bb-0310-9956-ffa450edef68

73d5ab1ec6d0dcffa7b4169282e656930660a9a3
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1ac183419252ac503baa309df8de529907c2d406
1242607361
William Barker
Sparse Matrix/Vector refactoring with mostly return types changed.

Thought that getSparcity was meaninful for SparseRealVector, and added a marker for SparseRealMatrix shape.  Feel free to -1 either ;).

I found an error in the unit tests, so will commit the changes there shortly, after a review.


git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@775784 13f79535-47bb-0310-9956-ffa450edef68

1ac183419252ac503baa309df8de529907c2d406
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446457d7747003d33d1a57db5bdd694b300d2f96
1242598370
William Barker
Initial refactoring of sparse matrix/vector

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@775768 13f79535-47bb-0310-9956-ffa450edef68

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23381b83eda18f37ec58f9590f98bb4479cf384a
1242591574
Luc Maisonobe
simplified DifferentiableMultivariateVectorialFunction
the gradient and partial derivaritves can be retrieved from the jacobian
and adding them at the interface level was cumbersome for implementing
optimization problems.
Now users need to provide only the jacobian method

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@775751 13f79535-47bb-0310-9956-ffa450edef68

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91d0741697127221a73d06315de1ab6753b160a3
1242484147
Phil Steitz
Javadoc fix.

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1241882995
Luc Maisonobe
suppressed two warnings

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Luc Maisonobe
check computed variances in test

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1241863024
Luc Maisonobe
completed internationalization of all error messages

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Luc Maisonobe
improved error messages

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1241602813
Luc Maisonobe
replaced matrix by vector where possible

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William Barker
Adding unit test for SparseFieldMatrix


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Luc Maisonobe
minor style fixes (braces, javadoc ...)

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William Barker
Adding unit test for SparseFieldVector

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William Barker
Adding equals and hashCode

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William Barker
Adding sparse field implememtations

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Luc Maisonobe
improved error messages

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Luc Maisonobe
fixed various checkstyle and findbugs errors

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1241292891
Luc Maisonobe
added a clustering package with an implementation of k-means++
JIRA: MATH-266

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@770979 13f79535-47bb-0310-9956-ffa450edef68

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Luc Maisonobe
Added distance1, distance and distanceInf utility methods for double and int arrays in MathUtils
JIRA: MATH-265

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Luc Maisonobe
updated documentation for ODE after recent changes

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Luc Maisonobe
simplified Nordsieck transformer
extended its domain to handle several layouts for multistep state

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Luc Maisonobe
added getNorm1, getNormInf, distance1 and distanceInf to the Vector3D class

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Luc Maisonobe
typo in HTML 4 entity

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1241030039
Luc Maisonobe
Added an utility equality method between double numbers using tolerance
in ulps (Units in Last Position) 
JIRA: MATH-264

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Luc Maisonobe
typo

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William Barker
Forgot to include licence :(

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William Barker
Adding unit test for OpenIntToFieldHashMap

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Luc Maisonobe
typo

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1240848243
Luc Maisonobe
event handlers in ODE now also provide the switching function variation
(increasing/decreasing) when an event occurs

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1240842745
Luc Maisonobe
reduced test size

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b53f5d7a42e64a8a2dc259f93f500a54447095b5
1240829512
Phil Steitz
Added AggregateSummaryStatistics class to support aggregation of SummaryStatistics. 
JIRA: MATH-224
Reported by Andre Panisson
Patched by John Bollinger


git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@768921 13f79535-47bb-0310-9956-ffa450edef68

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1240766099
Phil Steitz
Improved error messages.

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@768727 13f79535-47bb-0310-9956-ffa450edef68

6ae7eb040dc8b2aef45695cf6bf657d44b1a7a4a
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1240702096
William Barker
Javadoc fixes, sorry for the noise

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@768625 13f79535-47bb-0310-9956-ffa450edef68

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1240700109
William Barker
Need to find out why autoprops isn't working

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@768622 13f79535-47bb-0310-9956-ffa450edef68

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William Barker
Adding backing class for sparse Field vectors and matricies

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1240688378
Luc Maisonobe
added javadoc

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Luc Maisonobe
fixed an Adams-Moulton order error, it was one unit too large
and inconsistent with the order of the underlying predictor

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1240624883
Sebastian Bazley
Javadoc fixes

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1240624844
Sebastian Bazley
Unnecessary casts

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1240624726
Sebastian Bazley
Can't inheritDoc unless implementing or overriding something ...

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Sebastian Bazley
MATH-261 - start adding some generics to Frequency

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William Barker
Fix equals and hashcode to do exact comparisons

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Luc Maisonobe
replaced a Java6 specific signature with its Java5 counterpart
(Array.newInstance(Class<T>, int ...)  --> (Array.newInstance(Class<T>, int[])

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1240261113
Luc Maisonobe
fixed warnings about serial version ID

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Luc Maisonobe
fixed missing dimension checks

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Luc Maisonobe
deprecated tests for deprecated methods
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Luc Maisonobe
added DenseFieldMatrix

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1240258732
Luc Maisonobe
use the buildArray method from base class
it has better generic parameter specification
and does initialize array elements

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Luc Maisonobe
use a simpler syntax for a generic static test function

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Luc Maisonobe
converted buildArray to static, so it can be used from other static methods

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Luc Maisonobe
optimized isInfinite for NaN vectors
reverted hashcode back to its previous behavior to avoid breaking consistency with equals

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Phil Steitz
Removed tabs.

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Luc Maisonobe
fixed checkstyle errors

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Luc Maisonobe
removed TAB characters that crept in as of r762194 two weeks ago

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Luc Maisonobe
added support for any kind of field in linear algebra
we can now use FieldMatrix<Fraction> and use exact LU-decomposition
on such matrices to solve linear systems

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1240158877
Luc Maisonobe
Added the generic Field/FieldElement interfaces on top
of existing Complex, Fraction and BigFraction
Added a new BigReal class wrapping a BidDecimal and implementing FieldElement

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57efba92ca35ec177fd8c8b4a39e97188152ec6b
1240158719
Luc Maisonobe
added Field and FieldElement interfaces to allow algorithms
operate on any type of field.
This change is related to the discussion on dev list
http://markmail.org/message/h2rmq6wo7nwqzx4w

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@766482 13f79535-47bb-0310-9956-ffa450edef68

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003c98d087ddbe011263bf4882de190c7f3e6cbe
1240067832
Luc Maisonobe
fixed an error in SparseRealVector.isInfinite, NaN was not checked beforehand
fixed an error in SparseRealVector.hashcode, code did not depend on vector entries
fixed tests accordingly

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1240054676
Sebastian Bazley
Remove obsolete Maven1 files

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1240000312
Luc Maisonobe
removed tests not meaningful for sparse vectors
reactivated some commented-out tests

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Sebastian Bazley
Use UTF-8 encoding for copying resources to avoid platform dependency

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Sebastian Bazley
MATH-259 - throw IllegalArgument rather than ClassCast to better retain original behaviour

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1239975299
Sebastian Bazley
MATH-259 - check for Comparable when adding values

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1239973646
Sebastian Bazley
Make HashMap final as it is only set in the ctors
Document behaviour of getCount(Object v) if v is not comparable
Save value of getSumFreq() from DIV/0 check so we don't calculate it twice

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Sebastian Bazley
Remove non-thrown throws clauses

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Sebastian Bazley
Parameterise raw type

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Remove unnecessary semi-colons

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Sebastian Bazley
Unused import

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Sebastian Bazley
Remove unnecessary null checks

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Phil Steitz
Fixed some errors, improved content.

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Phil Steitz
Clarified javadoc, added tests. JIRA: MATH-258

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Phil Steitz
Fixed internal links and added covariance and correlation section.

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Phil Steitz
Made method names consistent, added methods to default bias-correction.

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Phil Steitz
Changed method name to be consistent with Covariance, added double[][] compute method.

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Phil Steitz
Fixed incorrect type spec, simplified references.

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Phil Steitz
Dropped extraneous parens.

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Phil Steitz
Dropped extraneous parens.

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Phil Steitz
Restored some double casts to improve ensure correctness does not depend on order of operations or literal conversion, dropped uneccesary parens.

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Luc Maisonobe
added a transformer between Nordsieck form and multistep form
for state history in multistep ODE integrators
(this will help implementing adaptive stepsize multistep integrators)

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Luc Maisonobe
removed unused import statements

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Luc Maisonobe
added a threshold for comparisons in Simplex solver
Jira: MATH-246

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Brent Worden
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fixed findbugs warnings and added more explanation about the corresponding behavior in javadoc

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Luc Maisonobe
added missing javadoc

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Luc Maisonobe
Fixed inconsistent access to multidimensional array in FastFourierTransformer

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Luc Maisonobe
fixed typo in error message

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Sebastian Bazley
Cannot be null here

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Sebastian Bazley
Make private static fields final.

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Sebastian Bazley
Remove unnecessary casts and unnecessary semi-colons

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Sebastian Bazley
Remove unnecessary casts, unnecessary throws and unnecessary semi-colons

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584e732456ca76a961ae296a1c2c059f0ddb2949
1238950415
Luc Maisonobe
Greatly improved multiplication speed for sparse matrices
Jira: MATH-248

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@762117 13f79535-47bb-0310-9956-ffa450edef68

584e732456ca76a961ae296a1c2c059f0ddb2949
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f46ebfe991c8078e254143385ffd61c42cb48f88
1238950133
Sebastian Bazley
Remove unnecessary casts

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@762116 13f79535-47bb-0310-9956-ffa450edef68

f46ebfe991c8078e254143385ffd61c42cb48f88
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55a5e54455c21833b407fbd52b5e66888f211ec7
1238945586
Luc Maisonobe
Fixed threading issues with MathException and MathRuntimeException
Jira: MATH-253

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@762107 13f79535-47bb-0310-9956-ffa450edef68

55a5e54455c21833b407fbd52b5e66888f211ec7
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382b57344ca9dbb3ef669d0fa41e3124c3867fb1
1238944563
Luc Maisonobe
Fixed threading issues with UnivariateRealSolverUtils factory
Jira: MATH-254

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@762102 13f79535-47bb-0310-9956-ffa450edef68

382b57344ca9dbb3ef669d0fa41e3124c3867fb1
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6fbda16e8533950829ef3ba09722d39672bfaf91
1238944047
Luc Maisonobe
fixed typo

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@762100 13f79535-47bb-0310-9956-ffa450edef68

6fbda16e8533950829ef3ba09722d39672bfaf91
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6750484753d78a0ff278506137aceccfa14ee4f0
1238942169
Luc Maisonobe
Reduced visibility of MessagesResources_fr.contents field to private
JIRA: MATH-255

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@762096 13f79535-47bb-0310-9956-ffa450edef68

6750484753d78a0ff278506137aceccfa14ee4f0
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da1a5916e45abd0fc0adcfb56eeeab8b14314a0e
1238941743
Luc Maisonobe
added Fraction.toString()
Jira: MATH-256

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@762095 13f79535-47bb-0310-9956-ffa450edef68

da1a5916e45abd0fc0adcfb56eeeab8b14314a0e
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9c8d2c79c1ef565337599849cd066ff63b8d5816
1238941218
Luc Maisonobe
added missing @Override annotations

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@762087 13f79535-47bb-0310-9956-ffa450edef68

9c8d2c79c1ef565337599849cd066ff63b8d5816
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3597812efa15c4422bd3c4900a86f4cc01105ee7
1238879293
Sebastian Bazley
Make private static fields final, as they are not changed currently.
[If they were mutable, this would make the class thread-hostile.]

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@762011 13f79535-47bb-0310-9956-ffa450edef68

3597812efa15c4422bd3c4900a86f4cc01105ee7
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b8711300e4923ede5450bdc89dfcf339445b3430
1238879101
Sebastian Bazley
Might as well make the variable final as it is private and not changed

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@762009 13f79535-47bb-0310-9956-ffa450edef68

b8711300e4923ede5450bdc89dfcf339445b3430
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d3cfb2ad596373fcef8ef0d1d16fcf133de1ae66
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Phil Steitz
Replaced JDK 1.6 constant.

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@761994 13f79535-47bb-0310-9956-ffa450edef68

d3cfb2ad596373fcef8ef0d1d16fcf133de1ae66
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9593ad61236471386d5ec2182257951ebfce1f38
1238686239
Luc Maisonobe
fixed a serialization warning

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@761325 13f79535-47bb-0310-9956-ffa450edef68

9593ad61236471386d5ec2182257951ebfce1f38
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d09782308cf5598cfedc6e1238e17312378da684
1238686185
Luc Maisonobe
moved multistep integrator and step interpolator base classes to their corresponding generic package

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@761323 13f79535-47bb-0310-9956-ffa450edef68

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c9255319a6f38f59cf590f30281d5caed4686d93
1238663156
Luc Maisonobe
fixed a missing absolute value in a test threshold

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@761213 13f79535-47bb-0310-9956-ffa450edef68

c9255319a6f38f59cf590f30281d5caed4686d93
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1238596158
Luc Maisonobe
removed the constraint on low degree polynomials
when building Chebyshev, Hermite, Laguerre or Legendre polynomials

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@760901 13f79535-47bb-0310-9956-ffa450edef68

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1238588129
Luc Maisonobe
Added  add/subtract/multiply/divide functions with integer parameters to Fraction

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Luc Maisonobe
optimized some fraction operations (mainly pow)
replaced pow(BigFraction) by pow(double) as it already converted the argument to double upon entry
added tests for pow

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Luc Maisonobe
Added some utility functions to compute powers with integral types (int, long, BigInteger)

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Luc Maisonobe
added a test parsing very large integers

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Luc Maisonobe
Fixed a comparison error when two different fractions evaluate to the
same double due to limited precision.
Jira: MATH-252


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Luc Maisonobe
added proper and improper formats for BigFraction (both parsing and display)

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Luc Maisonobe
removed an unneeded call to reduce()
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Luc Maisonobe
removed BigFraction.clone() as the class is guaranteed to be immutable

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Luc Maisonobe
Added a BigFraction class that does not overflow when big numerators or denominators are used.
Jira: MATH-251

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Luc Maisonobe
fixed an error in Simplex algorithm when several ambiguous solutions exist

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Luc Maisonobe
fixed javadoc error

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Luc Maisonobe
removed spurious import clause

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Luc Maisonobe
added an implementation of Dantzig's simplex algorithm
to solve constrained linear optimization problems
JIRA: MATH-246

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1238108427
Luc Maisonobe
fixed checkstyle and findbugs errors

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1237935409
Luc Maisonobe
updated documentation after changes in the optimization framework
JIRA: MATH-177

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Luc Maisonobe
improved consistency in class naming with respect to functions in the analysis package

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Luc Maisonobe
added an implementation of a non-linear conjugate gradient optimizer

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1237932908
Luc Maisonobe
updated general algorithms with latest interfaces definitions

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Luc Maisonobe
updated univariate algorithms with latest interfaces definitions

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Luc Maisonobe
updated direct algorithms with latest interfaces definitions

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e90541ee13c8623b54f66b50fad83b9a72b4bfa5
1237932752
Luc Maisonobe
added new simple convergence checkers implementations

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@758053 13f79535-47bb-0310-9956-ffa450edef68

e90541ee13c8623b54f66b50fad83b9a72b4bfa5
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069999454d6a538d14927e7e64c01609da4ba013
1237932676
Luc Maisonobe
improved consistency in class naming with respect to functions in the analysis package

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@758052 13f79535-47bb-0310-9956-ffa450edef68

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04afca038ee4a0c31b862e0e013c8a414db5f747
1237932616
Luc Maisonobe
removed spurious exception in optimization

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@758051 13f79535-47bb-0310-9956-ffa450edef68

04afca038ee4a0c31b862e0e013c8a414db5f747
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faecb297b9c67d111aae9a73553bc4ebec90491a
1237932574
Luc Maisonobe
improved consistency in class naming with respect to functions in the analysis package

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@758049 13f79535-47bb-0310-9956-ffa450edef68

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b219ec6d7d7d6302328f7185604eedabdaac7bbb
1237932399
Luc Maisonobe
removed spurious exception in optimization

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@758047 13f79535-47bb-0310-9956-ffa450edef68

b219ec6d7d7d6302328f7185604eedabdaac7bbb
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06d69c3273aa661eb931fa8466ab543f141d3a27
1237932313
Luc Maisonobe
use a single set of consistent functions definitions in the analysis package
instead of one set in the analysis and another one in optimization


git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@758046 13f79535-47bb-0310-9956-ffa450edef68

06d69c3273aa661eb931fa8466ab543f141d3a27
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a22972bab6b827f94bf2c5a644929418ae18b3c0
1237727945
Luc Maisonobe
fixed a forgotten counter update

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@757183 13f79535-47bb-0310-9956-ffa450edef68

a22972bab6b827f94bf2c5a644929418ae18b3c0
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a7faf40b61f445d15d9a210b23fa0008b87e25e2
1237726800
Luc Maisonobe
separated iteration counter from function evaluation counters,
some optimizers are based on gradient/jacobian only and cannot
reliably be protected by monitoring the objective function calls.

We now have two or three counters for each algorithm:
 - iteration counter, which is checked against a max allowance
   to prevent infinite loops if no convergence is reached
 - objective function evaluations, for user information only
 - objective function gradient/jacobian if the function is
   differentiable, for user information only

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@757181 13f79535-47bb-0310-9956-ffa450edef68

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794f8fb4805f2f4c9ec2604d8b9b23ece1453aa8
1237726485
Luc Maisonobe
renamed SimpleValueChecker into SimpleScalarValueChecker
for consistency with the vectorial checker name

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@757180 13f79535-47bb-0310-9956-ffa450edef68

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513511976ddc778f7c52d69bf43db3c3f4b88803
1237152938
Luc Maisonobe
fixed checkstyle and findbugs errors

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@754765 13f79535-47bb-0310-9956-ffa450edef68

513511976ddc778f7c52d69bf43db3c3f4b88803
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b5cf53f629502237cd09ce8ea152f0522198d0e4
1237152887
Luc Maisonobe
updated documentation after the redesign of the optimization package

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@754764 13f79535-47bb-0310-9956-ffa450edef68

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f32c25c23ab75ae08a616621e8a060c7f9ec4e66
1237152811
Luc Maisonobe
added all necessary multi-start optimizers types

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@754763 13f79535-47bb-0310-9956-ffa450edef68

f32c25c23ab75ae08a616621e8a060c7f9ec4e66
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a889c1a539a0834c787a2180e88ce622470348d3
1237151019
Luc Maisonobe
removed a spurious print statement

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@754750 13f79535-47bb-0310-9956-ffa450edef68

a889c1a539a0834c787a2180e88ce622470348d3
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b5783028ce133627ca332ea83ae6d8572c631d4d
1237149227
Luc Maisonobe
fixed typo in package documentation

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@754744 13f79535-47bb-0310-9956-ffa450edef68

b5783028ce133627ca332ea83ae6d8572c631d4d
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32f05fb5f66fa26c15f6e1e8a09d238d5085b101
1237145444
Luc Maisonobe
resurrected the estimation package but with all interfaces and classes deprecated
this will help users switch smoothly to the new optimization.general package

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@754732 13f79535-47bb-0310-9956-ffa450edef68

32f05fb5f66fa26c15f6e1e8a09d238d5085b101
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8541f303370cec9a25f2b32b3d660b3f188913f0
1237144262
Luc Maisonobe
adapted old Levenberg-Marquardt estimator to new top level optimizers API

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@754727 13f79535-47bb-0310-9956-ffa450edef68

8541f303370cec9a25f2b32b3d660b3f188913f0
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8cb418e7fa50aba9977fe073aec66ad3f6e4f07c
1237052307
Luc Maisonobe
adapted the Gauss-Newton optimizer to the new top-level optimization interfaces

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@754500 13f79535-47bb-0310-9956-ffa450edef68

8cb418e7fa50aba9977fe073aec66ad3f6e4f07c
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97686434d3664c6d04810bd746aa740071dd56a9
1237052149
Luc Maisonobe
updated optimization main interfaces to handle scalar and vectorial functions
and to handle functions with or without explicit derivatives

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@754499 13f79535-47bb-0310-9956-ffa450edef68

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1a47f53684b77146c807b20781b2e831523b0b6c
1236125271
Luc Maisonobe
continued refactoring of optimization framework:
 - improved general interfaces at top optimization level
 - added a simple implementation of ConvergenceChecker (ObjectiveValueChecker)
 - added a general multi-start wrapper
 - changed the direct search optimizers to the new interfaces

This work is still not complete yet. The general package classes
are very close to the former design, they have almost not been changed
structurally.

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@749850 13f79535-47bb-0310-9956-ffa450edef68

1a47f53684b77146c807b20781b2e831523b0b6c
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95836d833482615c11d46e2e655f3eea06a641d7
1235946082
Luc Maisonobe
added compareTo method with epsilon
JIRA: MATH-247

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@749139 13f79535-47bb-0310-9956-ffa450edef68

95836d833482615c11d46e2e655f3eea06a641d7
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fbe565694aa2721d4a8538eb053171cc8ecfde47
1235675859
Luc Maisonobe
started refactoring of optimization framework:
 - created subpackages optimization.direct, optimization.general,
   optimization.linear (currently empty) and optimization.univariate
 - removed packages analysis.minimization and estimation
 - renamed all Cost-related interfaces/classes into Objective
   (this allows both minimization and maximization)
 - added a few new general interfaces

This work is not complete yet. The direct and general packages classes
are very close to the former design, they have almost not been changed
structurally.

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@748274 13f79535-47bb-0310-9956-ffa450edef68

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911f0fe11146590554ec11d1277d6e2ba55bd7e9
1235532772
William Barker
epsilon needs to be set before calling isZero, plus copy epsilon for append

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@747650 13f79535-47bb-0310-9956-ffa450edef68

911f0fe11146590554ec11d1277d6e2ba55bd7e9
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2628b29e876bf69f58727a8ef9d63924f8f87a27
1235509181
Luc Maisonobe
minor code cleanups
(error messages, javadoc, avoiding array copies, final attributes ...)

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@747544 13f79535-47bb-0310-9956-ffa450edef68

2628b29e876bf69f58727a8ef9d63924f8f87a27
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7ff6d072ece0452874aa2ceeb94eba7305e02cf0
1235247698
Luc Maisonobe
fixed wrong word in javadoc

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@746583 13f79535-47bb-0310-9956-ffa450edef68

7ff6d072ece0452874aa2ceeb94eba7305e02cf0
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6eec202b7d66dbeb4e2c2b4fa4214b359134ea2f
1235247396
Luc Maisonobe
handle NaN and infinities correctly in the MathUtils.equals method with tolerance

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@746582 13f79535-47bb-0310-9956-ffa450edef68

6eec202b7d66dbeb4e2c2b4fa4214b359134ea2f
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8c8e46f65c08a168679b39a0b33a4155922bf3e2
1235246579
Luc Maisonobe
fixed exception type in a test

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@746579 13f79535-47bb-0310-9956-ffa450edef68

8c8e46f65c08a168679b39a0b33a4155922bf3e2
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7f88773d6c3c96c0a2fd24c3e50d1eb80daca11d
1235246474
Luc Maisonobe
replaced Object[] parameters by variable arguments in exceptions constructors
this allows simpler error declaration and removes the need for the strange
null argument with fixed messages

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@746578 13f79535-47bb-0310-9956-ffa450edef68

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58b5609fe8f99aabc990d885bf6c4d85631b7c79
1235224465
Luc Maisonobe
Fixed an error in computing gcd and lcm for some extreme values at integer range boundaries.
JIRA: MATH-243

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@746511 13f79535-47bb-0310-9956-ffa450edef68

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924b6d76a2d44baf858c3aee46ab1439c9641959
1235223368
Luc Maisonobe
Added a MathUtils method to check equality given some error bounds
JIRA: MATH-247

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@746506 13f79535-47bb-0310-9956-ffa450edef68

924b6d76a2d44baf858c3aee46ab1439c9641959
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Luc Maisonobe
added a no-args constructor for GaussNewtonEstimator

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@745188 13f79535-47bb-0310-9956-ffa450edef68

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Phil Steitz
Increased sensitivity of test and added another p-value verification.

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@744918 13f79535-47bb-0310-9956-ffa450edef68

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1234760989
Phil Steitz
Added Pearsons correlation implemendation. JIRA: MATH-114

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@744802 13f79535-47bb-0310-9956-ffa450edef68

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Phil Steitz
Changed to persist and expose the number of observations in the source dataset.

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Luc Maisonobe
moved the decomposition algorithms in a subpackage of the linear package

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@744768 13f79535-47bb-0310-9956-ffa450edef68

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36ce2d6c7f3547321ab8a31e58f32f69bc0f4986
1234725351
Luc Maisonobe
improved error messages consistency
fixed checkstyle warnings

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@744724 13f79535-47bb-0310-9956-ffa450edef68

36ce2d6c7f3547321ab8a31e58f32f69bc0f4986
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6fce0ba9870aedea135b2001720a9505a3e71a85
1234723231
Luc Maisonobe
fixed findbugs warning

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@744717 13f79535-47bb-0310-9956-ffa450edef68

6fce0ba9870aedea135b2001720a9505a3e71a85
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46b75fa18c316c8e5ad2a288aeaca2684c165429
1234723129
Luc Maisonobe
fixed checkstyle warnings

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@744716 13f79535-47bb-0310-9956-ffa450edef68

46b75fa18c316c8e5ad2a288aeaca2684c165429
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4b1e08ea11ba68f8900b6a6f0fd423715c2c0fd9
1234720412
Luc Maisonobe
added Cholesky decomposition

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@744708 13f79535-47bb-0310-9956-ffa450edef68

4b1e08ea11ba68f8900b6a6f0fd423715c2c0fd9
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0982dbed0d08323eca63a8b05fbe5bd55cb6bfca
1234712632
Luc Maisonobe
removed references to InvalidStateException, they are never thrown
cleaned up exception messages

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@744682 13f79535-47bb-0310-9956-ffa450edef68

0982dbed0d08323eca63a8b05fbe5bd55cb6bfca
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566b8c16d3adc9b60defb78a8dc8bf5b3bcf89e5
1234712390
Luc Maisonobe
moved NotPositiveDefiniteMatrixException to the linear package

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@744681 13f79535-47bb-0310-9956-ffa450edef68

566b8c16d3adc9b60defb78a8dc8bf5b3bcf89e5
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d07f552a2b13801bdef5b5a0b8d213fba7342b0a
1234680375
William Barker
Add working equals to SparseRealVector.

hashCode implementation is minimal, but I can't see a use case for using a SparseRealVector as a key.

Remove unused imports from OpenInToDoubleHashMap.

Some cleanup for optimized methods, and javadoc fixes.


git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@744614 13f79535-47bb-0310-9956-ffa450edef68

d07f552a2b13801bdef5b5a0b8d213fba7342b0a
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:100644 100644 fee502217dfa5ebba0b396ee1a38db84b7ffcb90 3b8c6c4665c20a17a4f13d9c21111640217b5e36 M	src/test/org/apache/commons/math/linear/SparseRealVectorTest.java

5f4e953b58f3e35ae21481e4df93bf26eea0c573
1234535928
Luc Maisonobe
Failed attempt to implement Strassen matrix multiplication on recursive layout as
described in Siddhartha Chatterjee, Alvin R. Lebeck, Praveen K. Patnala and Mithuna
Thottehodi paper "Recursive Array Layout and Fast Matrix Multiplication".

As of 2009-02-13, this implementation does not work! The padding at left and bottom
sides of the matrix should be cleared after some operations like scalerAdd and is not.
Also there is a limitation in the multiplication that can only process matrices with
sizes similar enough to have the same power of two number of tiles in all three
matrices A, B and C such that C = A*B. These parts have not been fixed since the
performance gain with respect to DenseRealMatrix are not very important, and the
numerical stability is poor.

This may well be due to a bad implementation.

This code has been put in the experimental directory for the record, putting it into
production would require solving all these issues.


git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@744126 13f79535-47bb-0310-9956-ffa450edef68

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2fcdbb07ce96a28d082acf86ee9891e5fb2a341d
1234437714
Phil Steitz
Added correlation package, Covariance class.  JIRA: MATH-114

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@743688 13f79535-47bb-0310-9956-ffa450edef68

2fcdbb07ce96a28d082acf86ee9891e5fb2a341d
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2ece00af52466502db7fcc6c00c6c6bb8f2dbbce
1234234958
William Barker
remove eclipse generated equals since it doesn't work.  Will add a working equals later

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@742837 13f79535-47bb-0310-9956-ffa450edef68

2ece00af52466502db7fcc6c00c6c6bb8f2dbbce
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0dfcb4f19d76ea36e0eaaca8d3ae90956e76f7ef
1234183280
William Barker
Fis some problems with equals for OpenInttoDoubleHashmap.


git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@742445 13f79535-47bb-0310-9956-ffa450edef68

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f24be14aaa099d18b15ee2cb295c8951a3154866
1234155027
William Barker
Mostly completing the methods that don't make sense if using a sparse vector in the first place.  Initial implementations for equals on the backing store, but it seems it will need more work (since still have to comment out junit tests).  
Making  checkVectorDimensions protected instead of public on all RealVector classes.


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1234121409
Phil Steitz
Exposed sums of squares.

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Phil Steitz
Moved matrix equality tests to TestUtils.

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1233755990
Luc Maisonobe
improved consistency between RealVector and RealMatrix API
JIRA: MATH-245

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1233691160
Luc Maisonobe
applied Cyril Briquet's patch (with slight changes) to improve FastFourierTransform efficiency
JIRA: MATH-216

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1233570620
Luc Maisonobe
javadoc typo

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1233543053
William Barker
revert accedental work-in-progress commit

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1233542568
William Barker
property sets 

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1233542427
William Barker
property sets mostly, some broken method fixes

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1233522835
Luc Maisonobe
added a PolynomialsUtils class providing factory methods for
Chebyshev, Hermite, Laguerre and Legendre polynomials
the code was extracted from mantissa and modified

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@739840 13f79535-47bb-0310-9956-ffa450edef68

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b1d89deddef03a6a3401b4cbf14608fe46a359ad
1233522415
Luc Maisonobe
fixed an error introduced by a recent change in PolynomialsFunction
(the coefficients array is automatically reduced if high degree coefficients are null)

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@739836 13f79535-47bb-0310-9956-ffa450edef68

b1d89deddef03a6a3401b4cbf14608fe46a359ad
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323475fd1cbfd2f59bde7506ef72d50ec501421f
1233521772
Luc Maisonobe
Added add, subtract, negate, multiply and toString methods to PolynomialFunction

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@739834 13f79535-47bb-0310-9956-ffa450edef68

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e4acfb1ab321d1101d2c7a4e24937a54029b225a
1233448087
William Barker
Adding constructors that allow specifing epsilon.
Remove the isZero(int) method, since it is inconsistant with the isZero(double) method, and this class is tightly bound to it's backing store.
Some javadoc fixes.


git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@739667 13f79535-47bb-0310-9956-ffa450edef68

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1233417222
Sebastian Bazley
Javadoc typos

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@739571 13f79535-47bb-0310-9956-ffa450edef68

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1233377477
William Barker
Initial checkin for the SparseRealVectorClass.

I know that it doesn't work 100% with the map*** methods that shouldn't be used with a sparse vector.  I'll clean those up shortly (including uncommenting unit tests).  Just want to get more eyes on this for the methods that matter.


git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@739504 13f79535-47bb-0310-9956-ffa450edef68

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e9daa97ee5b95002a42caad3dc0d72fea75c8203
1233122462
William Barker
Adding me to the list

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@738375 13f79535-47bb-0310-9956-ffa450edef68

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1233120031
William Barker
Correct bug that prevents replacing an element while using an iterator

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1232911701
Phil Steitz
Changed FractionFormat to extend NumberFormat.  JIRA: MATH-189

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Phil Steitz
Added 1.2 release.

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1232826669
Phil Steitz
Fixed project name.

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Phil Steitz
Replaced maven-generated ant build with standalone version adapted from [io].

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Phil Steitz
Eliminated advertised exceptions that are no longer thrown.

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Luc Maisonobe
various javadoc fixes

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be3dacd09f4fde7fc48fa93337ab458d59cc8982
1232737691
Luc Maisonobe
fixed missing word

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@737152 13f79535-47bb-0310-9956-ffa450edef68

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Luc Maisonobe
fixed missing javadoc parameter

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@737151 13f79535-47bb-0310-9956-ffa450edef68

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ff3bab11deea7386a9ac9e3c4675fcecff53d106
1232737461
Luc Maisonobe
fixed wrong subversion directory

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1232737421
Luc Maisonobe
fixed special xml characters

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e16786f252b63073accfd843c7a93505eea98985
1232710227
Phil Steitz
Changed NaN comparison tests to use TestUtils.assertSame.

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e16786f252b63073accfd843c7a93505eea98985
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e59742b4629a63a798c030db41f6276f716a23e6
1232537436
Phil Steitz
Forced symmetry in binomialCoefficientLog and added test cases for MathUtils.
JIRA: MATH-242
Reported and patched by Christian Semrau

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@736288 13f79535-47bb-0310-9956-ffa450edef68

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85a8ab2dcfc26e83be1514acdb11d3feaac3e73d
1232409122
Phil Steitz
Fixed error in binomial coefficient computation
JIRA: MATH-241
Reported and patched by Christian Semrau

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@735879 13f79535-47bb-0310-9956-ffa450edef68

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1232408414
Luc Maisonobe
added a Legendre-Gauss integrator

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@735876 13f79535-47bb-0310-9956-ffa450edef68

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6378fb99209275e2da4f15664d87bab2aff2e47f
1232400345
Phil Steitz
No code change.  Fixed spelling errors in comments.

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7cd3d822b65b7acdd1f6e1c82b291cd994f4fe05
1232394181
Phil Steitz
Fixed error in factorial accuracy.  JIRA: MATH-240.

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3112f69e1d789e00fb21a1dde901b313547fed60
1232312982
Luc Maisonobe
removed commented out code

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3112f69e1d789e00fb21a1dde901b313547fed60
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315778e8b53471f9ba12e82b8bd6d6eee49f143f
1232312775
Luc Maisonobe
improved consistency between solvers/integrators
by providing the integrand function as a parameter to integrate
rather that at construction, thus allowing reuse of a configured integrator
Jira: MATH-218

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@735545 13f79535-47bb-0310-9956-ffa450edef68

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47dbe73de639fac31d05faa4d11140c51cc3b075
1232311516
Luc Maisonobe
added absolute accuracy handling for integrators

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@735536 13f79535-47bb-0310-9956-ffa450edef68

47dbe73de639fac31d05faa4d11140c51cc3b075
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1232308132
Luc Maisonobe
trying to recover history for solvers

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1232297849
Luc Maisonobe
fixed various minor bugs identified by checkstyle and findbugs

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1232295192
Luc Maisonobe
added missing header

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fa15a15b9e45852dff7ebe2ae490dd78680862d3
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85387dc2d55dbbcc54063ff1ec2ab1f909bef7a4
1232293175
Luc Maisonobe
Added a new minimization package with an implementation of the Brent algorithm
contributed by Gilles Sadowski.
The implementation needs some testing as it seems to never use the parabola fitting
and only relying on golden section. This may be due to the refactoring I did on
the original patch.
Jira: MATH-177

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@735475 13f79535-47bb-0310-9956-ffa450edef68

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1422c5df3ce320396850bcf42e840c8714499804
1232290071
Luc Maisonobe
extracted a superinterface ConvergingAlgorithm from UnivariateRealSolver
for later reuse by upcoming minimization algorithms

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@735468 13f79535-47bb-0310-9956-ffa450edef68

1422c5df3ce320396850bcf42e840c8714499804
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5b6969f0980eb50a2b6aec9f6b193ecc6f5aa7a6
1232284678
Luc Maisonobe
split the analysis package into several sub-packages

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@735452 13f79535-47bb-0310-9956-ffa450edef68

5b6969f0980eb50a2b6aec9f6b193ecc6f5aa7a6
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1d1436557bcb21887d9b352dd0f5f3d3acb71e11
1232284042
Luc Maisonobe
split the analysis package into several sub-packages

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@735449 13f79535-47bb-0310-9956-ffa450edef68

1d1436557bcb21887d9b352dd0f5f3d3acb71e11
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3a8a9685ec252116dce375ae9ca61f4cd41fa70f
1232212090
Phil Steitz
javadoc formatting only.

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@735312 13f79535-47bb-0310-9956-ffa450edef68

3a8a9685ec252116dce375ae9ca61f4cd41fa70f
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a96e597894562c2cf01fc678f6c435d65ccc31c5
1232147192
Luc Maisonobe
fixed overflow error in gdc computation
JIRA: MATH-238

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@735178 13f79535-47bb-0310-9956-ffa450edef68

a96e597894562c2cf01fc678f6c435d65ccc31c5
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ee88057ba86b543c4f678f8e28b1620c22b19f0f
1231213589
Phil Steitz
Changed return type of nthRoot to List
Renamed getPhi to getArgument
Changed and documented behavior of nthRoot wrt NaN, infinite components
Improved nth root computation
Added some test cases

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@731822 13f79535-47bb-0310-9956-ffa450edef68

ee88057ba86b543c4f678f8e28b1620c22b19f0f
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9fafb86f4c4d34afd1fdf9df8c8e8b2ccb54f413
1231194772
Luc Maisonobe
removed two false positives from findbugs

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@731749 13f79535-47bb-0310-9956-ffa450edef68

9fafb86f4c4d34afd1fdf9df8c8e8b2ccb54f413
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ea2e132c223b45570d3e99babf69f6b886729e6e
1231193832
Luc Maisonobe
updated findbugs plugin version
fixed exclusion rule for some false positives

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@731746 13f79535-47bb-0310-9956-ffa450edef68

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Phil Steitz
Changed covariance matrix computation to use QR decomp.

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Phil Steitz
Added standard errors.

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Luc Maisonobe
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Luc Maisonobe
removed unused exception clause

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Luc Maisonobe
added missing header

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Luc Maisonobe
removed all external decomposition solvers

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Phil Steitz
Javadoc only.  Cleanup formatting.

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Luc Maisonobe
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Luc Maisonobe
fixed a dimension error with under-determined problems
removed IllegalStateException
create a DenseRealMatrix when solving A.X = B

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Luc Maisonobe
fixed a block width computation error

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Luc Maisonobe
fixed wrong matrix type in test ...
sorry

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Luc Maisonobe
new tests

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Luc Maisonobe
added a missing error message

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Luc Maisonobe
avoid ugly call to getDataRef that relies on vector internal implementation

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Luc Maisonobe
added copySubmatrix methods
use matrix visitors to implement some existing methods more efficiently

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Luc Maisonobe
added default implementations of the matrix visitors interfaces

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Phil Steitz
Added hat matrix computation.

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Phil Steitz
Changed to use updated decomp API.

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Luc Maisonobe
added a static method createBlocksLayout to prepare array before constructing the matrix

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Luc Maisonobe
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Luc Maisonobe
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Luc Maisonobe
added column walking order
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Luc Maisonobe
fixed typos

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Luc Maisonobe
fixed a forgotten scaling factor in inverse Hadamard transform
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note that the integer transform inverse is not always an integer transform

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Luc Maisonobe
replaced TeX formulas by HTML formulas

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b52302121bb18d9804b47722e92e08de31a946ef
1230487768
Luc Maisonobe
Added a RealTransformer interface on top of cosine, sine and Hadamard transforms.
The Fourier transform cannot implement this interface since it produces complex results.
Improved error messages.

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@729758 13f79535-47bb-0310-9956-ffa450edef68

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6120284c3713886137a3fc71e27606b8f32c9eb2
1230411312
Luc Maisonobe
Added method to walk matrix entries with or without changing them in the
visitor design pattern sense. Two different orders can be used, row by row
of following internal storage. Internal order should be preferred when no
specific order is needed, because it will be more cache efficient.


git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@729673 13f79535-47bb-0310-9956-ffa450edef68

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dd7ae1350ef823d8e6d7a0c77f847980fe24ca10
1230409445
Luc Maisonobe
added Fast Hadamard Transform
JIRA: MATH-215

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@729670 13f79535-47bb-0310-9956-ffa450edef68

dd7ae1350ef823d8e6d7a0c77f847980fe24ca10
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8ce4c00c1e3570ddd637b3c0fe8c5190912f999f
1230395023
Luc Maisonobe
added nth root computation for complex numbers
JIRA: MATH-236

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@729639 13f79535-47bb-0310-9956-ffa450edef68

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1230228379
Luc Maisonobe
fixed javadoc comment

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@729431 13f79535-47bb-0310-9956-ffa450edef68

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1230119782
Luc Maisonobe
removed unused method

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@729302 13f79535-47bb-0310-9956-ffa450edef68

72003ba2470a85fed35c104d4cce0adecc5bfc89
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1230119742
Luc Maisonobe
replaced use of deprecated method

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@729301 13f79535-47bb-0310-9956-ffa450edef68

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1230115673
Luc Maisonobe
fixed various errors and warnings detected by checkstyle and findbugs

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c95811b0a49700c8503e9e7dfc5532f728b4344e
1230075033
Luc Maisonobe
added new cache-friendly specializations of get/set/operate/premultiply methods

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@729174 13f79535-47bb-0310-9956-ffa450edef68

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ec4c52a56216055570ae9329f9984378e9d7eef2
1230074872
Luc Maisonobe
added a specialized implementation of premultiply
removed unneeded signatures with RelVectorImpl already handled efficiently by base class

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@729173 13f79535-47bb-0310-9956-ffa450edef68

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95d9854a37e740655c86b673c40a0e326562a438
1230074731
Luc Maisonobe
use direct array access where possible

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@729172 13f79535-47bb-0310-9956-ffa450edef68

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03a1d4d5fc2acd6480aa3d2176832721e2adf37c
1230074611
Luc Maisonobe
fixed javadoc

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@729171 13f79535-47bb-0310-9956-ffa450edef68

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8d4a233f7ec9341cfeb16343cfe2d680247a1f86
1230027473
Luc Maisonobe
added message for asymmetric matrices

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c52275ef9b7dc50d5afda235fc4a835521224c03
1230027431
Luc Maisonobe
removed evenPermutation and isSingular for consistency with other decomposition solvers

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@728917 13f79535-47bb-0310-9956-ffa450edef68

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0e91a5d499edfdc7af34a6b26bd657babf3649a7
1230027289
Luc Maisonobe
javadoc improvements

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@728916 13f79535-47bb-0310-9956-ffa450edef68

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4cce86a7a28b1037dc930d094f86854e56c6b3a7
1230027238
Luc Maisonobe
prepared interface for general eigendecomposition
we currently support only symmetric matrices and real eigenvalues
Jira issue MATH-235 asks for asymmetric matrices support, which needs
an API adaptation.
Preparing the interface yet avoids introducing incompatibility later.
The current status is explained in javadoc and matrix symmetry is checked
at runtime with an InvalidMatrixException triggered if asymmetry is detected.

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@728915 13f79535-47bb-0310-9956-ffa450edef68

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Luc Maisonobe
comments

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@728717 13f79535-47bb-0310-9956-ffa450edef68

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Luc Maisonobe
implemented solver as an internal class for efficiency

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@728716 13f79535-47bb-0310-9956-ffa450edef68

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19ceb4431cd859caa6dcd2593ba44af7a63580a2
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Luc Maisonobe
implemented solver as an internal class to avoid building decomposed matrices

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@728686 13f79535-47bb-0310-9956-ffa450edef68

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207b1dc03bdee99538f2bfc86006136293469b60
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Luc Maisonobe
replaced references to RealMatrixImpl

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Luc Maisonobe
removed a leftover print statement

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Luc Maisonobe
fixed loop unrolling error

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Luc Maisonobe
added getSolver() into LUDecomposition

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Luc Maisonobe
removed spurious exception clause

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Luc Maisonobe
fixed some javadoc

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Luc Maisonobe
reverted some changes introduced yesterday, as they lead to unexpected test failures

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Luc Maisonobe
reverted some changes introduced yesterday, as they lead to unexpected test failures

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Luc Maisonobe
decomposed fields can be set to final (this may help optimizer)

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@728483 13f79535-47bb-0310-9956-ffa450edef68

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b551cacc3db5a6d659d9e92911eb602163306deb
1229888159
Luc Maisonobe
recover performances lost with changes for r723496

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Luc Maisonobe
partially unrolled some computation loops to increase performance

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Luc Maisonobe
removed direct references to RealMatrixImpl and use factory

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415479d76a52bb1cdd482894e20d91f629e1df8a
1229731178
Luc Maisonobe
added a new DenseRealMatrix class intended to replace RealMatrixImpl
this class is more cache-friendly as it stores data from squares blocks
in flattened arrays. This allows algorithms that need cross-direction
navigation like multiplication or transpose) to be more efficient on
modern processors.


git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@728185 13f79535-47bb-0310-9956-ffa450edef68

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Luc Maisonobe
added the addToentry and multiplyEntry methods
to allow in-place operation for matrices

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Luc Maisonobe
removed overhead of Entry object allocation during OpenIntToDoubleHashMap iteration

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82aff3309c4021ada6ef93202a1649afe803dda9
1229267062
Luc Maisonobe
Added support for sparse real matrices
JIRA: MATH-230

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d67bfffac4309c66da129111a258c1471e128c6a
1229266610
Luc Maisonobe
Added an int/double hash map (OpenIntToDoubleHashMap) with much smaller
memory overhead than standard java.util.Map (open addressing and no boxing)

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@726459 13f79535-47bb-0310-9956-ffa450edef68

d67bfffac4309c66da129111a258c1471e128c6a
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8bf7df05e8df6530d6d47c21421ba026d9df0132
1228743642
Luc Maisonobe
removed obsolete comment

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@724343 13f79535-47bb-0310-9956-ffa450edef68

8bf7df05e8df6530d6d47c21421ba026d9df0132
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8f7a24947517068bd76ccefc6f9e878d2f6ecd91
1228684598
Luc Maisonobe
removed characters needing a specific encoding

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@724205 13f79535-47bb-0310-9956-ffa450edef68

8f7a24947517068bd76ccefc6f9e878d2f6ecd91
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e958565b02f003f85f203af89cf466e3358178eb
1228682880
Luc Maisonobe
Added support for multi-dimensional Fourier transform.
JIRA: MATH-152

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@724198 13f79535-47bb-0310-9956-ffa450edef68

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583dffc0ee383e9b5e1e08c574de10db8270fdb7
1228681450
Luc Maisonobe
The root solvers now take the function to solve as a parameter to
the solve methods, thus allowing to reuse the same solver for different
functions.

JIRA:MATH-218

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@724191 13f79535-47bb-0310-9956-ffa450edef68

583dffc0ee383e9b5e1e08c574de10db8270fdb7
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2466ed1d8402459cb2383a6fdb9188fce61320c8
1228681141
Luc Maisonobe
updated error generation

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@724189 13f79535-47bb-0310-9956-ffa450edef68

2466ed1d8402459cb2383a6fdb9188fce61320c8
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b8789b6e0983b49ed173bdabde6e9dcf005ae1b2
1228681065
Luc Maisonobe
fixed missing error checks

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@724187 13f79535-47bb-0310-9956-ffa450edef68

b8789b6e0983b49ed173bdabde6e9dcf005ae1b2
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d3101af1589268c96f806518ec797741700297aa
1228668785
Luc Maisonobe
added setter methods for rows and columns in matrices
JIRA: MATH-234

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@724158 13f79535-47bb-0310-9956-ffa450edef68

d3101af1589268c96f806518ec797741700297aa
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37bdc7e7085803070f7cda6ea19000dc67f34d27
1228664192
Luc Maisonobe
added Frobenius matrix norm
JIRA: MATH-232

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@724144 13f79535-47bb-0310-9956-ffa450edef68

37bdc7e7085803070f7cda6ea19000dc67f34d27
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c28099c6ede92badb1c26c003ea64c5f3f38377e
1228663263
Luc Maisonobe
added an abstract implementation of RealMatrix and used it for RealMatrixImpl
JIRA: MATH-231

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@724141 13f79535-47bb-0310-9956-ffa450edef68

c28099c6ede92badb1c26c003ea64c5f3f38377e
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8dfb5ce14aadc86299f134ee50a652c55738c72a
1228660770
Luc Maisonobe
renamed getValues() into getInternalValues() in ResizeableDoubleArray
(the old name is still there, but deprecated)

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@724136 13f79535-47bb-0310-9956-ffa450edef68

8dfb5ce14aadc86299f134ee50a652c55738c72a
:100644 100644 ad693aa220158d727ba2387872bdb4934e37a000 91fb88898462e97d2bed4f755705b0c304eb9af9 M	src/java/org/apache/commons/math/stat/descriptive/DescriptiveStatistics.java
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160fc1076ae568b4510fec50636fcb23740ee91b
1228586503
Luc Maisonobe
removed unneeded call to super()
removed spurious data copy (a copy was already done in the ResizableDoubleArray)

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@724020 13f79535-47bb-0310-9956-ffa450edef68

160fc1076ae568b4510fec50636fcb23740ee91b
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42009b0b42061253208086136aa4fc017bcc3b46
1228583467
Luc Maisonobe
added support for Zipf distribution
JIRA: MATH-178

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@724014 13f79535-47bb-0310-9956-ffa450edef68

42009b0b42061253208086136aa4fc017bcc3b46
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7790b9f4c744edb67f2e13f451735e3c83af42e3
1228487256
Luc Maisonobe
removed reference to non-existent version 1.3 in changes report

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@723737 13f79535-47bb-0310-9956-ffa450edef68

7790b9f4c744edb67f2e13f451735e3c83af42e3
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17238b2e4570213c4d31d4df6805b24dadc468c1
1228485950
Luc Maisonobe
improved matrix decomposition API.
solving a linear system AX = B is now done by a call like:
  RealVector x = new XyzSolver(new XyzDecomposition(a)).solve(b);

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@723736 13f79535-47bb-0310-9956-ffa450edef68

17238b2e4570213c4d31d4df6805b24dadc468c1
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1e04f22cbe919088d23cb284c6669a8f0dcad601
1228470565
Luc Maisonobe
make sure the abstract copy() method signature used is the restricted one
inherited from the StorelessUnivariateStatistic interface and not the
general one inherited from AbstractUnivariateStatistic.
The eclipse compiler generates an error without this.

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@723694 13f79535-47bb-0310-9956-ffa450edef68

1e04f22cbe919088d23cb284c6669a8f0dcad601
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fdb92c5b04d686cec898286ac943e3b48af60235
1228434977
Luc Maisonobe
moved the various solve function out of decomposition algorithms
and into a dedicated DecompositionSolver class

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@723500 13f79535-47bb-0310-9956-ffa450edef68

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1228434498
Luc Maisonobe
moved the various solve function out of decomposition algorithms
and into a dedicated DecompositionSolver class

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5faae53ac0050d4ceb0beec4872efa5dd5ccf09e
1228406031
Luc Maisonobe
removed unused Gershgorin circles class
Gershgorin circles are now handles (simply) inside the EigenDecomposition class

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@723363 13f79535-47bb-0310-9956-ffa450edef68

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7dcff7b38d6d987aef7307bd0ae775224020e251
1228405604
Luc Maisonobe
added (at least!) a first implementation of singular value decomposition.
JIRA: MATH-157, MATH-220, MATH-233

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@723361 13f79535-47bb-0310-9956-ffa450edef68

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e37e28a55d8a65a49213afbb0886468cc5eb5a7d
1228405317
Luc Maisonobe
improved error messages

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@723359 13f79535-47bb-0310-9956-ffa450edef68

e37e28a55d8a65a49213afbb0886468cc5eb5a7d
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6c051d60242db7e59ff82356709937476e1a856b
1228249972
Luc Maisonobe
renamed AbstractMultipleLinearRegressionTest into MultipleLinearRegressionAbstractTest
to match the pom.xml exclude rules and prevent an error in automatic builds

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@722612 13f79535-47bb-0310-9956-ffa450edef68

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0e09cbe2ed12d43286b776df17e635f99f755a87
1228249326
Luc Maisonobe
added a missing deprecated annotation

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@722605 13f79535-47bb-0310-9956-ffa450edef68

0e09cbe2ed12d43286b776df17e635f99f755a87
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559bc9e51d490cb51fa1aa3f2364e9ff07c9524d
1228228907
Luc Maisonobe
don't compute the expensive Q matrix until really needed

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@722476 13f79535-47bb-0310-9956-ffa450edef68

559bc9e51d490cb51fa1aa3f2364e9ff07c9524d
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5979df51f8b7165aebf6f839f683af25e9701656
1228228740
Luc Maisonobe
allow eigen decomposition of a matrix already in symmetric tridiagonal form

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@722473 13f79535-47bb-0310-9956-ffa450edef68

5979df51f8b7165aebf6f839f683af25e9701656
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1228228500
Luc Maisonobe
improved test coverage

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@722471 13f79535-47bb-0310-9956-ffa450edef68

274ead248b0ba564b8eb45c4062fd609975e6e29
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952b612547a5bcd7141820da95d3774b62c73cf5
1228228379
Luc Maisonobe
removed commented out code

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@722469 13f79535-47bb-0310-9956-ffa450edef68

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1b3341ce18fbac5aef67135cad5fa9d384a9190d
1228095296
Phil Steitz
Added rigging for checking eigenvalues and eigenvectors and some easy test cases.

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@721943 13f79535-47bb-0310-9956-ffa450edef68

1b3341ce18fbac5aef67135cad5fa9d384a9190d
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eea1a9d95d1e63e5aefd5897e9aeabcb552f1185
1227864338
Luc Maisonobe
fixed wrong loop bounds

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@721399 13f79535-47bb-0310-9956-ffa450edef68

eea1a9d95d1e63e5aefd5897e9aeabcb552f1185
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7d9003b91aacba77f91556a590163824838b8db0
1227801042
Luc Maisonobe
completed implementation of EigenDecompositionImpl.
The implementation is now based on the very fast and accurate dqd/dqds algorithm.
It is faster than Jama for all dimensions and speed gain increases with dimensions.
The gain is about 30% below dimension 100, about 50% around dimension 250 and about
65% for dimensions around 700.
It is also possible to compute only eigenvalues (and hence saving computation of
eigenvectors, thus even increasing the speed gain).
JIRA: MATH-220

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@721203 13f79535-47bb-0310-9956-ffa450edef68

7d9003b91aacba77f91556a590163824838b8db0
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8979969e30f2bb55c0835d40f92c2aafdea26914
1227466070
Phil Steitz
Added support for copying statistics
Changes to stats classes:
- copy constructor
- static copy(-,-)
- instance copy()
Added copy() to UnivariateStatistic and StorelessUnivariateStatistic
interfaces.

JIRA: MATH-212
Reported and patched by Jason C. HandUber 

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@720030 13f79535-47bb-0310-9956-ffa450edef68

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20b4a70d3637a287ec4153d7f7d085cc59fa7a80
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Phil Steitz
Added test case to ensure permuting arrays changes hash.

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@719995 13f79535-47bb-0310-9956-ffa450edef68

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Phil Steitz
Added test case to ensure nextPermutation fails for negative arguments.

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@719993 13f79535-47bb-0310-9956-ffa450edef68

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Phil Steitz
Clarified javadoc for nextPermutation (to match interface).

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@719991 13f79535-47bb-0310-9956-ffa450edef68

d69852bd95647bd188ff6058b2007e7109e92796
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Phil Steitz
Replace hashcode functions with JDK 1.5+ provided impls. Deprecate?

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@719909 13f79535-47bb-0310-9956-ffa450edef68

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Phil Steitz
Javadoc only.

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@719907 13f79535-47bb-0310-9956-ffa450edef68

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Phil Steitz
Added the following methods to ResizableDoubleArray to support MATH-212 
changes to stats classes:
copy constructor
static copy(-,-)
instance copy()
equals and hashcode

JIRA: MATH-212


git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@719894 13f79535-47bb-0310-9956-ffa450edef68

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edb9b626313abed465e7151127d56c978da2461e
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Luc Maisonobe
applied Cyril Briquet's patch adding an observations removal feature to descriptive statistics
JIRA: MATH-229

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@713093 13f79535-47bb-0310-9956-ffa450edef68

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Luc Maisonobe
fixed typo

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@713088 13f79535-47bb-0310-9956-ffa450edef68

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Luc Maisonobe
improved error messages

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@712430 13f79535-47bb-0310-9956-ffa450edef68

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aa08f8421622a27ffad8add27ef1deb60518366d
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Luc Maisonobe
allow chained IOExceptions even before Java 6

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@712187 13f79535-47bb-0310-9956-ffa450edef68

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ebac9b0dd11538aaad65fcd88c192d6ff526c662
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Luc Maisonobe
fixed a forgotten possible NPE

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@712178 13f79535-47bb-0310-9956-ffa450edef68

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Luc Maisonobe
improved error messages

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@712144 13f79535-47bb-0310-9956-ffa450edef68

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Luc Maisonobe
leverage null pointer handling,
exception classes can be built using null arguments arrays which
are automatically converted to zero-sized arrays to prevent null pointer exceptions

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@712142 13f79535-47bb-0310-9956-ffa450edef68

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Luc Maisonobe
added factory methods to simplify creation of runtime exceptions with helpful messages

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Luc Maisonobe
removed forgotten pre-JDK 1.4 stuff
added protection against null pointer exceptions

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Luc Maisonobe
added IEEE-754 related useful constants

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Luc Maisonobe
replaced RuntimeException by MathRuntimeException

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Luc Maisonobe
improved error handling in linear package with finer grained exceptions

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Luc Maisonobe
simplified a javadoc sentence

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Luc Maisonobe
remove pre Java 1.4 emulation stuff as we now need at least Java 5

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Luc Maisonobe
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.

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Luc Maisonobe
fixed checkstyle warnings

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Luc Maisonobe
added missing serialVersionUID

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Luc Maisonobe
replaced calls to deprecated methods from linear algebra package

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Luc Maisonobe
removed unneeded import statements

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Phil Steitz
Fixed error in javadoc.

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Luc Maisonobe
added a first version of eigen decomposition implementation
this version is not finished yet, but it does work when
eigenvalues are well separated and is faster than JAMA for
dimensions above 100.
It still needs work as the MRRR algorithm is not implemented
yet (only the basic parts with twisted factorization is there).
I continue working on this, but wanted to have a first version
committed to let people play with it and as a basis for comparison.

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@701897 13f79535-47bb-0310-9956-ffa450edef68

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1223239035
Luc Maisonobe
added methods to operate directly on double arrays

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Luc Maisonobe
removed unneeded multiplications by zero by separating
the first iteration from the following ones in a loop
(once again ...)

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Luc Maisonobe
removed unneeded multiplications by zero by separating
the first iteration from the following ones in a loop

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Luc Maisonobe
replaced an intermediate variable by its opposite for easier to read expression

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Luc Maisonobe
added a test ensuring the part of the symmetric matrix below the diagonal is never used

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Luc Maisonobe
improved javadoc

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Luc Maisonobe
fixed typo

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372619e520ceae34daa37db4b12c65c25debf5e1
1222787357
Luc Maisonobe
added interfaces for eigen decomposition and for singular value decomposition
the implementation for this interfaces is not ready yet, but it seems
important to show what the interface will look like.
JIRA: MATH-220

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@700492 13f79535-47bb-0310-9956-ffa450edef68

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Luc Maisonobe
improved javadoc

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Luc Maisonobe
updated userguide after deprecation of internal LU decomposition in linear algebra

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Luc Maisonobe
added a transformer from symmetric matrix to tri-diagonal matrix
(this is only for internal purposes only yet, it will be used later)

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Luc Maisonobe
fixed indentation (sorry)

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Luc Maisonobe
fixed an matrix mismatch error

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Luc Maisonobe
added a getQT() method to QRDecomposition interface
compute Q by transposing QT rather than the other way round for efficiency
JIRA: MATH-223

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Luc Maisonobe
slight optimization:
cached pointers to row vectors from double arrays
wherever the same row was used in a loop, to avoid
double index computation/range check

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1222617315
Luc Maisonobe
Replaced internal LU-decomposition by the external class.
Deprecated the direct call to these methods as users should
really be able to choose the type of solver they want.
LU-decomposition is only one possibility among others like
QR-decomposition.

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@699845 13f79535-47bb-0310-9956-ffa450edef68

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Luc Maisonobe
pulled some solve-related methods higher in the classes hierarchy
(isNonSinglular(), getInverse())

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1222567639
Phil Steitz
Fixed error in javadoc added in r699704
JIRA: MATH-207




git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@699762 13f79535-47bb-0310-9956-ffa450edef68

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1222538719
Phil Steitz
Eliminated the "mutation requirement" in nextGeneration method.
Added algorithm description in javadoc.
JIRA: MATH-207
Reported and patched by David Stefka




git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@699704 13f79535-47bb-0310-9956-ffa450edef68

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1222458673
Luc Maisonobe
propagated trunk changes from r699157 into branch 2.0
MATH-227.  fixed F distribution inverse CDF computation for small denominator degrees of freedom.

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1222398593
Brent Worden
MATH-227.  fixed F distribution inverse CDF computation for small denominator degrees of freedom.

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1221598828
Luc Maisonobe
Fixed an error in CorrelatedRandomVectorGenerator leading to a component of the generated vector being constant
JIRA: MATH-226

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@696054 13f79535-47bb-0310-9956-ffa450edef68

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1221410291
Luc Maisonobe
Greatly improved QR-decomposition speed using transposed matrices internally
JIRA: MATH-223

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1221127031
Luc Maisonobe
Fixed an infinite loop encountered in some backward integration cases for ODE solvers

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1221076508
Luc Maisonobe
added beta distribution
JIRA: MATH-222

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@693959 13f79535-47bb-0310-9956-ffa450edef68

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Luc Maisonobe
distribution factory was removed after 1.2 release

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1221058272
Luc Maisonobe
fixed typo

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1220993941
Luc Maisonobe
added Ted Dunning to the list of contributors (for probability density functions)

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9220f389803c2bdf86e41bebeea1466c8895e88e
1220992628
Luc Maisonobe
Added probability density functions computation for distributions for which it is feasible
JIRA: MATH-222

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Luc Maisonobe
added matrix transformer to bi-diagonal shape
(for later use by singular value decomposition)

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1220269328
Luc Maisonobe
typos

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Luc Maisonobe
removed spurious throws clause

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Luc Maisonobe
added a decompose method to the base DecompositionSolver interface
to allow a solver to decompose a matrix after construction.

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1220026653
Luc Maisonobe
Changed the equals() methods from RealMatrixImpl, RealVectorImpl and Vector3D
so that they consider +0 and -0 are equal, as required by IEEE-754 standard.
These were bugs similar to MATH-221 for Complex.

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@690314 13f79535-47bb-0310-9956-ffa450edef68

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1220024782
Luc Maisonobe
Changed the Complex.equals() method so that it considers +0 and -0 are equal,
as required by IEEE-754 standard.
JIRA: MATH-221

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@690308 13f79535-47bb-0310-9956-ffa450edef68

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1219277988
Luc Maisonobe
added JAMA-like LU-decomposition

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Niall Kegan Pemberton
Upgrade to latest clirr plugin version 2.2.2 (fixes problem downloading the old artifact from the repo)

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Niall Kegan Pemberton
Upgrade to latest clirr plugin version 2.2.2 (fixes problem downloading the old artifact from the repo)

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1219182077
Luc Maisonobe
Started work on JAMA-like interfaces.
This first step is an enhancement of the existing QR-decomposition interface and associated implementation in JAMA-style, i.e with added getH() method and most importantly various solve methods for least-squares solution of the A * X = B equation.
JIRA: MATH-220

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@687167 13f79535-47bb-0310-9956-ffa450edef68

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e2774b9140b16b1798fa6b2059786a40393fbbc6
1219144690
Luc Maisonobe
added removeData methods to 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.
JIRA: MATH-219

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@687021 13f79535-47bb-0310-9956-ffa450edef68

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1218062308
Luc Maisonobe
fixed typo

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1217779968
Luc Maisonobe
added createRealVector for consistency with Matrix factory methods

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@682190 13f79535-47bb-0310-9956-ffa450edef68

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1217188097
Luc Maisonobe
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 class for
input/output.

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@680172 13f79535-47bb-0310-9956-ffa450edef68

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a311dce47eb28360297655aefeac518cfac069a9
1217186122
Luc Maisonobe
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 class for
input/output.


git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@680166 13f79535-47bb-0310-9956-ffa450edef68

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1217185893
Phil Steitz
Javadoc fixes.

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@680165 13f79535-47bb-0310-9956-ffa450edef68

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76ab3aae807cc824cf7415f2966a2d99d3f07fe2
1217184758
Phil Steitz
Changed OLSMultipleLinearRegression implementation to use QR decomposition to
solve the normal equations.
JIRA: MATH-217



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1217176123
Luc Maisonobe
updated minimum java version required

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1217171857
Luc Maisonobe
improved explanation of NaN coordinates

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1217171503
Luc Maisonobe
fixed javadoc

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1217169277
Luc Maisonobe
fixed javadoc comments pasted from ComplexFormat without care

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@680113 13f79535-47bb-0310-9956-ffa450edef68

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1217169043
Luc Maisonobe
fixed typo

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@680111 13f79535-47bb-0310-9956-ffa450edef68

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d92c1b36754b7ce22c4cc6f4c78d1af4c64ae21b
1217102429
Luc Maisonobe
reverting a return type changed inadvertently

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@680036 13f79535-47bb-0310-9956-ffa450edef68

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2280928fca9bc42d9c6c0401065c8f759de76c8b
1217101676
Luc Maisonobe
added in user guide a reference to the Vector3DFormat class for input/output.

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@680034 13f79535-47bb-0310-9956-ffa450edef68

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1217100935
Luc Maisonobe
filtered out findbugs warnings for intentional and documented features

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1217097101
Luc Maisonobe
added a Vector3DFormat class

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@680029 13f79535-47bb-0310-9956-ffa450edef68

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1217096925
Luc Maisonobe
extracted a CompositeFormat base class from ComplexFormat

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@680026 13f79535-47bb-0310-9956-ffa450edef68

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1216662331
Niall Kegan Pemberton
change commons-parent to version 11

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1216662238
Niall Kegan Pemberton
change commons-parent to version 11

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8968ba2bf3326b4c0f295d2033fba66d000b0099
1216122803
Luc Maisonobe
fixed javadoc related checkstyle errors

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@676891 13f79535-47bb-0310-9956-ffa450edef68

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3dfb882621a212fd602500f966987c0e344c3b4b
1216121686
Luc Maisonobe
removed false comment
(coefficients are not cached, they are computed for each new instance)

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@676882 13f79535-47bb-0310-9956-ffa450edef68

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d7695b8695ee66b3807c13583603b4777e6e6ffc
1216070003
Luc Maisonobe
New ODE integrators have been added: the explicit Adams-Bashforth and implicit
Adams-Moulton multistep methods. These methods support customizable starter
integrators and support discrete events even during the start phase.
All these methods provide the same rich features has the existing ones:
continuous output, step handlers, discrete events, G-stop ...


git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@676737 13f79535-47bb-0310-9956-ffa450edef68

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034b1d68bd181fe876ae2106c428a80ee274a59d
1216048571
Luc Maisonobe
preparing test to work with multistep integrators

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@676622 13f79535-47bb-0310-9956-ffa450edef68

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6c1ed573db29625b1f89ffcfe497a17e8e7dda2f
1216048482
Luc Maisonobe
fixed test which did not bounce properly when convergence setting was low

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@676620 13f79535-47bb-0310-9956-ffa450edef68

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8dadbe008fda795fd622128d764b151e82a603f2
1216048356
Luc Maisonobe
fixed a problem preventing integration stop when end time was exactly 0

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@676618 13f79535-47bb-0310-9956-ffa450edef68

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02014066495c944c5d4da6a2c160e79ee5ef66b2
1216048131
Luc Maisonobe
fixed step size handling in borderline cases.
When an even occurred at step start, the step size dropped to zero
which put integration in an infinite loop

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@676615 13f79535-47bb-0310-9956-ffa450edef68

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aedc1272b6012b36267476bfb2a9ae518f64d7b8
1216047537
Luc Maisonobe
FixedStepHandler now extends Serializable.
This should have been done before when the integrator and problem
interfaces were changed too, but was forgotten.

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@676612 13f79535-47bb-0310-9956-ffa450edef68

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a94bf27be020fdc006232b51c0b036eb071799a9
1216047093
Luc Maisonobe
improved robustness in case of events just at integration start

When an event occurs exactly at integration start, the first truncated
steps ends up with zero size. This induced problems with forward/backward
sensing based on this step alone. This also induced an infinite loop in
the calling integrators.

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@676610 13f79535-47bb-0310-9956-ffa450edef68

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b35f8a1e58611f063e7fac5573050407da9ff98c
1215942901
Luc Maisonobe
fixed a problem introduced by recent changes,
thanks to Phil to spot it

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@676291 13f79535-47bb-0310-9956-ffa450edef68

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8bbdea576022e0374890c6800101fe7c8e8846c5
1215898877
Phil Steitz
Refactored data specification in multiple regression api. JIRA: MATH-255.  Patched by Mauro Televi.

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@676241 13f79535-47bb-0310-9956-ffa450edef68

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e7110eac1a03a118b7852659581a7a84b60f31af
1215699733
Luc Maisonobe
Simplified integration end handling using the same method as other integrators
(based on a dedicated event handler)

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@675589 13f79535-47bb-0310-9956-ffa450edef68

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e5f16ff92cba9e441de86d6cbc81cde15c2ddd0f
1215698777
Luc Maisonobe
prevent zero-length steps from generating NaN

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@675578 13f79535-47bb-0310-9956-ffa450edef68

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7385f7694cdf030c01a0f5b969e5bad87a98dcca
1215698701
Luc Maisonobe
updated test after step handling changes

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@675576 13f79535-47bb-0310-9956-ffa450edef68

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5b82c88097248ba7bda933c11b2b40838131e473
1215694194
Luc Maisonobe
allow root search even in reverse direction

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40c365e5cfaf905286ef478ab1362afbf4c8b53b
1215693750
Luc Maisonobe
Replaced size adjustment of all steps of fixed steps Runge-Kutta integrators by a truncation of the last step only.
JIRA: MATH-214

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@675552 13f79535-47bb-0310-9956-ffa450edef68

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0fa1692279761d744d08181ab6eacbf09c348515
1215693644
Luc Maisonobe
Replaced size adjustment of all steps of fixed steps Runge-Kutta integrators by a truncation of the last step only.
JIRA: MATH-214

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@675551 13f79535-47bb-0310-9956-ffa450edef68

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2384ac70e8740ec3c4ec764c5351df751d3f658b
1215524367
Luc Maisonobe
introduced an upper level interface for all ODE integrators

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@674821 13f79535-47bb-0310-9956-ffa450edef68

2384ac70e8740ec3c4ec764c5351df751d3f658b
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c557eb22d4e8b8b99b3b73be7684cf5346f142fa
1215524229
Luc Maisonobe
introduced an upper level interface for all ODE integrators

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@674820 13f79535-47bb-0310-9956-ffa450edef68

c557eb22d4e8b8b99b3b73be7684cf5346f142fa
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6c905a3aea0377431de5e69dbb340635801fc97f
1215523920
Luc Maisonobe
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.

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@674817 13f79535-47bb-0310-9956-ffa450edef68

6c905a3aea0377431de5e69dbb340635801fc97f
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72e8eb5cb889e7a21d53acd6306c9cd6370a0916
1215523619
Luc Maisonobe
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.


git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@674814 13f79535-47bb-0310-9956-ffa450edef68

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24588ac80204331d1e7f8e21812e09ff7aca7998
1215159926
Luc Maisonobe
fixed javadoc links

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@673953 13f79535-47bb-0310-9956-ffa450edef68

24588ac80204331d1e7f8e21812e09ff7aca7998
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6a6be729d16515d1286e3975dad80df1eb79ed2f
1215113518
Luc Maisonobe
renamed AbstractStepInterpolatorTest into StepInterpolatorAbstractTest
to match existing maven exclusion patterns

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@673772 13f79535-47bb-0310-9956-ffa450edef68

6a6be729d16515d1286e3975dad80df1eb79ed2f
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69b9c638d218796f3f4ea057a32a4556ec0810d4
1215111398
Luc Maisonobe
added a common abstract class for testing time-derivatives consistencies in step interpolators

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@673762 13f79535-47bb-0310-9956-ffa450edef68

69b9c638d218796f3f4ea057a32a4556ec0810d4
:000000 100644 0000000000000000000000000000000000000000 4401d092b16cb0c6797d52311ecca9b1f767c6c0 A	src/test/org/apache/commons/math/ode/nonstiff/AbstractStepInterpolatorTest.java

a717386116e3d69fb9df72e9935b990ea87a0737
1215111116
Luc Maisonobe
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.


git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@673759 13f79535-47bb-0310-9956-ffa450edef68

a717386116e3d69fb9df72e9935b990ea87a0737
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97e55988bdb1189df54ad4e32a05c7056bdc126b
1215110163
Luc Maisonobe
pushed common code up in the AbstractIntegrator base class

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@673755 13f79535-47bb-0310-9956-ffa450edef68

97e55988bdb1189df54ad4e32a05c7056bdc126b
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:100644 100644 1b1f353bfce4a697236fdbe8bb82be32432d22ad 4e89bea62fa9494ce89e96be79e2b7fb4affecf5 M	src/java/org/apache/commons/math/ode/nonstiff/RungeKuttaIntegrator.java

23b0de6c94675e57f58f33a58175d89347b04405
1215109772
Luc Maisonobe
added a way to retrieve the meta-data associated with event handlers
(max iteration count, convergence, check interval)

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@673752 13f79535-47bb-0310-9956-ffa450edef68

23b0de6c94675e57f58f33a58175d89347b04405
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a792a2de0f3309571086e0670f69b22a544a5e71
1215109530
Luc Maisonobe
fixed typos

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@673751 13f79535-47bb-0310-9956-ffa450edef68

a792a2de0f3309571086e0670f69b22a544a5e71
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b6a0d050502fc6fe25030446ec6690fe6dca5ab3
1214915780
Luc Maisonobe
added a top-level AbstractIntegrator class to manage events and step handlers

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@673069 13f79535-47bb-0310-9956-ffa450edef68

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7a43f4b5b32279691b28770e6f7648a0712b38d6
1214915658
Luc Maisonobe
added missing keywords

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@673068 13f79535-47bb-0310-9956-ffa450edef68

7a43f4b5b32279691b28770e6f7648a0712b38d6
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:100644 100644 5e60d25ea4052979e710d1c4091303b2285265f4 9447ee23563ba8bc590fbb06484d547e28e6d9aa M	src/test/org/apache/commons/math/MaxIterationsExceededExceptionTest.java

e703a2cb78692922f7c08576bfd1ecdcc0b350a5
1214314708
Luc Maisonobe
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).

JIRA: MATH-213


git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@671168 13f79535-47bb-0310-9956-ffa450edef68

e703a2cb78692922f7c08576bfd1ecdcc0b350a5
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ed492bd0c5c5c3a0258a65cb31cc8723d8f011fd
1214228806
Luc Maisonobe
ported all changes from trunk between r6152100 (branch 2.0 creation) and r670469 (today)
These changes contain fixes for MATH-204 and MATH-205


git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@670569 13f79535-47bb-0310-9956-ffa450edef68

ed492bd0c5c5c3a0258a65cb31cc8723d8f011fd
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:100644 100644 ea1ba6857a5616b4586f0686418f9ca3974822ff 49c93aa0be67aa1904d219ac71be391a1ff8ad16 M	src/test/org/apache/commons/math/analysis/BrentSolverTest.java

7cf0c980d5d814daf187502bc07da0542ed7a828
1214208098
Luc Maisonobe
clarified the ODE package by breaking in into several sub-packages and renaming
classes. This also prepares future work for non-stiff solvers.

SwitchingFunctions is now known as EventHandler
SwitchingFunctionsHandler is now known as CombinedEventsManager

The user manual as also been slightly improved, both to reflect these changes
and to make it easier to grasp the underlying principles in our implementation
of ODE solving


git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@670469 13f79535-47bb-0310-9956-ffa450edef68

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f485a1c7ebca34d5f365f870ddf0ff0e683bd769
1213959573
Luc Maisonobe
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.

JIRA: MATH-210


git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@669851 13f79535-47bb-0310-9956-ffa450edef68

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a0f3e0435c405ec842240413e2165863c9c76a16
1213729776
Luc Maisonobe
fixed dimension error in operate method for RealMatrixImpl and BigMatrixImpl
JIRA: MATH-209

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@668798 13f79535-47bb-0310-9956-ffa450edef68

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26cf6d543deeb2e59564ba23568c83eda2b389bd
1213615714
Luc Maisonobe
replaced inefficient constructors Character(char) by Character.valueOf(char)

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@668117 13f79535-47bb-0310-9956-ffa450edef68

26cf6d543deeb2e59564ba23568c83eda2b389bd
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4eca0cc5c19035441975c4acde9bce59336279d1
1213613270
Luc Maisonobe
missing dot at end of javadoc first sentence

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@668107 13f79535-47bb-0310-9956-ffa450edef68

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4b6cf793fe4fc3037897e01da5bfd71e5505530e
1213613204
Luc Maisonobe
The FirstOrderDifferentialEquations and FirstOrderIntegrator interfaces now extends Serializable.
This allows users to embed implementations of these interfaces in their objects when their
objects needs to be serializable.

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@668106 13f79535-47bb-0310-9956-ffa450edef68

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311979527c16c996520521965493ed5cb4d7377a
1213612812
Luc Maisonobe
fixed javadoc link

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@668105 13f79535-47bb-0310-9956-ffa450edef68

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aaaa530a35e21f88b6002d66ca67f3e6bc461cdb
1213477171
Phil Steitz
Added another OLS test case.

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@667880 13f79535-47bb-0310-9956-ffa450edef68

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e9ee0abc4a4c715f2bd6ae28255760cb44326ea6
1213477123
Phil Steitz
Made assertEquals display difference between arguments.

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@667879 13f79535-47bb-0310-9956-ffa450edef68

e9ee0abc4a4c715f2bd6ae28255760cb44326ea6
:100644 100644 181b966f4c1e8804924b7c76c3b7646d7b2231e9 c952774851d0c346c9c6dc01e9c5000255def6d9 M	src/test/R/testFunctions

1ec0634086270d2beac90b963ba4443355561af1
1213471844
Luc Maisonobe
putting the <project> tag on one line as recommended by the commons wiki

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@667869 13f79535-47bb-0310-9956-ffa450edef68

1ec0634086270d2beac90b963ba4443355561af1
:100644 100644 a50780c4d9795617c05c28ce94ecff70713dcf7e 8a7a3b22ef960f805af76b69c5add26d33d69882 M	pom.xml

fd0f87590d1c88c18f669e9b168c8fd20631f23c
1213126372
Luc Maisonobe
replaced inefficient use of constructors for Integer, Long, Float and Double
by the recommended static valueOf methods that cache results

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@666292 13f79535-47bb-0310-9956-ffa450edef68

fd0f87590d1c88c18f669e9b168c8fd20631f23c
:100644 100644 45d3561ec96d053cec67218984be2ee5abf7217e 0d9efed601a719e6c882031c3426c011fbcbc98c M	src/experimental/org/apache/commons/math/function/DefaultContext.java
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:100644 100644 c748bfe25a9c280c89f04f35a7d684d521e91e97 5e60d25ea4052979e710d1c4091303b2285265f4 M	src/test/org/apache/commons/math/MaxIterationsExceededExceptionTest.java
:100644 100644 2260a0906ccda3133e0ca8a0b44c2a8482b94568 3c2ac5e96fb44033281a586f23e96b94a4fb5c8b M	src/test/org/apache/commons/math/complex/ComplexFormatAbstractTest.java
:100644 100644 6844fd9b90258279d67248071e3e508c02972d0a 7eb2bbdecd2b5d2c82be920f8cc943e6cf15d061 M	src/test/org/apache/commons/math/fraction/FractionTest.java
:100644 100644 be201b9679033638c940496fe6dc30ca20f0319a 5ccb4b80d981e7ac98ca767b175b53ad0da15215 M	src/test/org/apache/commons/math/ode/HighamHall54IntegratorTest.java
:100644 100644 ef40af1344a3c68fb2769502a215dacf6b12f36e 03ef1678bf84ba37720fc09f98d8d3d086880ee0 M	src/test/org/apache/commons/math/random/RandomDataTest.java
:100644 100644 7aaca0b4bb89d66c6286f383e139882fa7d6bba3 31c6bbb66aa19fd4becaed234d93645a790a47b0 M	src/test/org/apache/commons/math/stat/FrequencyTest.java
:100644 100644 77af4d7e058926a68b6ea747b2fb88e269ddaa8f 252a95acd7b34e595c887d37a219243a1a9a460d M	src/test/org/apache/commons/math/stat/data/CertifiedDataAbstractTest.java
:100644 100644 c0d9eb03785b1129a0ab5ae42b742006cb08c052 7f1f84678c044d314bfd3c0c6483718e0a682403 M	src/test/org/apache/commons/math/stat/descriptive/ListUnivariateImpl.java
:100644 100644 2a5c93ed076776876c7ea5fd58202c79e845aad5 f9fdf81d9cd91ff4b7d9a7dea2fe1d1089e921e2 M	src/test/org/apache/commons/math/stat/descriptive/ListUnivariateImplTest.java
:100644 100644 210d2a461ae395e9cdec4f8c9a03db80baa083b5 c7f74759fb928725d91d688023f13d5e796d6f4f M	src/test/org/apache/commons/math/stat/descriptive/MixedListUnivariateImplTest.java
:100644 100644 b2b3d5e6e080048c2131d15d0874f9415a2451bc 493a0ea4f74791ece56c5e454f046786e41ed869 M	src/test/org/apache/commons/math/stat/descriptive/MultivariateSummaryStatisticsTest.java
:100644 100644 3b8c99640704588a5e56d9ef0b9708ae1d0c20f8 4261bba80a5989be9eca9cbf95dd03789a0005bd M	src/test/org/apache/commons/math/stat/descriptive/StatisticalSummaryValuesTest.java
:100644 100644 20b72a05941a4bcb550fd425e1614003be1310af 4d11cf45d03da3a7dc10552622408cbb12d3d73b M	src/test/org/apache/commons/math/stat/descriptive/SummaryStatisticsTest.java
:100644 100644 a906975bff7c7cdb265c7d9f615eb73c1657a545 7193946ac1432acb96108cb691b4ccfc9918da36 M	src/test/org/apache/commons/math/util/DefaultTransformerTest.java
:100644 100644 3cef10d9205c6ab8b6f451c9bcc607d8dae9a001 484b57550e27345366cf22bdbc3bc3795e7e5a4d M	src/test/org/apache/commons/math/util/TestBean.java

98a349691da7f332042ec9bafe9973f35baf5f13
1213125684
Luc Maisonobe
fixed a type error in array parameter
(String[] instead of Object[] as in super constructor ... and all other exceptions)
fixed a typo

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@666287 13f79535-47bb-0310-9956-ffa450edef68

98a349691da7f332042ec9bafe9973f35baf5f13
:100644 100644 4233b3c349239ff7fd7c242f3869b98d2ecc07a4 b7bf3f79025c8020bffcb747251394fb8a24c7e2 M	src/java/org/apache/commons/math/ode/DerivativeException.java

e511f759c4b626c4b884500fe4280885dbdaf453
1213021041
Luc Maisonobe
Improved usability of the geometry package.
From a developer point of view, all the changes are related.
From a user point of view, they are independent changes.

 - added several convenience methods for Vector3D and Rotation
 - replaced public no argument constructors with IDENTITY or ZERO
   static instances for immutable classes Vector3D and Rotation
 - fixed inconsistencies in the naming scheme for static fields in
   Vector3D and Rotation with respect to the overall library


git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@665700 13f79535-47bb-0310-9956-ffa450edef68

e511f759c4b626c4b884500fe4280885dbdaf453
:100644 100644 118a07dc08edd24738f12df94ac2b550ae5ae897 7f2dba7861add8250bd4df164d9c75e213612204 M	src/java/org/apache/commons/math/geometry/Rotation.java
:100644 100644 34e12a148d53f9100a0674c59769932bb27dfff8 519b42e4069355ba05e3dc995864cff88e454c0b M	src/java/org/apache/commons/math/geometry/RotationOrder.java
:100644 100644 8616bc11d67a760190200cf3337aee27ebb180fe a6d3af4d550b84d54254b21e9ed53ebae612215b M	src/java/org/apache/commons/math/geometry/Vector3D.java
:100644 100644 acd5465eb2ad1e64676a1fc28bf548c7739438eb 2289caa88ae52343e0f8752b32e3e98e517e80c8 M	src/site/xdoc/changes.xml
:100644 100644 3f6c11cd53553a66bc7b2ff97592f0736cc62bdf ca355f4e01be59477bdf4b34083b1c7652170a6c M	src/test/org/apache/commons/math/geometry/RotationTest.java
:100644 100644 8d4430daf46807e252e02720f9cb79b7627344f7 e75397ee16c6ba732033863780affd4432eabf2a M	src/test/org/apache/commons/math/geometry/Vector3DTest.java

ef53729e7cd5004d691f6dc029cdb48216d90413
1212976662
Phil Steitz
Added some initial tests for regression parameters and residuals.

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@664602 13f79535-47bb-0310-9956-ffa450edef68

ef53729e7cd5004d691f6dc029cdb48216d90413
:100644 100644 76f4d96d8409bf84e64abb2383c8956c80510393 6f349f2c13384c672bb7bd20ddbef3fec9f30fda M	src/test/org/apache/commons/math/stat/regression/OLSMultipleLinearRegressionTest.java

9bb7dd6e0c7c0ca40cdbeb265272f906275cc534
1212940340
Phil Steitz
Added some initial OLS multiple regression tests.

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@664519 13f79535-47bb-0310-9956-ffa450edef68

9bb7dd6e0c7c0ca40cdbeb265272f906275cc534
:000000 100644 0000000000000000000000000000000000000000 832de4eccf665c65f095e5d3e2212cc63f5b16df A	src/test/R/multipleOLSRegressionTestCases
:100644 100644 2ac1f5388e91f26385d8aa3073a6a8416f8a9bcf e7f66bf29bb4f2d58b488faa7092689651ba5a38 M	src/test/R/testAll

ff3dc2bbb200e38f68df0bbc0bebbc06ebc59be1
1212938986
Phil Steitz
Support NaN, na, NULL values in assertEquals.

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@664513 13f79535-47bb-0310-9956-ffa450edef68

ff3dc2bbb200e38f68df0bbc0bebbc06ebc59be1
:100644 100644 b18571f4cf66e2345f2bdb833debbdb4b083ff70 181b966f4c1e8804924b7c76c3b7646d7b2231e9 M	src/test/R/testFunctions

2708b20351fb0fbb98fd0bc11d2aab1ecc89ba50
1212436417
Luc Maisonobe
changed fields visibility to protected,
to allow users to extend the implementation

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@662538 13f79535-47bb-0310-9956-ffa450edef68

2708b20351fb0fbb98fd0bc11d2aab1ecc89ba50
:100644 100644 09eaf78b6917c1da6127e3641e8c39e78200bc1d ce92c40b1dae38e0ded1abbe43bc241165671298 M	src/java/org/apache/commons/math/linear/BigMatrixImpl.java
:100644 100644 97599f50917efbe4e46435e5ecfd81c15fbb2501 79106442514c0e1b0496b4067c936039937823ff M	src/java/org/apache/commons/math/linear/RealMatrixImpl.java

6f6ae291d5bd1d130e39f0023d2b1f850e0a5256
1212349216
Luc Maisonobe
avoid array copy

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@662274 13f79535-47bb-0310-9956-ffa450edef68

6f6ae291d5bd1d130e39f0023d2b1f850e0a5256
:100644 100644 8e5fe1ad0abb3b8ad6c19c313d5a3c294cbdf3b3 a0676c7e78744d0fcdb76589a70720c6f75891ed M	src/java/org/apache/commons/math/estimation/AbstractEstimator.java

7b37de8d8ce8145f933537db67070dc91e19d86b
1212337339
Luc Maisonobe
Improved linear RealMatrixImpl and BigMatrixImpl performances.
The main changes are the following ones:
 - use directly the storage array when possible for
   diadic operations (add, subtract, multiply), as
   suggested by Phil, this avoids the cost of the
   generic getEntry method
 - replaced custom indices checks by simple use of
   the JVM checks and ArrayIndexOutOfBoundException
 - put row arrays reference in local variables to
   avoid multiple checks in double loops
 - use final variables where possible
 - removed unneeded array copying
 - added a constructor to build a matrix from an
   array without copying it where it makes sense

The speed gain is about 3X for multiplication. Performances
for this operation are now on par with Jama.

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@662241 13f79535-47bb-0310-9956-ffa450edef68

7b37de8d8ce8145f933537db67070dc91e19d86b
:100644 100644 2363c143130463b44d1265658658cf77a7889f33 09eaf78b6917c1da6127e3641e8c39e78200bc1d M	src/java/org/apache/commons/math/linear/BigMatrixImpl.java
:100644 100644 6f08dd0a183ba17702e9fe9a4073e6eb1e927c0c 2f9bf3e3d18150d8f79ded553af2ba3dc52b2278 M	src/java/org/apache/commons/math/linear/MatrixUtils.java
:100644 100644 8c5b96c127de1e0089ed40110654591c37256bc7 97599f50917efbe4e46435e5ecfd81c15fbb2501 M	src/java/org/apache/commons/math/linear/RealMatrixImpl.java
:100644 100644 7b8d6837602b55a3a1d5445d5579a8ae5873ab03 acd5465eb2ad1e64676a1fc28bf548c7739438eb M	src/site/xdoc/changes.xml
:100644 100644 b1b98291423eea91887922fca4f39eea0c8797b3 f30e04b9c3f2513e3b5da840e5be0913d8022ccd M	src/test/org/apache/commons/math/linear/BigMatrixImplTest.java
:100644 100644 90cba3a4b327f22618ac1c715793a8065e0a74ab bc251f41b9689a48af36d83bfdd7d92660fe12c2 M	src/test/org/apache/commons/math/linear/MatrixUtilsTest.java
:100644 100644 c0604c2caa6292a74ad64dc719f78ed21d232770 1147a2a83d7852012311f4d68ee39fdcd64b8bbc M	src/test/org/apache/commons/math/linear/QRDecompositionImplTest.java
:100644 100644 38fafd6b27517768c4d72acad97af2560921b724 7553f3675b991d16c0e0179e07674f4a3e618ed0 M	src/test/org/apache/commons/math/linear/RealMatrixImplTest.java

cc7a071357da904cd6ac16ff50d29e7b2ee2433d
1212000038
Luc Maisonobe
typo

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@661042 13f79535-47bb-0310-9956-ffa450edef68

cc7a071357da904cd6ac16ff50d29e7b2ee2433d
:100644 100644 3739b836530a5beee552c03d0c5b3cf87a15e7dc 9bbc26ce7479b944f24e7b502ef803728f752b19 M	src/java/org/apache/commons/math/analysis/DividedDifferenceInterpolator.java

6656e6da9f8248f7f7b405f73f640debe6f6b771
1211523277
Niall Kegan Pemberton
COMMONSSITE-30 - fix the checkstyle configuration to work for multi-module and review/update <reporting> plugin version numbers for the poms being changed.
 - pom's need to use ${basedir} for configuration files as the multi-module profile is run from commons-parent, so if not specified it can't find those files
 - the checkstyle configuration file needs to use ${checkstyle.header.file} for the headerFile property and  <headerFile> element added to the plugin config in the pom.xml
 - fix m1 checkstyle config to reflect the above where appropriate (specify header file property)


git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@659441 13f79535-47bb-0310-9956-ffa450edef68

6656e6da9f8248f7f7b405f73f640debe6f6b771
:100644 100644 4c39a7f944978d5d6cd10efbb4196e2ca336a0d4 db1e638ef927089e528392e200c18ad88570676e M	checkstyle.xml
:100644 100644 fa5f85cbf664d8c3eb916931a1e07074e27ebd35 a50780c4d9795617c05c28ce94ecff70713dcf7e M	pom.xml
:100644 100644 6c00c155b2893ca3d2d61e7175b92b1476c05bc1 772a6a08b7f3a0000607cf8aa2cfe8220f47e15f M	project.properties

a2fb21f1e934ed0cc5593ca26b88a4b280622826
1211523000
Niall Kegan Pemberton
COMMONSSITE-30 - fix the checkstyle configuration to work for multi-module and review/update <reporting> plugin version numbers for the poms being changed.
 - pom's need to use ${basedir} for configuration files as the multi-module profile is run from commons-parent, so if not specified it can't find those files
 - the checkstyle configuration file needs to use ${checkstyle.header.file} for the headerFile property and  <headerFile> element added to the plugin config in the pom.xml
 - fix m1 checkstyle config to reflect the above where appropriate (specify header file property)


git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@659438 13f79535-47bb-0310-9956-ffa450edef68

a2fb21f1e934ed0cc5593ca26b88a4b280622826
:100644 100644 e7c7a3387094a61809a6da9b71f5119baa8b386c 3e3d05fe3d0b90d5a43c3c2ad611fbc6afb258d4 M	checkstyle.xml
:100644 100644 aa31ff8ab1fd2d7f6e691307b73e21027344e2d1 f6f35da5cb71b327e9a32165b0edab74d83a5305 M	pom.xml
:100644 100644 cc4f520f48799cd5390b1484e8d5627b5167babb 79ffe9691b725c72641f37e621d4679df4dcb06f M	project.properties

b1e827390dc2d374e49703d3955b4160ceb488fd
1211374695
Luc Maisonobe
Configured checkstyle to stop complaining about incomplete Javadoc in some very specific cases.

This problem has been discussed previously here:
  http://markmail.org/message/pmbiyiqssjesq7tm

The solution implemented with this modification is to configure checkstyle
in such a way the errors can be filtered out using dedicated comments in the
source code:

  // CHECKSTYLE: stop JavadocMethodCheck

  // a bunch of functions known to trigger warnings
  // that we explicitly REFUSE to fix

  // CHECKSTYLE: resume JavadocMethodCheck

The checks are still performed normally in file parts not bracketed by
these comments. Hence the first few methods in o.a.c.m.stat.inference.TestUtils are
still checked for correct javadoc, and only for the last ones in the same files
are the checks relaxed.

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@658671 13f79535-47bb-0310-9956-ffa450edef68

b1e827390dc2d374e49703d3955b4160ceb488fd
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c69860b9a17bb5f90d331d381141515999e9324d
1211372007
Luc Maisonobe
added error handling for multiple linear-regression
added documentation for multiple linear-regression
JIRA: MATH-203

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@658645 13f79535-47bb-0310-9956-ffa450edef68

c69860b9a17bb5f90d331d381141515999e9324d
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79a13f97bab612e5f2695da4c70344e169d93c95
1211181221
Luc Maisonobe
changed groupId from commons-math to org.apache.commons
as suggested in http://markmail.org/message/hxdsteovws7lalsa

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@657736 13f79535-47bb-0310-9956-ffa450edef68

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ebedf3011fbe22af05da0229eb9bb23acd0e0848
1211142925
Luc Maisonobe
set up svn:keywords property as the other java files

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@657633 13f79535-47bb-0310-9956-ffa450edef68

ebedf3011fbe22af05da0229eb9bb23acd0e0848
65f63d07d3ad83873527890c1e6ca4cdb9bc396f
1211142083
Luc Maisonobe
fixed many checkstyle errors about javadoc

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@657629 13f79535-47bb-0310-9956-ffa450edef68

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60c93e73be76beece194a332b25e375973408a95
1211139443
Luc Maisonobe
Replaced Raw types by Parameterized types where appropriate.
The various ArrayList, HashSet and HashMap used in math have
be restricted to the content they are intended for.
This removes lots of warnings that have appeared after the
switch to Java 5, and improves safety (for example the categories
used by OneWayAnova are guaranteed to be double arrays at compile
time).
Two difficult cases where not handled here: the Frequency class
and the Fitness interface. The first one mixes types and needs to
be studied before any change is attempted. The second one generates
some side effects on the overall package which is still under development.

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@657612 13f79535-47bb-0310-9956-ffa450edef68

60c93e73be76beece194a332b25e375973408a95
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33ca1f2d8d1dbf241ada24c5521700a0e79960ca
1211124000
Luc Maisonobe
fixed javadoc links

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@657572 13f79535-47bb-0310-9956-ffa450edef68

33ca1f2d8d1dbf241ada24c5521700a0e79960ca
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75ba92f2b2fb958ddc04828445fae86039382f38
1211123912
Luc Maisonobe
added missing newline at end of file

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@657571 13f79535-47bb-0310-9956-ffa450edef68

75ba92f2b2fb958ddc04828445fae86039382f38
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99d6a903c741d0893f207b8a7d1ffa447bd9b3ee
1211123129
Luc Maisonobe
added Mauro's patch to support multiple regression
there is still some work to do on this new feature
JIRA: MATH-203

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@657570 13f79535-47bb-0310-9956-ffa450edef68

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7693648a526d64261d524d65e9422289870bc3db
1211122852
Luc Maisonobe
changed minimum java platform version to Java5
this change was discussed in the following thread:
http://markmail.org/message/3v5imgkeh72ypm5v

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@657568 13f79535-47bb-0310-9956-ffa450edef68

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1210881292
Luc Maisonobe
fixed formula in fast cosine transformer javadoc comments
JIRA: MATH-205

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@656814 13f79535-47bb-0310-9956-ffa450edef68

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Niall Kegan Pemberton
Upgrade to commons-parent-10 pom

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Brent Worden
MATH-204.  added root checks for the endpoints.

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Henri Yandell
Fixing the headerFile location as per CODEC-67 and Benjamin's patch

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Phil Steitz
Updated javadoc links.

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Luc Maisonobe
added a way to handle errors in user-defined switching functions
previously, only the function evaluation could trigger errors,
not the other functions of the interface

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Luc Maisonobe
added the getSwitchingFunctions and clearSwitchingfunctions to the integrator interface
JIRA: MATH-202

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@651282 13f79535-47bb-0310-9956-ffa450edef68

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Luc Maisonobe
removed references to discovery

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Luc Maisonobe
announced a whole bunch of deprecation removals

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1209043506
Luc Maisonobe
removed deprecated methods
this does not belong to commons-math yet, but will probably be merged some day

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Luc Maisonobe
removed the deprecated getIdentity method

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Luc Maisonobe
removed deprecated implementations
the implementation is now in the base class, and can be modified by setter injection

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@651254 13f79535-47bb-0310-9956-ffa450edef68

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1209043050
Luc Maisonobe
removed deprecated exceptions constructors

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@651252 13f79535-47bb-0310-9956-ffa450edef68

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Luc Maisonobe
removed factories

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@651251 13f79535-47bb-0310-9956-ffa450edef68

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Luc Maisonobe
removed tests on removed deprecated methods

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@651250 13f79535-47bb-0310-9956-ffa450edef68

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1209041837
Luc Maisonobe
removed deprecated functions that have been moved to the Complex class itself

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@651249 13f79535-47bb-0310-9956-ffa450edef68

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1209040181
Luc Maisonobe
changed the field TOO_SMALL from protected to private static

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/branches/MATH_2_0@651244 13f79535-47bb-0310-9956-ffa450edef68

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1209040034
Luc Maisonobe
changed an internal test class to private static, for the sake of cleanliness

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Luc Maisonobe
removed dependency on discovery

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Luc Maisonobe
removed dependency on discovery

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Luc Maisonobe
removed deprecated factory methods and classes
they were replaced by setter injection as of 1.2

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Luc Maisonobe
replaced deprecated protected real/imaginary fields by private final fields

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Luc Maisonobe
configured pom for development in branch 2.0

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Luc Maisonobe
branching for initial work on 2.0
starting from a copy of trunk, shortly after 1.2 release

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Brent Worden
MATH-201.  Fixed truncation error in t-test classes for large t values.

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Brent Worden
set subversion properties on new files.

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Brent Worden
added beginning of genetics framework.

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1206734814
Luc Maisonobe
fixed crashes in AbstractEstimator when some parameters are bound.
getCovariances() and guessParametersErrors() now only give result
about unbound parameters
JIRA: MATH-200

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Luc Maisonobe
removed warnings

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Luc Maisonobe
added an error message for Levenberg-Marquardt

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Luc Maisonobe
detect numerical problems in Q.R decomposition for Levenberg-Marquardt estimator
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JIRA: MATH-199

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1206274979
Luc Maisonobe
added an error detection for missing imaginary character while parsing complex string
JIRA: MATH-198

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Henri Yandell
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Niall Kegan Pemberton
Upgrade to version 9 of commons-parent

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Brent Worden
MATH-193.  javadoc and style fixes.

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Brent Worden
replace string concatenation with StringBuffer.append calls.

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Luc Maisonobe
fixed javadoc typos

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Niall Kegan Pemberton
Rool Math version number to 1.3-SNAPSHOT following 1.2 release

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Niall Kegan Pemberton
Remove OSGi configuration in maven-jar-plugin (now handled by maven-bundle-plugin configured in commons-parent)

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Niall Kegan Pemberton
Add Issue Tracking and Download pages generated by commons-build-plugin

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Niall Kegan Pemberton
Upgrade to commons-parent-8 and add configuration properties for OSGi (maven-bundle-plugin) and commons-build-plugin

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Phil Steitz
Made builtBy attribute configurable.

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Phil Steitz
Dropped reference to 1.1 release.

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Phil Steitz
Added LICENSE.txt to jar, changed jar name to 1.2.

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Phil Steitz
Dropped extraneous elements causing problems for maven 1.1.

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Phil Steitz
Commented out reference to currently defunct nightlies.

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Phil Steitz
Prepare for 1.2-RC2.

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Phil Steitz
Changed version to RC2, added pointer to build instructions.

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Luc Maisonobe
fixed a javadoc link that used the wrong method name

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Luc Maisonobe
fixed wrong javadoc links

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Luc Maisonobe
minor javadoc changes (ith -> i<sup>th</sup>, removed extra curly brace)

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Luc Maisonobe
removed javadoc links to the addValue method which does not belong to the interface

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Luc Maisonobe
fixed functions names (minimizes -> minimize)

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Luc Maisonobe
improved consistency between Vector3D and RealMatrix API (multiply -> scalarMultiply)
improved javadoc

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Luc Maisonobe
fixed exception messages arguments types

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Luc Maisonobe
improved javadoc (null norm => zero norm)
improved exception consistency
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1203069842
Luc Maisonobe
changed ArrayListe to List
made fields final

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Luc Maisonobe
improved SOC between AbstractEstimator and its derived classes
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1202756419
Luc Maisonobe
fixed typo

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1202724884
Niall Kegan Pemberton
Add license-header.txt to source distro assembly

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Phil Steitz
Reordered javadoc links, prepared for 1.2 release.

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1202705537
Phil Steitz
Preparing for 1.2-RC1.

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4bab561059df57a4bc8e8d4f3475dc6986360146
1202692719
Phil Steitz
Made numerator and denominator final in Fraction and
deprecated protected real and imaginary parts fields in Complex,
making Fraction immutable and preparing Complex to become fully
immutable in 2.0.
JIRA: MATH-188
Reported and patched by Sebastian Bazley


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41014f0439b962a0246920346ca64f38c8714a47
1202692105
Phil Steitz
Added deprecations summary.

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1202691888
Phil Steitz
Fixed AbstractIntegerDistribution cumulativeProbablility(-,-)
to correctly handle double arguments.
JIRA: MATH-184
Reported by Yegor Bryukhov


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1202677830
Phil Steitz
Javadoc. Removed obsolete comment.
JIRA: MATH-187
Reported by Sebastian Bazley


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Phil Steitz
Improved javadoc for implementation setters / getters.

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Phil Steitz
Javadoc only. Added @since tags.

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4f354fa0698a9c196e67e10e079a12d384e90231
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Luc Maisonobe
added a line about multivariate summary statistics.

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Luc Maisonobe
removed references to the StatisticalMultivariateSummaryValues class

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Luc Maisonobe
improved javadoc according to Phil's changes in the implementation class
added the missing getGeometricMean method

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Luc Maisonobe
removed the StatisticalMultivariateSummaryValues class

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Phil Steitz
Fixed typo in header comment.

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Phil Steitz
Edited javadoc.

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ad94f87d49767e481381952243bffbd6e0e346e2
1202600564
Phil Steitz
Added getSumOfLogs method to SummaryStatistics and made
sum of logs instance used by GeometricMean configurable.
JIRA: MATH-191


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Phil Steitz
Cleaned up to prepare for 1.2 release.

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Phil Steitz
Added description for upcoming release, reclassed some changes from update to add.

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Phil Steitz
Dropped references to unreleased RCs.

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Phil Steitz
Updated changes.xml file location.

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Luc Maisonobe
added dimension checks
removed findbugs warnings about internal representation exposition

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Luc Maisonobe
removed remnants of development tests

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1202488954
Luc Maisonobe
added multivariate summary statistics

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Luc Maisonobe
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Luc Maisonobe
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Luc Maisonobe
fixed typo in javadoc

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Luc Maisonobe
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Luc Maisonobe
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Luc Maisonobe
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Luc Maisonobe
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Luc Maisonobe
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Luc Maisonobe
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1202234946
Luc Maisonobe
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1202156948
Luc Maisonobe
fixed svn properties
JIRA: MATH-190

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Luc Maisonobe
fixed javadoc

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Luc Maisonobe
fixed typo

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Sebastian Bazley
Ignore Findbugs preferences file

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1202079337
Luc Maisonobe
really fixed the equals/hashcode issue
JIRA: MATH-186

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53483bccb065d5798528e40915aaa1b833e1a021
1202078918
Phil Steitz
Added OneWayAnova methods to TestUtils and updated User Guide
to cover One-way Anova tests.
JIRA: MATH-173


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53483bccb065d5798528e40915aaa1b833e1a021
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4f57455d53f8f7cb2b25aae014ab73237fbd41a3
1202078633
Luc Maisonobe
changing the order of data to be less sensitive to numerical problems on different JVM
JIRA: MATH-186

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f54e5bbf25bc15054c5625c3aa75f4d0db1802d2
1202074748
Luc Maisonobe
moved synchronized setters/getters from SummaryStatistics to SynchronizedSummaryStatistics
JIRA: MATH-183

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1202067063
Luc Maisonobe
updated junit version

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Luc Maisonobe
removed warnings about unused variables

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Phil Steitz
Updated build instructions.

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1202065134
Luc Maisonobe
added a missing synchronized bloc
JIRA: MATH-183

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Phil Steitz
Javadoc only.  Added missing </p>'s

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d838e256d9e4ad88221b2230612e78165fee5de5
1201976239
Luc Maisonobe
make sure immutable PointCostPair internal representation is not accessible
JIRA: MATH-183

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@617855 13f79535-47bb-0310-9956-ffa450edef68

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1201975670
Luc Maisonobe
changed an internal class to static as suggested by findbugs
JIRA: MATH-183

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fa601ee57b549eabdd099489b7cb09d2af08b5dc
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9283a8ae9db16e08e9447139bc95f7b7aab82a37
1201975289
Luc Maisonobe
throw EOFException when using empty files with ValueServer in replay and digest modes
JIRA: MATH-185

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96ef54d716955b6e8f8e232813a0470d982ad1af
1201970358
Luc Maisonobe
added comments in the code to explain use of real number equality tests
JIRA: MATH-183

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1201918235
Niall Kegan Pemberton
Update m2 build:
 - add findbugs-exclude-filter.xml to source distro
 - exclude Cobertura javascript files with license issues
 - remove NOTICE/LICENSE file resources (already in commons-parent pom)
 - update copyright year in NOTICE file to 2008

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1201883503
Niall Kegan Pemberton
MATH-180 - Add support for OSGi to the m2 build

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Luc Maisonobe
fixed typo

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1201867332
Luc Maisonobe
added checks for integer overflows during double to Fraction conversion
JIRA: MATH-182

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Luc Maisonobe
still javadoc ...

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Luc Maisonobe
announced fix for MATH-181

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1201859002
Luc Maisonobe
fixed javadoc

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afcb345fba17a8ccf58541d3094e130c38fe80ae
1201858754
Luc Maisonobe
replaced maxDenominatorDigit by maxDenominator in constructor
it is more straightforward and avoid an exception
JIRA: MATH-181

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Luc Maisonobe
removing unneeded call to reduce()
(convergents are already reduced by construction)

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1201544353
Luc Maisonobe
fixed an array type error

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49c73ce8e4cbbe2fad5ec4cc4ff49bf60d629d66
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1201521475
Luc Maisonobe
added new constructors for Fractions
JIRA: MATH-181

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1201500603
Phil Steitz
Javadoc only. Added missing </p>'s

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1201407730
Phil Steitz
Removed JDK 1.5-dependent code.
JIRA: MATH-173


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1201387363
Phil Steitz
Added one-way ANOVA implementation.
JIRA: MATH-173
Contributed by Bob MacCallum.


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1201035773
Luc Maisonobe
add change notice
JIRA: MATH-179

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1201035500
Luc Maisonobe
added Niall's patch for improved double constructor test
added test for construction failure (golden-ratio)
JIRA: MATH-179

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Luc Maisonobe
removed duplicated "The"

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Phil Steitz
Fixed section title.

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Luc Maisonobe
added missing javadoc

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b609686dc766987d05c9dbaa760387bdc6227334
1200845210
Luc Maisonobe
fixed array type from String[] to Object[] according to base class

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@613587 13f79535-47bb-0310-9956-ffa450edef68

b609686dc766987d05c9dbaa760387bdc6227334
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e045f37c79b3f77ab0fd04d27dbe41a0add21965
1200844332
Luc Maisonobe
fixed an exception type in javadoc

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@613577 13f79535-47bb-0310-9956-ffa450edef68

e045f37c79b3f77ab0fd04d27dbe41a0add21965
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d76a581764f63cf8841173cf1527216ca19aa558
1200841404
Luc Maisonobe
fixed keywords used in @version tags to match checkstyle-enforced rule

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@613570 13f79535-47bb-0310-9956-ffa450edef68

d76a581764f63cf8841173cf1527216ca19aa558
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718a708ecfd5ac3f2d3091b2ea60e87d0d72f6a4
1200782896
Luc Maisonobe
Added general methods to guess errors on estimated parameters
JIRA: MATH-176

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@613474 13f79535-47bb-0310-9956-ffa450edef68

718a708ecfd5ac3f2d3091b2ea60e87d0d72f6a4
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Luc Maisonobe
fixed javadoc typos

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Luc Maisonobe
removed lazy building of the instance
it was not needed since the instance is small
it introduced synchronization problems

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Rahul Akolkar
Fix global search+replace error.


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"mathuage" eqyivalent of geek-speak for math devs? Sorry but for ASF licensing you have to communicate like the rest of us!

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upgrade to commons-parent-7

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Luc Maisonobe
added an exclusion filter file for findbugs, to prevent false positives from being displayed

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Luc Maisonobe
fixed javadoc typos

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Luc Maisonobe
be more restrictive on ignored exceptions for the test
added a long to double conversion to also test the getN() methods

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Luc Maisonobe
javadoc typo fix

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Luc Maisonobe
removed the static qualifier for inner class NaturalComparator,
the class *really* should be static, but this triggers a bug in the clirr plugin

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Luc Maisonobe
replaced array sharing by array copying to remove a findbugs warning
(this is used only for exception, so there should be no performance problems here)

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Luc Maisonobe
NumberTransformer classes should be Serializable
since they are used as fields of the Serializable TransformerMap class

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d65cde69ff76003ce1ed238b5455cf04cb2af9f3
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Luc Maisonobe
RandomGenerator classes should be Serializable
since they are used as fields of both Serializable RandomAdaptor
and RandomDataImpl classes

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Luc Maisonobe
replaced serialization to temporary file by serialization to byte array
and simplified the error handling to remove a findbugs warning

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Luc Maisonobe
replace getClass by the exact class,
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Luc Maisonobe
UnivariateStatistic classes should be Serializable
since they are used as fields of the Serializable DescriptiveStatistics class

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Luc Maisonobe
the internal class NaturalComparator now implements Serializable
to remove a findbugs warning

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Luc Maisonobe
removed a serialization warning from findbugs

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Luc Maisonobe
commented out currently unused private code to remove warnings

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Luc Maisonobe
added serialVersionUID to remove warning

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Luc Maisonobe
removed warnings about field coming from deprecated base class

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Luc Maisonobe
fixed comments typos

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Luc Maisonobe
replaced calls to deprecated SummaryStatistics.newInstance() method

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Luc Maisonobe
replaced calls to deprecated SummaryStatistics.newInstance() method

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Luc Maisonobe
removed unneeded import clauses

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Luc Maisonobe
replaced calls to deprecated DescriptiveStatistics.newInstance()
and SummaryStatistics.newInstance() methods

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Luc Maisonobe
replaced calls to deprecated DescriptiveStatistics.newInstance() method

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Luc Maisonobe
removed unneeded import clauses

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Luc Maisonobe
replaced calls to deprecated SummaryStatistics.newInstance() method

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Luc Maisonobe
replaced calls to deprecated SummaryStatistics.newInstance() method

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1199972348
Luc Maisonobe
replaced deprecated ComplexUtils methods
JIRA: MATH-171

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Luc Maisonobe
deprecated tests concerning deprecated methods, to remove numerous warnings
JIRA: MATH-171

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1199863813
Luc Maisonobe
MATH-164 add a special handling for multiplication of complex
numbers with infinite parts

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1199855760
Phil Steitz
Added check and rescaling of expected counts to sum to sum of expected
counts if necessary in ChiSquare test.
JIRA: MATH-175
Reported and patched by Carl Anderson.


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fixed typos

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[MATH-171] updated documentation according to new behavior

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fixed typos

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fixed typos

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fixed typos

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Luc Maisonobe
added SynchronizedSummaryStatistics class (and tests)

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Luc Maisonobe
javadoc typos

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Luc Maisonobe
fixed typo in javadoc link

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Phil Steitz
Clean up reflection exception handling.

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1197082793
Phil Steitz
Changed Mean.evaluate() to use a two-pass algorithm, improving accuracy
by exploiting the the fact that this method has access to the full
array of data values.


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Phil Steitz
javadoc

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Phil Steitz
Deprecated abstract factory methods and made SummaryStatistics
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Made implementations of statistics configurable via setters.


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Phil Steitz
Fixed javadoc typo.

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1196627330
Phil Steitz
javadoc only.

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1196627241
Phil Steitz
Changed to extend non-deprecated, now-concrete DescriptiveStatistics.

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Phil Steitz
Added some descriptive statistics verification tests.

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1196543953
Phil Steitz
Cleaned up some errors / omissions from r598133
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* Eliminated unecessary import
* Eliminated lazy initialization
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* Added tests for percentile impl injection 


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Phil Steitz
Deprecated abstract factory methods and made DescriptiveStatistics a concrete
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this class. Made implementations of statistics configurable via setters.


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1196053955
Phil Steitz
updated clirr plugin version.

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Luc Maisonobe
removed an unneeded import clause

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Phil Steitz
Moved misplaced element.

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Phil Steitz
Merged most functions from ComplexUtils into Complex class, added
static factory method to Complex.
JIRA: MATH-171
Reported and patched by Niall Pemberton


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Niall Kegan Pemberton
Update m2 build

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Luc Maisonobe
added missing Apache license

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Luc Maisonobe
typo

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9aeabf6a381ae0f69de6f4d0218f758e54f336fd
1194468773
Luc Maisonobe
renamed the RungeKuttaFehlbergIntegrator base class to EmbeddedRungKuttaIntegrator
since it is more general than the single method designed by Fehlberg
renamed some misleading private fields in the corresponding derived classes

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@592894 13f79535-47bb-0310-9956-ffa450edef68

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Luc Maisonobe
improved test coverage

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@592705 13f79535-47bb-0310-9956-ffa450edef68

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Luc Maisonobe
improved test coverage

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Luc Maisonobe
renamed DescriptiveStatisticsTest into DescriptiveStatisticsAbstractTest
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git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@592121 13f79535-47bb-0310-9956-ffa450edef68

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Luc Maisonobe
improved test coverage

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Luc Maisonobe
add tests for Gauss-Newton estimator

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@591692 13f79535-47bb-0310-9956-ffa450edef68

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1194121419
Luc Maisonobe
allow switching functions to trigger FunctionEvaluationException
let the low level errors in switching functions find their way to upper level

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@591674 13f79535-47bb-0310-9956-ffa450edef68

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1194115637
Luc Maisonobe
improved tests coverage

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@591662 13f79535-47bb-0310-9956-ffa450edef68

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1194115571
Luc Maisonobe
delayed integrator internal state update after the call to step handler
to ensure integrator.getStepStart() and interpolator.getPreviousTime()
are consistent.
renamed getStepsize() into getSignedStepsize()

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@591661 13f79535-47bb-0310-9956-ffa450edef68

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Luc Maisonobe
removed unused FSAL flag for simple Runge-Kutta schemes
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Luc Maisonobe
removed the static suite() method which cannot create a test instance anymore
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Brent Worden
set subversion properties on new files.

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Luc Maisonobe
improved test coverage

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Luc Maisonobe
make sure to use setSafety instead of changing the attribute
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Luc Maisonobe
improved test coverage

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Luc Maisonobe
Replaced the misused clone method in step interpolators
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automatically and hence may trigger DerivativeException.
This should simplify usage and avoid nasty errors caused
by forgotten finalization

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@590660 13f79535-47bb-0310-9956-ffa450edef68

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Brent Worden
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Brent Worden
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Brent Worden
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Brent Worden
MATH-170.  added SynchronizedDescriptiveStatistics class.

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Luc Maisonobe
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Luc Maisonobe
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Luc Maisonobe
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Luc Maisonobe
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Luc Maisonobe
fixed typos

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Luc Maisonobe
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Luc Maisonobe
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Luc Maisonobe
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Luc Maisonobe
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Luc Maisonobe
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1189435183
Luc Maisonobe
replaced arbitrarily small thresholds by 0 where it was sensible with respect to IEEE754
removed unnecessary else clauses
removed double indices where possible
fixed some comments


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Luc Maisonobe
removed an unneeded else

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Luc Maisonobe
improved test coverage

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Luc Maisonobe
removed an unneeded else

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1189409935
Luc Maisonobe
fixed javadoc

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Luc Maisonobe
improved test coverage

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1189373893
Luc Maisonobe
fixed visibility of setMultiStart,
it should be called only from within the minimizes methods

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Luc Maisonobe
fixed javadoc errors introduced with r574049

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1189363598
Luc Maisonobe
[MATH-160] introduced a new UnknownDistributionChisSquareTest interface
to hold the new methods without creating binary incompatibilities with
commons-math 1.1
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Henri Yandell
Changing name to 'Commons Xxx'

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Luc Maisonobe
removed an uneeded throw declaration

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Luc Maisonobe
removed warnings about internal test classes that should have been declared static

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Luc Maisonobe
changed getWindowSized to synchronized since setWindowSize was already synchronized

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Luc Maisonobe
fixed an integer division error (should have been a float division)

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Phil Steitz
Updated commons parent version to 4.

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Luc Maisonobe
removed warnings about unused return values/fields

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1187540102
Luc Maisonobe
fixed a missing initialization

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Luc Maisonobe
added missing Apache header

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Luc Maisonobe
[MATH-165] basic implementation of a SimpleEstimationProblem

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Luc Maisonobe
fixed a warning about a missing serialVersionUID

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Luc Maisonobe
fixed a non-static call to a static method

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Luc Maisonobe
fixed numerous warnings in test code (unused fields/results, fields only set to null)

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Luc Maisonobe
replaced some references to Jakarta after commons switched as TLP

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:100644 100644 83a7d8b9bacc029035e72f59b61fd49ea1990bcf 4e2720ca71a8569d80310ca16564e9730d362e60 M	src/test/R/README.txt
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0e29ee4b25a07f4ed3087eeccc485ecd9448d4cc
1186579126
Luc Maisonobe
fixed a mixed case error (setup vs. setUp) that prevented tests setup
fixed the associated tolerance for some failing tests

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@563850 13f79535-47bb-0310-9956-ffa450edef68

0e29ee4b25a07f4ed3087eeccc485ecd9448d4cc
:100644 100644 90fd5a482c17c850712e9643112c8104d273d8ff 863aedc99f6bece7b74ec8ff64a952c791fd17a9 M	src/test/org/apache/commons/math/distribution/ChiSquareDistributionTest.java
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:100644 100644 4f6884cac086a1bbe3c9cc41f61d5da4d3e02c77 dfbcbf56cbbff678057f4b2c5bbbaac3842a90a3 M	src/test/org/apache/commons/math/distribution/GammaDistributionTest.java
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:100644 100644 39084fc47b075a9fa340571f80254f7ff89c5de8 d29eef96749b0855ed7833f04e6ceea011b0e0e0 M	src/test/org/apache/commons/math/stat/inference/TTestFactoryTest.java

3667e4b4991dcc6d915bedf1fdfb2018df294dc2
1186355310
Phil Steitz
Temporarily disabled clirr compatibility check.

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@562983 13f79535-47bb-0310-9956-ffa450edef68

3667e4b4991dcc6d915bedf1fdfb2018df294dc2
:100644 100644 83c6deebaea6a0c0adfde0943680aa52a6e821e0 d7447e7aec6c2e9d7b90ede942d63796ff516643 M	pom.xml

1cc65391ff6fd356f5424961b99568a71f134ad5
1186354803
Phil Steitz
Removed coberta coverage check. Was causing install to fail

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@562981 13f79535-47bb-0310-9956-ffa450edef68

1cc65391ff6fd356f5424961b99568a71f134ad5
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9f754568e23a947aed5c879c06560956a2769aec
1186354355
Phil Steitz
Step coberta back down to 2.0 - was causing build failures.

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@562980 13f79535-47bb-0310-9956-ffa450edef68

9f754568e23a947aed5c879c06560956a2769aec
:100644 100644 9abdb34e28e224b2463d60fed74a98f25907f550 ac73c2eeb5f433961d2511a10f13fc037fd9321a M	pom.xml

23e6c25d30c55a1c73dc8a5a793d3d9e118a55ea
1186351176
Brett Porter
don't need to use SSL for a read-only connection


git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@562975 13f79535-47bb-0310-9956-ffa450edef68

23e6c25d30c55a1c73dc8a5a793d3d9e118a55ea
:100644 100644 edf28d32d8459fac9cfba7d9523462fe20bd77bb 9abdb34e28e224b2463d60fed74a98f25907f550 M	pom.xml

3cde8bea4c41d22ba50e84e28e7c8b6d6265678a
1186348251
Niall Kegan Pemberton
TLP Move change wiki URLs from "wiki.apache.org/jakarta-commons" to "wiki.apache.org/commons"

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@562963 13f79535-47bb-0310-9956-ffa450edef68

3cde8bea4c41d22ba50e84e28e7c8b6d6265678a
:100644 100644 b2a6a86e0efb19d3b4ea4986d652b03dce016e6f 2ba95fac2c3ae8d99af37caa3df3147bf6af315b M	src/site/site.xml
:100644 100644 0f24905b29c2759ed465bb4b5df0f706c8d1ff90 1c61449c703c6a3044c074dab934d6fa327e08ef M	xdocs/developers.xml
:100644 100644 25216a262ae3feabe9ca4e41274fd1172afe4244 6ec7fd13652d16263611066fd23f31d7191626d8 M	xdocs/navigation.xml

fdd7622fa74ac059c9fd9feec7c0e573ddce38fe
1186343127
Luc Maisonobe
new attempt to fix an encoding error

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@562944 13f79535-47bb-0310-9956-ffa450edef68

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4ced68e8ac5b8b68c1f8eac78b1f59a335041184
1186008994
Niall Kegan Pemberton
Add missing license headers

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4ced68e8ac5b8b68c1f8eac78b1f59a335041184
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ca8706d9f2f2b1d2b148d0aa0c428e8ed58877c4
1185919147
Niall Kegan Pemberton
Correct missing = signs in due-to

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@561566 13f79535-47bb-0310-9956-ffa450edef68

ca8706d9f2f2b1d2b148d0aa0c428e8ed58877c4
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e9918edb46aad273476b73bcbcd48ddbaebe71ab
1185915746
Matthew Jason Benson
Apache Apache

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e39b43efed72d10a7c68a75330e1cab2e2b3a435
1185905605
Niall Kegan Pemberton
Move Commons TLP changes

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@561417 13f79535-47bb-0310-9956-ffa450edef68

e39b43efed72d10a7c68a75330e1cab2e2b3a435
:100644 100644 7966fe996e7cb500146e2829bcaa9cb50df9164a 4ae41fc963b583251c609ae7daf403b4342881e1 M	xdocs/index.xml
:100644 100644 85f93b13b4acee36b6d97ec75e3a75ae0728622a 109646dcc0c382b50800e0891b41c06de481ad7f M	xdocs/issue-tracking.xml
:100644 100644 06b3bd0f685a01c189fa883d11f9347b1ac2c643 25216a262ae3feabe9ca4e41274fd1172afe4244 M	xdocs/navigation.xml

477ae4b5fa019563190d1c11b23e1ac65ebedf44
1185861009
Henri Yandell
Fixing svn locations after TLP move

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@561233 13f79535-47bb-0310-9956-ffa450edef68

477ae4b5fa019563190d1c11b23e1ac65ebedf44
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c501fb2d4c5d59a334ab3d5e19bdc9d7d3cae2cb
1185855429
Rahul Akolkar
TLP related blanket changes:

s:jakarta.apache.org/commons:commons.apache.org:
s/commons-user@jakarta.apache.org/user@commons.apache.org/
s/commons-dev@jakarta.apache.org/dev@commons.apache.org/
s/Jakarta Commons/Apache Commons/
s:svn.apache.org/viewcvs/jakarta/commons:svn.apache.org/viewvc/commons:
s:svn.apache.org/viewcvs.cgi/jakarta/commons:svn.apache.org/viewvc/commons:
s:svn.apache.org/viewvc/jakarta/commons:svn.apache.org/viewvc/commons:
s:svn.apache.org/repos/asf/jakarta/commons:svn.apache.org/repos/asf/commons:

I'd appreciate another pair of eyes on this. There are some categories we probably don't want to change ATM (hopefully, none of these snuck in):
 * Historicals (proposals etc.)
 * URLs that shouldn't change (DOCTYPE fragments etc.)
 * Test cases where namespace URLs matter etc. (I'll track any related nightly failures)


git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@561230 13f79535-47bb-0310-9956-ffa450edef68

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220df444872eb275120310453daa5f881713af24
1185767853
Henri Yandell
Moving to a css on the Commons site

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220df444872eb275120310453daa5f881713af24
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d23e587908f7855e5d162bda2f28b5343b9f58a0
1185740062
Henri Yandell
Fixing the mailing list addresses

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d23e587908f7855e5d162bda2f28b5343b9f58a0
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7d4a882dfcfa248e3bdfc95f85d1b05317815e19
1185726173
Luc Maisonobe
changed a character from isolatin-1 to UTF-8 encoding
as specified in the XML header

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@560755 13f79535-47bb-0310-9956-ffa450edef68

7d4a882dfcfa248e3bdfc95f85d1b05317815e19
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c3b43a9cf7e570e5341308266fdcd2c305d54010
1185680554
Henri Yandell
Moving to TLP

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@560660 13f79535-47bb-0310-9956-ffa450edef68

c3b43a9cf7e570e5341308266fdcd2c305d54010
13d155c5c8b61d35119e28b20edf2920f07328a9
1185680441
Henri Yandell
Moving to TLP

git-svn-id: https://svn.apache.org/repos/asf/commons/commons/proper/math/trunk@560657 13f79535-47bb-0310-9956-ffa450edef68

13d155c5c8b61d35119e28b20edf2920f07328a9
908eab2317349c8b53a569248a15dfb84db95115
1185610377
Henri Yandell
Updating to reflect website change

git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@560518 13f79535-47bb-0310-9956-ffa450edef68

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03ff69df9b0bd172180e35e2e07a973976c6ee94
1185558724
Niall Kegan Pemberton
Remove jakarta references from m1 and m2 builds

git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@560337 13f79535-47bb-0310-9956-ffa450edef68

03ff69df9b0bd172180e35e2e07a973976c6ee94
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:100644 100644 30732b3364ee484c33688ae59cf827810dfda1cd 62fe6bd04976463484dbabd1084105a8a92a9218 M	project.xml

4ce05bcd51ec956d789d20b59c743603d24a8ab7
1185071588
Phil Steitz
Modified NormalDistributionImpl.cumulativeProbablity to catch
MaxIterationsExceededException and return 0 or 1, resp. if the argument
is more than 20 standard deviations from the mean.

JIRA: MATH-167


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@558450 13f79535-47bb-0310-9956-ffa450edef68

4ce05bcd51ec956d789d20b59c743603d24a8ab7
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b8058233e92ad635fe204f450235cad597cd70f2
1184548905
Phil Steitz
Added test to confirm that nextUniform excludes endpoints.

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b8058233e92ad635fe204f450235cad597cd70f2
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85997f7fbb91829fa3c7c51c137f4bd35117f254
1184548812
Phil Steitz
Corrected error in exception text.

git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@556484 13f79535-47bb-0310-9956-ffa450edef68

85997f7fbb91829fa3c7c51c137f4bd35117f254
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a14ed1ddb4060424212fecee12e7926332a3be3a
1183825054
Phil Steitz
Added recent contributors - should have been in r554220.

git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@554224 13f79535-47bb-0310-9956-ffa450edef68

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bfeade88d27ef890d238abcf5a2defbf233e0c6c
1183822583
Phil Steitz
Added recent contributors.

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bfeade88d27ef890d238abcf5a2defbf233e0c6c
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972a35af7d8f8ff20130095234696f08291ad12a
1183660485
Luc Maisonobe
trivial javadoc fix

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972a35af7d8f8ff20130095234696f08291ad12a
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b0f473cd04ae3fee722f57a7344fb80aeec3bf3a
1183582149
Luc Maisonobe
slightly improved documentation for random vectors generation

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2d12081d150331bf00ac745b9b01e894d0ae4725
1183573587
Rahul Akolkar
Update NOTICE files in trunks-proper in light of TLP move (and add component names to NOTICEs where missing).


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@553294 13f79535-47bb-0310-9956-ffa450edef68

2d12081d150331bf00ac745b9b01e894d0ae4725
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b7ce18afa4bb3bac1687a3a200442d4df10b8159
1182719419
Phil Steitz
Added two-sample (binned comparison) ChiSquare test
JIRA: MATH-160
Thanks to: Matthias Hummel



git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@550285 13f79535-47bb-0310-9956-ffa450edef68

b7ce18afa4bb3bac1687a3a200442d4df10b8159
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2cdf068a537c077dbb795b2c91c6d05b860c5482
1182382790
Phil Steitz
Added log function.
JIRA: MATH-158



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1182378244
Phil Steitz
Increased default epsilon for Gamma, Beta function evaluation.
JIRA: MATH-166
Reported and patched by Lukas Theussl


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Henri Yandell
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1181536976
Phil Steitz
Javadoc only.  Made it clear that increment-getResult uses a different,
less accurate, computing formula than evaluate for Variance.
JIRA: MATH-163


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Brent Worden
Removed dependency on DistributionFactory.

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1181224536
Brent Worden
Removed dependency on DistributionFactory.  Added settable normal distribution field.

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Brent Worden
Removed dependency on DistributionFactory.  Added settable gamma distribution field.

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Brent Worden
Removed dependency on DistributionFactory.  Added settable chi-squared distribution field.

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Brent Worden
Removed dependency on DistributionFactory.  Added settable t distribution field.

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Brent Worden
Removed dependency on DistributionFactory.  Added settable t distribution field.

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Phil Steitz
Added clirr check and report.

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Phil Steitz
Javadoc; changed string double generator to use valueOf.

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Phil Steitz
Added missing license headers.

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Phil Steitz
Added site deployment config.

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Phil Steitz
Initial commit.

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Phil Steitz
Fixed name.

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Phil Steitz
Configured reports.

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Phil Steitz
Added resources for m2 site.

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Phil Steitz
Javadoc formatting and minor edits.

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Phil Steitz
Made license headers conistent.

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26eda01f7ee614985e9bc6c35d0b204f7542bcee
1172685198
Luc Maisonobe
replaced a corrupted non-ASCII character by an entity

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56b8cf436b6577383562dfd2706a831f46bc5712
1172609626
Luc Maisonobe
moved notice information from Mantissa to commons-math
(concerning Levenberg-Marquardt and Gragg-Bulirsch-Stoer algorithms implementations)

git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@512386 13f79535-47bb-0310-9956-ffa450edef68

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a833c458eb7cd71998bc664647c3e1a9bde15a21
1172609519
Luc Maisonobe
removed remnants of code transfered from Mantissa to commons-math

git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@512385 13f79535-47bb-0310-9956-ffa450edef68

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1075771d110f4d153cc8c1a45ec23530d93e180d
1172609280
Luc Maisonobe
identified myself as a developer

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49caee49ed165a30dc453e478c4056ef2cde7a9f
1172607832
Luc Maisonobe
added the optimization package from Mantissa

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17950753e1bc76c050ee0ab1509fb83dec3096fc
1172607752
Luc Maisonobe
added the geometry package from Mantissa

git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@512380 13f79535-47bb-0310-9956-ffa450edef68

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921a27954aca829468930f6ff70419b7a03da8fa
1172531560
Luc Maisonobe
added the ode package from Mantissa

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2a1acbb5c6c293d4d705fa58e59ebd8625cfd074
1172531184
Luc Maisonobe
specialized exception for mismatched vectors or matrices dimensions

git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@512064 13f79535-47bb-0310-9956-ffa450edef68

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6d21abba54a9b3a0cca222abfacd26cabd88561c
1172530785
Luc Maisonobe
added the estimation package from Mantissa

git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@512061 13f79535-47bb-0310-9956-ffa450edef68

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8ce6b30d7126356da4e18fb73f0bd836b921ce1c
1172529858
Luc Maisonobe
deprecated the no argument constructor

git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@512050 13f79535-47bb-0310-9956-ffa450edef68

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d53fbcb626be3bf5f4c2315060e56e91471e6dbc
1172529216
Luc Maisonobe
updated errors prior to Mantissa integration

git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@512045 13f79535-47bb-0310-9956-ffa450edef68

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f9304678e3550c5ef6b8077abff7f5606a45a43a
1172529130
Luc Maisonobe
fixed javadoc typos

git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@512042 13f79535-47bb-0310-9956-ffa450edef68

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09743354a6cbde7d5c2b927512fa0273e3ead804
1172528573
Luc Maisonobe
added support for generation and analysis of random vectors

git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@512039 13f79535-47bb-0310-9956-ffa450edef68

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1172418528
Luc Maisonobe
fixed a wrong unicode encoding

git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@511532 13f79535-47bb-0310-9956-ffa450edef68

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1172418487
Luc Maisonobe
make the code java 1.3 compatible

git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@511531 13f79535-47bb-0310-9956-ffa450edef68

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1171404390
Luc Maisonobe
allow using locales with different variants

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1171319708
Luc Maisonobe
set eol-style property to native

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1171318647
Luc Maisonobe
set eol-style property to native

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1171310602
Luc Maisonobe
added missing license headers (sorry)

git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@506614 13f79535-47bb-0310-9956-ffa450edef68

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93cef035bc8de890039f9df0bd0cdcafa1ed0528
1171309069
Luc Maisonobe
fixed some missing serialVersionUID

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b852a8e794727f4a99a0058dd8830bebd0dcca4a
1171308959
Luc Maisonobe
use properly the top level exceptions for too specific cases which don't need a devoted exception class

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1171308537
Luc Maisonobe
Added and used a specialized exception for arguments outside domains

git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@506595 13f79535-47bb-0310-9956-ffa450edef68

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1171308436
Luc Maisonobe
Added and used a specialized exception for duplicate abscissas in sampled functions

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1171308197
Luc Maisonobe
Added and used a specialized exception for continued fraction convergence errors

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1171307861
Luc Maisonobe
Added and used a specialized convergence exception for exceeded iteration counts

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84f1ef1d4578d2a8be6972e7172b308277911faa
1171306464
Luc Maisonobe
- refactored top level of Exception hierarchy,
- added getPatern(), getArguments() and getMessage(Locale)
  (names chosen for consistency with java.text.MessageFormat)
- deprecated some raw constructors as the top level exception are too
  coarse grained and intended only as base classes for easier to use classes
- added several constructors for use by more fine grained derived classes

git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@506576 13f79535-47bb-0310-9956-ffa450edef68

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02c96d8aeab2d3246dcf97e33df7df3b95724a88
1170313432
Henri Yandell
Maven 2 pom for Math. Tests that use getClass().getResource(String) don't work at the moment, unsure how to fix currently. 

git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@502139 13f79535-47bb-0310-9956-ffa450edef68

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1168894731
Luc Maisonobe
added missing files from previous patches (JIRA:MATH-161 and JIRA:MATH-162)

git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@496489 13f79535-47bb-0310-9956-ffa450edef68

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676c203843a2b968236da27702eb8789051a9784
1166566267
Phil Steitz
Updated contributed sources - Mantissa 7 upgrade. JIRA: MATH-162

git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@488828 13f79535-47bb-0310-9956-ffa450edef68

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934db34b321f6ab78583d2f6b56eb2dae9a6c2fb
1165961501
Henri Yandell
Setting the maven repo - apologies if this borks anything

git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@486363 13f79535-47bb-0310-9956-ffa450edef68

934db34b321f6ab78583d2f6b56eb2dae9a6c2fb
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2798f0ffa570a0218442f483016d08ba12da6574
1164784954
Henri Yandell
Fixed copyright header (committing in parts as the full commit timed out)

git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@480443 13f79535-47bb-0310-9956-ffa450edef68

2798f0ffa570a0218442f483016d08ba12da6574
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ed7ae79dd2dae5df1554108f2bc59023cf9b1172
1164784882
Henri Yandell
Fixed copyright header (committing in parts as the full commit timed out)

git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@480442 13f79535-47bb-0310-9956-ffa450edef68

ed7ae79dd2dae5df1554108f2bc59023cf9b1172
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05f7f6059bd0cbb69b5dd49c061f1f3520e0ee1e
1164784452
Henri Yandell
Fixed copyright header (committing in parts as the full commit timed out)

git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@480440 13f79535-47bb-0310-9956-ffa450edef68

05f7f6059bd0cbb69b5dd49c061f1f3520e0ee1e
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18f8949e2315cda27e421a40fd7bf3a8c01ce9e3
1164784099
Henri Yandell
Fixed copyright header (committing in parts as the full commit timed out)

git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@480437 13f79535-47bb-0310-9956-ffa450edef68

18f8949e2315cda27e421a40fd7bf3a8c01ce9e3
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55fd222f5844fb75017c985adec847e933642db8
1164783995
Henri Yandell
Fixed copyright header (committing in parts as the full commit timed out)

git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@480435 13f79535-47bb-0310-9956-ffa450edef68

55fd222f5844fb75017c985adec847e933642db8
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53be0bb35a1f831f10bf02ec31f2c3ad8f25053f
1164783206
Henri Yandell
Fixing the license header. Something is up with this file, in svn diff it has a odd set of bytes on the front of the file. Possibly Windows BOM UTF-8 issue?

git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@480433 13f79535-47bb-0310-9956-ffa450edef68

53be0bb35a1f831f10bf02ec31f2c3ad8f25053f
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e6191b661d08496d313f1da0e8854df2258b3ceb
1164783098
Henri Yandell
Fixed header. Switched from Windows to Unix line endings as a part of this - not sure if that's problematic or not, but I don't trust that I can hack this to remain windows specific

git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@480432 13f79535-47bb-0310-9956-ffa450edef68

e6191b661d08496d313f1da0e8854df2258b3ceb
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3009748f133d47fb5f3b09c4c2cc9dd3ec7c2469
1164473016
Phil Steitz
Formatting only. Eliminated tabs.

git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@479144 13f79535-47bb-0310-9956-ffa450edef68

3009748f133d47fb5f3b09c4c2cc9dd3ec7c2469
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:100644 100644 edfe945a8e2e6e314c4fba2d72c0084b7e31564f 623e989768a1dee7ae9fcb62a4e485aa3397ce54 M	src/test/org/apache/commons/math/fraction/FractionFormatTest.java

ca79137f55a7278e761ffc6022c61941e019d01e
1164255433
Phil Steitz
Collection of patches to initial Mantissa sources:
- Fixed a problem when switching functions triggered derivatives
  discontinuities
- Removed methods and classes that were deprecated in Mantissa
  and do not need to be preserved in commons-math as backward compatibility
  is not a problem for this newly integrated code
- Changed Vector3D and Rotation to immutable classes for ease of use
- Improved some javadoc in class Rotation
JIRA: MATH-161
Submitted (with patches) by Luc Maisonobe


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@478458 13f79535-47bb-0310-9956-ffa450edef68

ca79137f55a7278e761ffc6022c61941e019d01e
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89ac173c2b467e6289df0e62f2a43ed1730fbad5
1163972175
Phil Steitz
Initial commit

git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@476930 13f79535-47bb-0310-9956-ffa450edef68

89ac173c2b467e6289df0e62f2a43ed1730fbad5
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1163031991
Rahul Akolkar
Point DOAP files to JIRA.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@472714 13f79535-47bb-0310-9956-ffa450edef68

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9b45c75cff86a52785ef34062c85c83f736dce47
1163031284
Rahul Akolkar
Missing SVN properties, possibly some large diffs, no functional change.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@472712 13f79535-47bb-0310-9956-ffa450edef68

9b45c75cff86a52785ef34062c85c83f736dce47
493539adfe0b14c4dcad2421b6429c6651845078
1163029153
Rahul Akolkar
Peg Commons at JCL 1.0.4. Have only looked at proper for lack of cycles, can follow up with sandbox and dormant components as they graduate or get revived.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@472702 13f79535-47bb-0310-9956-ffa450edef68

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1155186733
Henri Yandell
Switching viewcvs url to viewvc

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1155186545
Henri Yandell
Switching viewcvs url to viewvc

git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@430245 13f79535-47bb-0310-9956-ffa450edef68

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1154585968
Henri Yandell
Fixing typo as pointed out by Remi Arntzen on commons-dev

git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@428255 13f79535-47bb-0310-9956-ffa450edef68

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Phil Steitz
Made constructors public in transform package.

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1153036118
Henri Yandell
Changing cvs.apache.org to people.apache.org. None of these locations appear to point to an svn or cvs url

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1153035931
Henri Yandell
Changing cvs.apache.org to people.apache.org. None of these locations appear to point to an svn or cvs url

git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@422396 13f79535-47bb-0310-9956-ffa450edef68

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1152928739
Niall Kegan Pemberton
Changes to Math maven site/build:
- removed dependency on commons-build
- correct Jira --> JIRA
- project specific JIRA links (all open Math issues etc)


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@422131 13f79535-47bb-0310-9956-ffa450edef68

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fc21b26f84312e4f75e8b144238618c73a8b091f
1152162649
Phil Steitz
Modified getSumSquaredErrors method in SimpleRegression to always 
return a non-negative result.
JIRA: MATH-85
Reported by Mark Osborn
Patched by Luc Maisonobe


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@419439 13f79535-47bb-0310-9956-ffa450edef68

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1152161243
Phil Steitz
Fixed bad issue attribute.

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1152047327
Phil Steitz
Javadoc fixes.

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1152046870
Phil Steitz
Improved javadoc for nextAfter.

git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@419099 13f79535-47bb-0310-9956-ffa450edef68

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1152046734
Phil Steitz
Added Fast Fourier transform
JIRA: MATH-140
Contributed by Xiaogang Zhang


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@419098 13f79535-47bb-0310-9956-ffa450edef68

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a6ab98b9867145c7d4eccab43c9ab8927aab06a7
1152000565
Phil Steitz
Added a nextAfter method in MathUtils to return the next
machine-representable number in a specified direction from a given
floating point number.  Used this to ensure that MathUtils.round does
not return incorrect results for numbers with bad IEEE754 
representations.
JIRA: MATH-151
Reported by Buza Zoltán
Patch submitted by Luc Maisonobe


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@418934 13f79535-47bb-0310-9956-ffa450edef68

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1151872285
Phil Steitz
Suspended setSecureAlgorithm test, since it takes several minutes on Ubuntu.

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Phil Steitz
Changed issue ids from BZ to Jira.

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41ba9e00e3bbde990f6821f67f0da2a5575b9ac3
1149476812
Phil Steitz
Modified ProperFractionFormat to reject embedded minus signs.
JIRA: MATH-60
Reported by Nhung Nnguyen


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@411647 13f79535-47bb-0310-9956-ffa450edef68

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5de83dca70afabf12bd46bb9ab438753c14c7453
1149476569
Phil Steitz
Eliminated tab character.

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1149470884
Phil Steitz
Added Pascal distribution implementation.
JIRA: MATH-148
Contributed by Joni Salonen


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Phil Steitz
Changed maven changes plugin template to work with Jira.

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Phil Steitz
Changed Bugzilla -> Jira.

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Robert Burrell Donkin
Corrected site host name.

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Henri Yandell
Switched url from bugzilla to jira

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Phil Steitz
Removed jdk 1.4 dependency in FractionFormatTest.

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Phil Steitz
Moved R test sources to src/test.

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1141999230
Phil Steitz
Marked optional dependencies.

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Phil Steitz
Javadoc. Complete change partially included in r385437.

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Phil Steitz
Eliminated main method.

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Phil Steitz
Added comments to dependencies and added xdoc 1.9.2 dependency.

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Phil Steitz
Added Todd Parnell as contributor.

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Phil Steitz
Adding PascalDistributionImpl inadvertently omitted in r381115.  Thanks, Gump!

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Phil Steitz
Added Pascal distribution contributed in BZ #38766.

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1139879714
Niall Kegan Pemberton
Modify maven build to add two non-standard attributes to the jar's manifest file to indicate the values of "maven.compile.source" and "maven.compile.target". Also modify the build to include an "Implementation-Vendor-Id" of "org.apache" in the jar's manifest.

The two non-standard entires created in the manifest file will look something like the following:

X-Compile-Source-JDK: 1.3
X-Compile-Target-JDK: 1.3

This change serves two purposes:

  1) To provide comfort to users regarding JVM compatibility.
  2) Enable releases to be checked more easily for JVM compatibility.

The manifest specification indicates that "unknown" entries in the manifest file are ignored. These entries have been prefixed with "X-" which is a sometimes used "convention" for indicating non-standard entries.

See thread: http://tinyurl.com/839zh

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Henri Yandell
fixing pmc from name to url

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1138032775
Henri Yandell
Adding doap files for each component for the projects.apache.org site

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1136306858
Brent Worden
PR: 38091
ComplexFormat was not formatting double values with the provided NumberFormat.  Instead, the real part format was always used.


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1136181330
Phil Steitz
Simplified code, eliminated unecessary parameters in private methods.

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1136181033
Phil Steitz
Replaced clover with cobertura, added pmd report.

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1136141030
Phil Steitz
Changed wiki link.

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1135723849
Joerg Pietschmann
Fix doc regressions caused by marging back the 1.1 branch.


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1135659935
Phil Steitz
Javadoc.

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1135637637
Phil Steitz
Coding style changes to match the rest of [math].

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1135627254
Phil Steitz
Removed dependency on ordering of roots using TestUtils.assertContains.

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1135627162
Phil Steitz
Added assertContains methods.

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Phil Steitz
Added file build customization properties file.

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1135289642
Phil Steitz
Merged userguide updates from MATH_1_1 release branch.

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Phil Steitz
Merged build fixes from MATH_1_1 release branch.

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Phil Steitz
Merged (final) src changes from MATH_1_1 release branch r321516-358399

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Joerg Pietschmann
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Brent Worden
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Phil Steitz
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Phil Steitz
Added description for 1.1 release.

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Phil Steitz
Formmatting, changed a couple of 'updates' to 'fixes'.

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Phil Steitz
Eliminated JDK 1.4 dependency.

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Phil Steitz
Emasculated MathException secalization test to work under jdk 1.3.

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Phil Steitz
Changed Fraction(double) to correctly handle near-integral arguments.
PR # 35434
Submitted by: Jörg Weimar


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Phil Steitz
Changed lcm to throw ArithmeticException (instead of returning bogus
value) if the result is too large to store as an integer.
PR # 35431
Submitted by: Jörg Weimar


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Javadoc.

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Phil Steitz
Formatting to make checkstyle happy.

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Phil Steitz
Revert inadvertent change from last commit.

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Phil Steitz
Added factory for TTest, ChiSquareTest and TestUtils class with
static methods to create instances and execute tests.
PR #32663



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Phil Steitz
Add 34042 fix.

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Phil Steitz
Eliminated redundant endpoint function evaluations in BrentSolver, SecantSolver. BZ #35042.

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Phil Steitz
Add id for Al.

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Put site (and coming distro) on a diet - limit maven image copy.

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Phil Steitz
Update content.

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Phil Steitz
Formatting, fix errors and typos.

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Phil Steitz
Fix typos.

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Phil Steitz
Update content, fix typos.

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Phil Steitz
Javadoc, formatting.

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Phil Steitz
Added RandomAdaptor to complete PRNG pluggability framework, updated User Guide.

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Phil Steitz
Added [math] prefix to Bugzilla templates.

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Phil Steitz
Added config to support jar deployment.

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Phil Steitz
Added setSubMatrix methods to RealMatrix, BigMatrix.
Modified copyIn methods to use setSubMatrix and moved array argument checking
from constructors and copyIn to setSubMatrix.
PR # 35007
Base implementation contributed by Rodrigo di Lorenzo Lopes


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Brent Worden
added @since tag to new methods.

git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@178166 13f79535-47bb-0310-9956-ffa450edef68

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38b48a8c9f4e9368b30c51eaab95f2ffee3f749f
1116790185
Phil Steitz
Minor site updates
* Changed scm link to point to cgi
* Edited down content on main page
* Added direct link to svn on nav
* Changed download link to point directly to math page


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@171363 13f79535-47bb-0310-9956-ffa450edef68

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1116739544
Brent Worden
fixed javadoc comments, added @since tags to new classes and methods, corrected hyperlinks in user guide, add fraction unit tests.

git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@171283 13f79535-47bb-0310-9956-ffa450edef68

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674d4c5ae5afe8fecf4069fcdc1067988adee906
1116692959
Phil Steitz
Added createXIdentityMatrix methods to MatrixUtils and deprecated getIdentity
methods in RealMatrixImpl, BigMatrixImpl.
Modified RealMatrixImpl, BigMatrixImpl constructors to throw
IllegalArgumentExceptions instead of ArrayIndexOutOfBounds when dimension
arguments are not positive.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@171229 13f79535-47bb-0310-9956-ffa450edef68

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2cb671bd661fab68c6ce6c2cf36de45a3cf9805d
1116181415
Phil Steitz
Made PRNG pluggable for classes in the random package.  
* Added RandomGeneratorinterface extracted from java.util.random.
* Added and abstract implementation, AbstractRandomGenerator providing default
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* Added a constructor taking a RandomGenerator as an argument to RandomDataImpl
* Changed ValueServer to use a RandomData in its constructor.
* Changes to 1.0 classes should be backward compatible
  (including serialization).


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@170243 13f79535-47bb-0310-9956-ffa450edef68

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984f58332c9929da498b9efe8a972e2071649c16
1116181322
Phil Steitz
Fixed javadoc typo

git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@170242 13f79535-47bb-0310-9956-ffa450edef68

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79f07ad259b6affa511e588b216dec3936925c36
1115528157
Phil Steitz
Fixed order of entries, added due-to in last update.

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1115528058
Phil Steitz
Added C. Scott Ananian to contributors.

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20786a617657c0c20315005c621052a2735dfe67
1115183699
Phil Steitz
Ported numerics improvements in commons lang Fraction implementation.
Added utility methods for overflow-checked integer arithmetic and
improved gcd method in MathUtils.


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12643c4a91cd155f1230591936e430064d152903
1115010889
Phil Steitz
Fixed error in TTestImpl.homoscedasticTtest. Implementation was
incorrectly using heteroscedastic t statistic. Also improved sensitivity
of test cases.
BZ #34677
Reported by: Gilles Gaillard


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@165583 13f79535-47bb-0310-9956-ffa450edef68

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bf1152fd53cae540ad17069ca39516a526c69098
1115010104
Phil Steitz
Removed unused import.

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b2ba9651dc4dd89411750872eb2c49e95195be9d
1113714735
Phil Steitz
Updated copyright dates.

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6cb6e91df66f822a8077ef6ed3c88970fd6c893b
1113688185
Phil Steitz
Fixed javadoc errors. One-sided t-test significance adjustment was
reversed in javadoc for boolean-valued test methods.
BZ #34448
Reported by: Gilles Gaillard


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@161613 13f79535-47bb-0310-9956-ffa450edef68

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ad8d86c5470c0daab831a2dc1b8652ad79cb73e0
1113687779
Phil Steitz
Updated to reflect 34448 fix.

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f880bad0259c747139d50761a16d78ef6a69dd53
1112388567
Brent Worden
updating copyright

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f880bad0259c747139d50761a16d78ef6a69dd53
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06117fcdf9c186896a42205ca4e10ec8ad2843e9
1112388321
Brent Worden
PR: 34230
Fixed bug in PolynomialSplineFunction to allow evaluation of the function at the last knot point.

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d1c8fbb244891deb7cf4deb285a4d4729655b0a6
1111985949
Phil Steitz
Changed siteAddress to cvs.apache.org and changed mailing list archive links to match commons site.

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dc7eb2daa10ca3aeed9884a3aba329878b4d0fe5
1111029612
Brent Worden
added weibull distribution

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be419b4e8378754b4e6cab1898ccc7dec3dac50c
1109567562
Phil Steitz
Added subversion links

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8cb39ac93cacc74e1f035cee0647a51e999f967f
1109567523
Phil Steitz
Created separate javadoc links for 1.0 release, 1.1-dev.

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1109425521
Dirk Verbeeck
convert .cvsignore to svn:ignore

git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@155505 13f79535-47bb-0310-9956-ffa450edef68

3b9ba210bab427311bfba99da87ccd4d17db73e6
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65b65f88b74de6b3462b04b2cf2a69f064a77557
1109423512
Dirk Verbeeck
svn:keywords correction

git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@155427 13f79535-47bb-0310-9956-ffa450edef68

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0f41c723d4cbf02192ce0ed07e8912aec88a0e93
1109279005
Brent Worden
fixed incorrect test data that was causing test failures.

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1109217545
Brent Worden
added cauchy distribution

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1107584660
Brent Worden
added rounding methods.

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41598b038509e9cdb7f6dbeefdb2a2876d2708a6
1107582585
Brent Worden
added fraction class and fraction formatting classes.

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351f0eabe385899e1c15651d24fe914c603a6160
1107205382
Dirk Verbeeck
change http://nagoya.apache.org/bugzilla
to http://issues.apache.org/bugzilla

git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@149300 13f79535-47bb-0310-9956-ffa450edef68

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7a47b8d6ca39efd88a377ea213aa0a9966989807
1107126148
Dirk Verbeeck
Use SVN changelog

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94b067575b74d6873dc75f1b760ee4f9930d99bd
1105422082
Brent Worden
Removed references to nagoya.  Replaced with issues and mail-archives


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865f9cbdd813a581ae4d028cecc10d63ceab3bee
1102913605
Phil Steitz
Include LICENSE.txt and NOTICE.txt in jars.


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51b3625a2cb8156c2b298094e97b1602a79a2ba7
1102910837
Phil Steitz
Get NOTICE.txt included in META-INF of distribution jars.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141521 13f79535-47bb-0310-9956-ffa450edef68

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858b0837ba9825cad2817be43a9abda6fa10199e
1102657637
Phil Steitz
Initial commit - R verification tests.


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152880ce8f296e126b439425e349dbc1df1ae646
1102655896
Phil Steitz
Increased precision of target values used in tests.


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be0c69f70755b15f7e7c7a48bd4594cfd3eaf7ad
1102655812
Phil Steitz
Fixed error in comment.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141518 13f79535-47bb-0310-9956-ffa450edef68

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10f16f9ce57806ec24840a7e50e3088f02469899
1102655572
Phil Steitz
Post-1.0 update.


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Prepare for 1.0 release.


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Phil Steitz
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Phil Steitz
Removed JDK 1.4 dependent code.
PR# 32538.


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Phil Steitz
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Partially addresses PR# 32538 (JDK 1.4 dependencies).


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Phil Steitz
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 - Complex equals uses Double.doubletoRawLongBits (fixing would make
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 - Beta fails compilation (easy to fix)


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Phil Steitz
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Phil Steitz
Removed STATUS file obsoleted by project.xml, changes.xml


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Phil Steitz
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Phil Steitz
Updated for 1.0 release.


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Phil Steitz
Updated for 1.0 release.


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Phil Steitz
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Increased accuracy of target values in one test case.


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Phil Steitz
Fixed bug in ChiSquareTest isNonNegative function that was incorrectly
rejecting 2-way tables with zero counts.
Fixes PR #32531
Reported by: Hans van der Heijden


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Phil Steitz
Fixed spelling.


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Phil Steitz
Prepare for Rc2.


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Phil Steitz
Prepare for RC2.


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Phil Steitz
Fixed broken javadoc link.


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Phil Steitz
Removed broken link.


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Phil Steitz
Fixed copyright date.


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Phil Steitz
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Phil Steitz
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PR #31713


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Phil Steitz
Updated to reflect distribution package changes.


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Phil Steitz
Added Fredrik Norin to contributors.


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Phil Steitz
Refactored distribution package so that more general distributions can be
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1) Added Distribution, AbstractDistribution
2) Added IntegerDistribution, AbstractIntegerDistribution
3) Added PoissonDistribution contributed by Fredrik Norin (PR #31688)


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Phil Steitz
Removed unused import.


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Phil Steitz
Removed unused import.


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Phil Steitz
Removed empty loop.


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Phil Steitz
Updated to reflect BigMatrix changes.


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Phil Steitz
Added methods to create BigMatrix instances.


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Phil Steitz
Added checks for validity of arrays supplied to constructors.


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Phil Steitz
Modified tests to work with immutable BigMatrix.


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Phil Steitz
Removed entry mutators, making BigMatrix instances immutable (like RealMatrix).


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Phil Steitz
Added tests for row, column, subMatrix accessors, equals and hashcode, toString.


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1098670880
Phil Steitz
Added Matrix-valued row, column, and subMatrix accessors as suggested
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Implemented equals and hashcode.
Modified toString() to handle empty matrix.


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Phil Steitz
Fixed hashcode computation so elements in first row, col contribute.


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Phil Steitz
Fixed test compile bug introduced in last commit.


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Phil Steitz
Fixed typo.


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Phil Steitz
Pr #31860 fix.


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Phil Steitz
Fixed bugged test (pr #31860), added more R certified tests


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1098599234
Phil Steitz
Fixed error in slope parameter significance estimate
Pr #31860
Reported by: Kim van der Linde


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Phil Steitz
Updated to reflect recent changes.


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Phil Steitz
Changed factorial methods to return 1 for argument = 0.
Pr #31687
Reported by: Fredrik Norin


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Phil Steitz
Initial commit of MatrixUtils, including RealMatrix factory methods.


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Phil Steitz
Removed data mutators from RealMatrix interface and RealMatrixImpl.


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Phil Steitz
Added support for population standard deviation.


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Phil Steitz
Javadoc.


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Phil Steitz
Javadoc.


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Phil Steitz
Improved coverage in population variance test.


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Phil Steitz
Added support for population variance computation.


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1097431276
Phil Steitz
Added test for toString.


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Phil Steitz
Formatting, javadoc, plus fix for toString to handle empty matrix.


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Phil Steitz
Implemented equals and hashCode.


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1097361562
Phil Steitz
Added row and column matrix accessors. Pr #30897.


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1097356902
Phil Steitz
Added Kim van der Linde to contributors, changed version to RC2.


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1097356556
Phil Steitz
Added submatrix accessors.
Pr #30897
Submitted by: Kim van der Linde
Reviewed by: Phil Steitz


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1097217201
Phil Steitz
Set changes.issue.template property.


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1097216718
Phil Steitz
Fix issue attribute name.


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1097216151
Phil Steitz
Updated to reflect recent changes.


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2ea3d91a1965b8ec2adb4ba5c55e22d155931c63
1097215041
Phil Steitz
Add Ken Geis as contributor.


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4f92fd25bd851573559a1d7405c34753bb239748
1097214798
Phil Steitz
Improved performance of logGamma.
Pr #31522
Submitted by: Ken Geis
Reviewd by: Phil Steitz


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0412df24e84e53397b3b5a6516aee1a4e12109c4
1097212101
Phil Steitz
Renamed .univariate -> .descriptive, .multivariate -> .regression


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141454 13f79535-47bb-0310-9956-ffa450edef68

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Phil Steitz
Added ComplexFormat fix.


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1095742268
Brent Worden
Added locale support to complex format.  Added test cases for specific locales.
PR: 31325


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1095741955
Brent Worden
Added locale support to complex format.  Added test cases for specific locales.
PR: 31325


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Phil Steitz
Added test case to ensure Integers passed to addValue as Object references are converted to Longs.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141450 13f79535-47bb-0310-9956-ffa450edef68

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1095735754
Phil Steitz
Modified addValue(Object) to convert Integers to Longs, completing (hopefully ;-) fix of problem with integral type conversions reported to commons-dev by Jon Langlois.


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Phil Steitz
Prepare for 1.0 release.


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Phil Steitz
Prepare for 1.0 release. Turned on changes plugin report.


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Phil Steitz
Initial commit.


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1095634047
Phil Steitz
Fixed error computing cumulative frequencies when actual parameter is an Integer.  Reported to commons-dev list by Jon Langlois.


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Phil Steitz
Fixed "premature" 1.0 download links.


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Phil Steitz
Changed matrix indexing to be 0-based.


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1094087442
Phil Steitz
Added public PGP keys file for signing releases.


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1094073971
Phil Steitz
Made standard matrix entry addressing explicit in javadoc.


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1094055791
Phil Steitz
Javadoc.


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7847852f7ea96bb2293101ac0914a91cebf54cd0
1094055561
Phil Steitz
Modified regression section to reflect class name change.


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af98e93bd2b12bd3a4a5627155b8f626bff962fe
1094054079
Phil Steitz
Made assumption about precomputed mean explicit in javadoc.  Added missing method.


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1094054032
Phil Steitz
Javadoc. Made assumption about precomputed mean explicit.


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1094053899
Phil Steitz
Javadoc. Made assumption about precomputed mean in variance computations explicit.


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1094051972
Phil Steitz
Renamed BivariateRegression to SimpleRegression.


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1093619367
Mark R. Diggory
info on creating patches


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1093138978
Phil Steitz
Fixed javadoc typos.


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1093138890
Phil Steitz
Removed method marked for removal prior to release.


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ea8e7afff1c8c018d2dddbf8e148578f5c7e1ad2
1093138775
Phil Steitz
Added link to Wiki, edited contributing section.


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Mark R. Diggory
Adding postGoal to copy css stylesheets from commons-build when site is generated. Please maintain this modification for consistent look and feel across commons subprojects.


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1092749255
Mark R. Diggory
When content is generated, the stylesheets are copied out of commons-build instead of being linked to, this allows independent stylesheets to be used in distributions. Maintains look and feel when jakarta site is inaccessable.


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Phil Steitz
Added pregoals to copy NOTICE.txt to both distributions and to drop /experimental from source distro.


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Phil Steitz
Added top level link to Javadoc


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1092601413
Phil Steitz
Prepare for RC1.


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60cefe3bc6ce5f3f2f3fb2eb4216aa5544c44138
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Phil Steitz
Suppressed regeneration of build.xml; path bug still present in ant plugin 1.8.


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1092593388
Phil Steitz
Preparing for Release 1.0


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Phil Steitz
Preparing for 1.0 release.


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Phil Steitz
Added missing semicolon in example.


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57ef80caca376d86e8dbf5d0b7124547e141c86e
1092324819
Phil Steitz
Fixed two errors reported on commons-user / commons-dev:
1. addValue(object) and getXxx methods failing or returning incorrect results for Integer arguments when the freq table is not empty
2. getXxx methods failing / returning inconsistent values when invoked on an empty table.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141420 13f79535-47bb-0310-9956-ffa450edef68

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1092071279
Brent Worden
added default goal.


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Phil Steitz
Removed boolean equalVariances flag from t-test API.


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Phil Steitz
Corrected inverseCumulativeProbability(0).


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1090768657
Phil Steitz
Changed Task list label.


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cd321472def83a7e405eeee4bba21274318a818c
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Phil Steitz
Changed statements about references to allow inline definitions, algorithm descriptions.


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Phil Steitz
Removed completed tasks, added Rational/Fraction class task for next release.


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Phil Steitz
Minor edits, formatting.


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Phil Steitz
Changed inverseCumulativeProbability to return correct values for p=0,1 as discussed on commons-dev.


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1090705225
Phil Steitz
Removed basedir property, causes updated plugin to fail.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141411 13f79535-47bb-0310-9956-ffa450edef68

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ccca505ed22099594ee3b3248f377c1caeb20c48
1090701809
Phil Steitz
Changed inverseCumulativeProbability to correctly handle p=0,1 as discussed on commons-dev.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141410 13f79535-47bb-0310-9956-ffa450edef68

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16310dc2210c020955db09bd41e27a2978d20a27
1090560156
Phil Steitz
Changed implementation to return correct inverse probabilities for p=0,1 (per discussion on commons-dev).


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141409 13f79535-47bb-0310-9956-ffa450edef68

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f25e3602099eeb8ccea425f9bb5b841905085436
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Phil Steitz
Changed to allow p=1 as argument to inverseCumulativeProbability.


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1090559683
Phil Steitz
Formatting, minor edits / updates.


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1090463665
Phil Steitz
javadoc


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329c20906cf315d8435a44abab0dd064bb88fbd3
1090463545
Phil Steitz
Add test for getN.


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f76a976abc491d264d605912c2050215a41db744
1090463401
Phil Steitz
Added test for toString().


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141404 13f79535-47bb-0310-9956-ffa450edef68

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1090463361
Phil Steitz
Fixed typo in toString(), added median.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141403 13f79535-47bb-0310-9956-ffa450edef68

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Phil Steitz
Added *last* missing sections :-)


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Phil Steitz
Added test class for PolynomialSplineFunction.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141401 13f79535-47bb-0310-9956-ffa450edef68

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1090328101
Phil Steitz
javadoc.


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Phil Steitz
Javadoc.


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Phil Steitz
Changed some methods to return interface types. Improved javadoc.


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Phil Steitz
Added constructor.


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Phil Steitz
Moved instance field initialization into constructor.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141396 13f79535-47bb-0310-9956-ffa450edef68

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Phil Steitz
Changed wrapped Variance instance to private.


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Phil Steitz
Changed implementation to wrap, rather than extend SumOfLogs.


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Phil Steitz
Removed unused import.


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Phil Steitz
Added geometric mean to StatUtils.


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Phil Steitz
-Changed UnivariateRealFunction.solve() to throw FunctionEvaluationException.
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  IllegalArgumentException if endpoints do not (appear to) bracket a root
  FunctionEvaluationException if an error occurs evaluating the function
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 instead of MathException when input property values are out of range.
-Changed AbstractContinuousDistribution.inverseCumulativeProbability to handle
 corner cases where solution equals domain lower or upper bound.
-Improved javadoc.
-Improved test coverage.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141391 13f79535-47bb-0310-9956-ffa450edef68

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Phil Steitz
Dropped serialization.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141390 13f79535-47bb-0310-9956-ffa450edef68

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Phil Steitz
Added argumentless constructor.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141389 13f79535-47bb-0310-9956-ffa450edef68

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Phil Steitz
Javadoc.


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Phil Steitz
Javadoc.


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dbb024cd5cd1549179222a1e7f1f81ac0480015e
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Phil Steitz
Renamed RealSolverTest to BrentSolverTest.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141386 13f79535-47bb-0310-9956-ffa450edef68

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Phil Steitz
Added FunctionEvaluationException and test class.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141385 13f79535-47bb-0310-9956-ffa450edef68

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ed015661d458a1e098099d5cdf34a1bf46d7d5cd
1089592029
Phil Steitz
Renamed ComplexMath to ComplexUtils.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141384 13f79535-47bb-0310-9956-ffa450edef68

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449fb86fa272ce3b5ddf05c180e0115a6c0da503
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Phil Steitz
Removed redundant null check.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141383 13f79535-47bb-0310-9956-ffa450edef68

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Phil Steitz
Removed [lang] dependency.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141382 13f79535-47bb-0310-9956-ffa450edef68

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Phil Steitz
Eliminated [lang] dependency.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141381 13f79535-47bb-0310-9956-ffa450edef68

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Phil Steitz
Eliminated [lang] dependency and local path reference.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141380 13f79535-47bb-0310-9956-ffa450edef68

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Phil Steitz
Changed to extend RuntimeException, removing [lang] dependency.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141379 13f79535-47bb-0310-9956-ffa450edef68

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Phil Steitz
Added tests for methods computing variance from mean, removed obsolete tests.


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Phil Steitz
Added methods for computing variance using precomputed mean, javadoc.


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Phil Steitz
javadoc only.


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Phil Steitz
Added missing method for computing variance from mean with no subarray specified.


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Phil Steitz
Added methods allowing exact values to be set using string representations.


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Phil Steitz
Added tests for printStackTrace(), serialization.


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Phil Steitz
Eliminated [lang] dependency.


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Phil Steitz
Added test for getN() and evaluate/getResult consistency test for small samples.


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Phil Steitz
Removed tests for factory methods that have been removed.


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Phil Steitz
Added test to make sure NaN is returned when it should be.


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053c5e0d0dd276b5d0ee8d6c958c8fba88576f67
1089479348
Phil Steitz
Changed getN() to return long.


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3771c80880835b4e294a67eab962686d8386dc74
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Phil Steitz
Changed getN() to return long. Changed evalutate() to return NaN if sample size is less than 3 (consistent w/ getResult()).


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Phil Steitz
Eliminated dependency on [logging].


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Phil Steitz
Caught NoClassDefFound Error when DiscoverClass is not present, eliminating
runtime dependency on [discovery], [logging].
Removed factory method taking string class name (use of Class.ForName()).


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Phil Steitz
Catch NoClassDefFound Error when DiscoverClass not present, eliminating runtime dependency on [discovery], [logging]


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Phil Steitz
Add evaluate/increment consistency test.


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Phil Steitz
Added evaluate method taking mean as a parameter. Changed implementation to wrap, rather than extend Variance.


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Phil Steitz
Added evaluate method taking mean as a parameter.


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Phil Steitz
Changed evaluate method to use embedded moments instead of duplicating code.


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Phil Steitz
Added incrementAll(double[]) methods.


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Phil Steitz
javadoc


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Phil Steitz
Made Sum instance local to evaluate. Improved javadoc.


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Phil Steitz
Made fields final.


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Phil Steitz
Removed link to external definition, as formula has been added to javadoc.


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Phil Steitz
Made NaturalComparator member class static.


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Phil Steitz
Added tests for NaN, infinite values, n=0,1.


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Phil Steitz
Fixed, documented NaN handling; changed internal counter to long; replaced pow with *.


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Phil Steitz
Added tests for NaN, infinite values, n=0,1


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Phil Steitz
Fixed, documented NaN handling.


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Phil Steitz
Added small sample tests for 2nd+ order moments.


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Phil Steitz
Added tests for n=0, 1.


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Phil Steitz
Added tests for NaNs, infinite values.


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Phil Steitz
Documented and fixed NaN handling.


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Phil Steitz
javadoc


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Phil Steitz
Changed implementation to use TreeMap directly, eliminating [collections] depenency.


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Phil Steitz
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Phil Steitz
Enforced bounds on quantile, improved javadoc.


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Javadoc.


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Made increment, evaluate consistent wrt NaN, improved javadoc.


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Phil Steitz
Uncommented previously failing tests.


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Made increment and evaluate methods consistent wrt NaN values, improved javadoc, formatting.


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Added tests for special values.


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Phil Steitz
Improved javadoc, implementation.


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Phil Steitz
Added tests for special values.


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Improved efficiency and javadoc.


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Formatting only. Eliminated tabs.


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Phil Steitz
Javadoc.


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Phil Steitz
Added tests to ensure NaN is returned for n<4


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Phil Steitz
Improved javadoc.
Eliminated unecessary / unused data members.
Made increment() and clear() throw IllegalStatException when the
statistic is based on an external moment.
Ensured that Double.NaN is returned for n < 4.


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Phil Steitz
Eliminated no-op increments which will throw once *silent* increment does.


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Phil Steitz
Added serialization tests.


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Phil Steitz
Added missing statistics in toString.


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Phil Steitz
Added tests for serialization, equals and hashcode.


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Phil Steitz
Implemented equals and hashcode, making summaries with identical statistics equal.


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Phil Steitz
Added tests for equals and hashcode.


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Phil Steitz
Implemented equals and hashcode.


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Phil Steitz
Added method to verify that serialization / deserialization preserves equals and hashCode (when this is supported).


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Phil Steitz
Changed getUnivariateStatistic() implementation to return a new instance (so tests can use multiple instances).


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Added equals and hash methods for comparing / hashing double values.


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Phil Steitz
Changed test class names to match implementation classes.


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Phil Steitz
Javadoc.


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Phil Steitz
Javadoc, formatting.


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Phil Steitz
Dropped load method taking string file path as argument.


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Phil Steitz
Dropped (unimplemented) load / saveDistribution methods.


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Phil Steitz
Dropped load / save methods taking string file paths as arguments.


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Phil Steitz
Formatting only. Removed tabs.


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Phil Steitz
Formatting only. Removed tabs and trailing spaces.


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Phil Steitz
Combined Expandable, ContractableDoubleArrays into ResizableDoubleArray and dropped FixedDoubleArray.


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Brent Worden
removed some condition logic by changing the continued fraction representation.


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08aeba4f0355ae6806f71bb92e9f81004cdbe6fe
1086892067
Brent Worden
PR: 29414
I changed the continued fraction used in regularizedBeta resulting in faster 
convergence.  I added the test case provided by scott and ran all units tests 
with all of them passing.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141289 13f79535-47bb-0310-9956-ffa450edef68

08aeba4f0355ae6806f71bb92e9f81004cdbe6fe
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43dcbb2433f06e0a1263d37a91f08c02561a99dc
1086704380
Phil Steitz
Javadoc only.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141288 13f79535-47bb-0310-9956-ffa450edef68

43dcbb2433f06e0a1263d37a91f08c02561a99dc
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f34385f6186718e8461f4f3a7a91ff8603071cf3
1086673063
Phil Steitz
Removed BeanUtils from list of dependencies.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141287 13f79535-47bb-0310-9956-ffa450edef68

f34385f6186718e8461f4f3a7a91ff8603071cf3
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a25f1e4515b215f4510088cd1787725479390b14
1086640216
Brent Worden
PR: 29419
Added an implementation of regularized gamma function, Q(a, x) = 1 - P(a,x), based on a continued fraction.  This converges much faster for the large x case.  I added the example submitted by Scott as a test case and ran all the test cases with everything passing.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141286 13f79535-47bb-0310-9956-ffa450edef68

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adc70eb37887e7036fd8395f489c26175546af45
1086578791
Phil Steitz
Formatting only, Eliminated tabs and trailing spaces.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141285 13f79535-47bb-0310-9956-ffa450edef68

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6d67900fb9862d1f33608f9985068d0eaeaef15d
1086563649
Phil Steitz
Cached DistributionFactory instance.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141284 13f79535-47bb-0310-9956-ffa450edef68

6d67900fb9862d1f33608f9985068d0eaeaef15d
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9c25e76e251bd7d5a8597c841005b4c72e9fc385
1086560905
Phil Steitz
Cached DistributionFactory instance used to create TDistribution instances.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141283 13f79535-47bb-0310-9956-ffa450edef68

9c25e76e251bd7d5a8597c841005b4c72e9fc385
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165783a737a69801fd245ff8555f909fc960f673
1086539946
Phil Steitz
Modified to extend ContinuousDistributionAbstractTest.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141282 13f79535-47bb-0310-9956-ffa450edef68

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1e1006a4d0e6ff24c91ed8acc442f99ea28e5e38
1086539885
Phil Steitz
Modified to extend AbstractContinuousDistribution.
Changed to throw IllegalArgumentException instead of returning NaN for
inverseCumulativeProbability argument not in [0,1].


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141281 13f79535-47bb-0310-9956-ffa450edef68

1e1006a4d0e6ff24c91ed8acc442f99ea28e5e38
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72d63d7ea2ee079eba6d5520ddcd7ac2d92d054d
1086538132
Phil Steitz
Corrected copyright date.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141280 13f79535-47bb-0310-9956-ffa450edef68

72d63d7ea2ee079eba6d5520ddcd7ac2d92d054d
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bee3b2bf43e36a9b07296b02b045842f43b8ff4a
1086495645
Phil Steitz
Initial Commit of BigMatrix classes.
PR #28819
Submitted by Matthew Inger


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141279 13f79535-47bb-0310-9956-ffa450edef68

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d96ef142ea5815d99f8f732966f570fb88a154bf
1086474676
Phil Steitz
Converted tabs to spaces.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141278 13f79535-47bb-0310-9956-ffa450edef68

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53b67deb0fe6aa6d275d6cd05fffda942fd8b69a
1086474490
Phil Steitz
Dropped rank method.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141277 13f79535-47bb-0310-9956-ffa450edef68

53b67deb0fe6aa6d275d6cd05fffda942fd8b69a
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c4510caf977e874dc5d462558e0eb5e948955eac
1086466266
Phil Steitz
Dropped serialization.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141276 13f79535-47bb-0310-9956-ffa450edef68

c4510caf977e874dc5d462558e0eb5e948955eac
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562545da7ffacdefe4a252ea1d9a57efb63c61aa
1086463723
Phil Steitz
Updated t-test docs to include paired, homoscedastic tests.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141275 13f79535-47bb-0310-9956-ffa450edef68

562545da7ffacdefe4a252ea1d9a57efb63c61aa
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04aa59dae1db76fdaa26fc85a2e7c744a7131864
1086357243
Mark R. Diggory
Removed unused imports


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141274 13f79535-47bb-0310-9956-ffa450edef68

04aa59dae1db76fdaa26fc85a2e7c744a7131864
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dc3d1506f8b49d341a3954cc5aad6fd23dbd6b93
1086357192
Mark R. Diggory
This call to StringUtils did very little for the following conditional structure. Consolidated code and removed dependency on lang.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141273 13f79535-47bb-0310-9956-ffa450edef68

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8a9722dad6954246a5b7efa45b934fabee17bb5f
1086187623
Mark R. Diggory
My local settings forced downloads in Ant to Apache instead of Ibiblio. I've corrected this.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141272 13f79535-47bb-0310-9956-ffa450edef68

8a9722dad6954246a5b7efa45b934fabee17bb5f
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455f95bcf76059c4c31e28d2928a9315b4108534
1086181735
Phil Steitz
Added support for equal variances tests.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141271 13f79535-47bb-0310-9956-ffa450edef68

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94d130188d16bd3a1ca2560bd372bdcf48999172
1086135892
Mark R. Diggory
Adding serialversionUID to control versioning and allow for implementations that would like to maintain serialization.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141270 13f79535-47bb-0310-9956-ffa450edef68

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1a46b43aed7d8ee2541e294ed6c11c178de3241e
1086135316
Mark R. Diggory
Adding serialversionUID to control versioning and allow for implementations that would like to maintain serialization.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141269 13f79535-47bb-0310-9956-ffa450edef68

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71c867a4af6deab5dc7cd6373461b13cad409883
1086135255
Mark R. Diggory
This class doesn't benefit from serialization, it has no internal state.


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9095d345ef747c4e11c10d90a8a9b0dc14d04d8c
1086135121
Mark R. Diggory
Test Example for serialization of Solvers and Functions.


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1086134131
Mark R. Diggory
Removed Dependency on BeanUtils and regenereated build.xml to reflect changes.


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1086133996
Mark R. Diggory
These Bean Classes have been added to experimental as internal classes in BeanListUnivariateImplTest


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6b35f287f032e2cc78f75109069073d1370d9ad5
1086133511
Mark R. Diggory
Now that we have BeanUtils "free" versions of these they do not need to be maintained in experimental.


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87f9a6994157acad8dbc3f83151d4136e88167d2
1086133229
Mark R. Diggory
Exception is getting exposed where it wasn't shown before.


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8c6718b9ae454fe78c7110ccae32e470de06a6aa
1086132092
Mark R. Diggory
Using standard jva.bean.Expression API to coerce property value in BeanTransformer.


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133b7ee9f5d62847c8417159f7fa6dc5d8f43459
1086128151
Mark R. Diggory
Removing Dependency on BeanUtils


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1086127817
Mark R. Diggory
Moving BeanTransformer to Experimental


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63c36c4dc2d8598ee28590dd49de2074bc269faf
1086125713
Mark R. Diggory
Added Serialization UID where required.


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1086125675
Mark R. Diggory
Consolidated AbstractDescriptiveStatistics into DescriptiveStatistics. Added Serialization interfaces where required.


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1086125286
Mark R. Diggory
Removing BeanListUnivariate example from test cases. Improving ListUnivariate Serialization Example.


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322706393973a99fc70f0cbd8cadee38bae3aa94
1086097637
Brent Worden
PR: 29000
Made ComplexFormat extend java.text.Format providing complex object formatting and parsing.


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322706393973a99fc70f0cbd8cadee38bae3aa94
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af6140fde695b8619531d04deb6d3e078f8cbfd1
1086050664
Phil Steitz
Added implementation for paired t-test boolean method.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141255 13f79535-47bb-0310-9956-ffa450edef68

af6140fde695b8619531d04deb6d3e078f8cbfd1
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1ffdfcd9b750da404b0a379620c1e592e0ae0744
1086037032
Phil Steitz
Javadoc fixes.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141254 13f79535-47bb-0310-9956-ffa450edef68

1ffdfcd9b750da404b0a379620c1e592e0ae0744
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14455961630d51d1dca0b818649d18e2123b2c36
1085964922
Phil Steitz
Modified to extent ContinuousDistributionAbstractTest.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141253 13f79535-47bb-0310-9956-ffa450edef68

14455961630d51d1dca0b818649d18e2123b2c36
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8686325727251cd77b77e54adcfba660620488bd
1085955215
Phil Steitz
Modified to extend ContinuousDistributionAbstract test, improved coverage.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141252 13f79535-47bb-0310-9956-ffa450edef68

8686325727251cd77b77e54adcfba660620488bd
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da13ce96f28a5f4019ab5476471a9eb933662350
1085896483
Phil Steitz
Modified to extend ContinuousDistributionAbstractTest, improved coverage.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141251 13f79535-47bb-0310-9956-ffa450edef68

da13ce96f28a5f4019ab5476471a9eb933662350
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a08439459a8a559007f51e8540f045200511176f
1085886480
Phil Steitz
Fixed some typos, formatting.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141250 13f79535-47bb-0310-9956-ffa450edef68

a08439459a8a559007f51e8540f045200511176f
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149f30e1d97c9e6893db500da876b292a37a238d
1085881173
Phil Steitz
Modified to extent ContinuousDistrbutionAbstractTest. Improved coverage.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141249 13f79535-47bb-0310-9956-ffa450edef68

149f30e1d97c9e6893db500da876b292a37a238d
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dd54604e2a7c1359c60c47426829a30138bf77e2
1085880242
Phil Steitz
Added endpoint order check to cumulativeProbability(double, double).


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141248 13f79535-47bb-0310-9956-ffa450edef68

dd54604e2a7c1359c60c47426829a30138bf77e2
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e9b8d5cf7d0bbcdf2c00b9d20717ac9eb69a6801
1085871164
Phil Steitz
Modified to extend ContinuousDistributionAbstractTest, improved coverage.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141247 13f79535-47bb-0310-9956-ffa450edef68

e9b8d5cf7d0bbcdf2c00b9d20717ac9eb69a6801
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dd45e40550aeb34d2ce3eb4098b9cc540e6b0ea3
1085871092
Phil Steitz
Initial commit.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141246 13f79535-47bb-0310-9956-ffa450edef68

dd45e40550aeb34d2ce3eb4098b9cc540e6b0ea3
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8dcee5909981e6af930e7f64c0a656c28358cc83
1085376870
Phil Steitz
Added tests for paired t-tests.
PR #29049


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141245 13f79535-47bb-0310-9956-ffa450edef68

8dcee5909981e6af930e7f64c0a656c28358cc83
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763ba3da98c9508e445af50204648cdc6f560fa3
1085376822
Phil Steitz
Added paired difference stats necessary
to support paired t-test computations
efficiently.
PR #29049


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141244 13f79535-47bb-0310-9956-ffa450edef68

763ba3da98c9508e445af50204648cdc6f560fa3
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bf5ff18001f65c85cbbf146b10ef8dafa4652989
1085376545
Phil Steitz
Added support for paired t-tests.
PR #29049
Reported by: Joel Freyss


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141243 13f79535-47bb-0310-9956-ffa450edef68

bf5ff18001f65c85cbbf146b10ef8dafa4652989
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f29d2289da81417e41f0479b0b8fe3f380aea656
1085348059
Timothy O'Brien
Addressed exception "swallowing" in test coverage.  From Phil's recent
email: "If the test case throws an unexpected exception, the test 
should fail.  ....[fix] these by changing the test method signature to 
throws Exception.  This also eliminates the need to import 
MathException everywhere."


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982271aec9c23c2a6a6e31a43b6165d217cb708b
1085291111
Phil Steitz
Javadoc fixes missed in PR #29050 changes.


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83ca7aaf105498bfdf942bdd4713edb4a21ab40a
1085288780
Phil Steitz
Added test case for small samples, adjusted for PR #29050 changes.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141240 13f79535-47bb-0310-9956-ffa450edef68

83ca7aaf105498bfdf942bdd4713edb4a21ab40a
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5ac2a29c8eb73d4119f0af8ecaf6faa81857cd0c
1085288688
Phil Steitz
Modified t-test procedures to allow samples as small
as 2 observations.
PR # 29050
Reported by: Joel Freyss


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141239 13f79535-47bb-0310-9956-ffa450edef68

5ac2a29c8eb73d4119f0af8ecaf6faa81857cd0c
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9942747e88518323443f79abc3fc4ca57228b0b3
1085273775
Timothy O'Brien
Pre Issue 29012, getKurtosisClass() did not have a tolerance; therefore,
any non-zero kurtosis was consistently mesokurtic.  Instead of getting 
into this level of detail, getKurtosisClass() has been removed, it is a
subjective measure not appropriate for DescStat.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141238 13f79535-47bb-0310-9956-ffa450edef68

9942747e88518323443f79abc3fc4ca57228b0b3
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de3e1206da887b91e055e48b5ef13f13765f06a3
1085273552
Timothy O'Brien
ComplexFormat now handles situations where either the real or 
imaginary part is NaN, POSITIVE_INFINITY, or NEGATIVE_INFINITY.
Three new tests were added to address these situations.
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git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141237 13f79535-47bb-0310-9956-ffa450edef68

de3e1206da887b91e055e48b5ef13f13765f06a3
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3484ff78aa1e37350bf0e91e00bb9506064f6b76
1085272421
Timothy O'Brien
Got rid of a number of those pesky "Auto-generated catch block" comments from test code.
PR:
Obtained from:
Submitted by:	
Reviewed by:	
CVS: ----------------------------------------------------------------------
CVS: PR:
CVS:   If this change addresses a PR in the problem report tracking
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CVS:   If you have not had it reviewed then delete this line.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141236 13f79535-47bb-0310-9956-ffa450edef68

3484ff78aa1e37350bf0e91e00bb9506064f6b76
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f7649bcc9f1f61b889b943c2ea71e8db435e9d1d
1085272201
Timothy O'Brien
Removed a series of unused imports in various classes both source and test.
PR:
Obtained from:
Submitted by:	
Reviewed by:	
CVS: ----------------------------------------------------------------------
CVS: PR:
CVS:   If this change addresses a PR in the problem report tracking
CVS:   database, then enter the PR number(s) here.
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CVS:   then name the system in this line, otherwise delete it.
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CVS:   they sent us a patch or a new module, then include their name/email
CVS:   address here. If this is your work then delete this line.
CVS: Reviewed by:
CVS:   If we are doing pre-commit code reviews and someone else has
CVS:   reviewed your changes, include their name(s) here.
CVS:   If you have not had it reviewed then delete this line.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141235 13f79535-47bb-0310-9956-ffa450edef68

f7649bcc9f1f61b889b943c2ea71e8db435e9d1d
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:100644 100644 f44cd312279254c75260d678ff33904ff4b0c850 ec6eb671730e8c6f228077d384f6047a4749b678 M	src/test/org/apache/commons/math/stat/univariate/DescriptiveStatisticsTest.java
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88f8675121ec780b7c2eb68d3c6d4208a7259aa7
1085255962
Phil Steitz
Improved efficiency.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141234 13f79535-47bb-0310-9956-ffa450edef68

88f8675121ec780b7c2eb68d3c6d4208a7259aa7
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7840ab4febd13f7c25d060a034d59790939942e8
1085149302
Phil Steitz
Javadoc.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141233 13f79535-47bb-0310-9956-ffa450edef68

7840ab4febd13f7c25d060a034d59790939942e8
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4456f88239df225ae680b27a9165fbb3c65f9942
1084979204
Brent Worden
Fixed javadoc warnings.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141232 13f79535-47bb-0310-9956-ffa450edef68

4456f88239df225ae680b27a9165fbb3c65f9942
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206201617aae648e12f63d4ab8aa9751157e7e63
1084976192
Brent Worden
Documented some runtime exceptions.
PR: 29013


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141231 13f79535-47bb-0310-9956-ffa450edef68

206201617aae648e12f63d4ab8aa9751157e7e63
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b16e7475445879a703a34e8af515e00b6ffd8995
1084854088
Phil Steitz
Added tests for getSummary() added to SummaryStatistics.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141230 13f79535-47bb-0310-9956-ffa450edef68

b16e7475445879a703a34e8af515e00b6ffd8995
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801524ee8416c759a42a397db6682c4495aa399e
1084853993
Phil Steitz
Added getSummary method returning StatisticalSummaryValues VO.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141229 13f79535-47bb-0310-9956-ffa450edef68

801524ee8416c759a42a397db6682c4495aa399e
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41007260becdf39a970625aea55193cb6c006044
1084853849
Phil Steitz
Initial commit -- value object representing statistical summary.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141228 13f79535-47bb-0310-9956-ffa450edef68

41007260becdf39a970625aea55193cb6c006044
:000000 100644 0000000000000000000000000000000000000000 bb05fd68e6fbec5039909e3bea9904738311f34a A	src/java/org/apache/commons/math/stat/univariate/StatisticalSummaryValues.java

10f49bc2c3b25f0aa61d32ef6d22de6fc788a98f
1084853318
Phil Steitz
Added tests corresponding to examples in user guide.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141227 13f79535-47bb-0310-9956-ffa450edef68

10f49bc2c3b25f0aa61d32ef6d22de6fc788a98f
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809ae375c746b0d51bb5867b89db8ed8adae9185
1084773554
Phil Steitz
Updated missing user guide sections.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141226 13f79535-47bb-0310-9956-ffa450edef68

809ae375c746b0d51bb5867b89db8ed8adae9185
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4b29763e68ada52b522d81cfd9d05f5924fa83ad
1084773515
Phil Steitz
Added overview, removed statistical utilities (covered in stat section).


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141225 13f79535-47bb-0310-9956-ffa450edef68

4b29763e68ada52b522d81cfd9d05f5924fa83ad
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5e4fca4bf69fe6048b53b7a9eb5269990ca687f9
1084773458
Phil Steitz
Added missing sections.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141224 13f79535-47bb-0310-9956-ffa450edef68

5e4fca4bf69fe6048b53b7a9eb5269990ca687f9
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8d825e475b702a65e1568590161bea6bc8f0103f
1084241948
Phil Steitz
javadoc typos.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141223 13f79535-47bb-0310-9956-ffa450edef68

8d825e475b702a65e1568590161bea6bc8f0103f
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e2882045231f6d29a6ffa9b2be9ff18b1698db87
1084241531
Phil Steitz
Modified to extend DiscreteDistributionAbstractTest. Added degenerate test cases.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141222 13f79535-47bb-0310-9956-ffa450edef68

e2882045231f6d29a6ffa9b2be9ff18b1698db87
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2ba7fa4d102f0c42ceb70946d6d91ff8c2d056d6
1084241354
Phil Steitz
Initial commit.


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Phil Steitz
Added consistency checks for constructor parameters.


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Phil Steitz
Improved documentation.


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Phil Steitz
Improved documentation. Added x0 <= x1 check in cumulativeProbability. Required p < 1 in inverseCumulativeProbability.


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Phil Steitz
Changed binomial coeffient computations to allow n = k = 0,
returning 1 in this case.  This is standard and also required
for degenerate hypergeometric distribution computations.


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Phil Steitz
Updated missing userguide sections.


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Phil Steitz
Added significance tests section.


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Brent Worden
Replaced normal CDF routine with one based on the error function.


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Phil Steitz
Removed pending license investigation.


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Brent Worden
Added unit tests.


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Brent Worden
Removed failing test.  Should never have been committed.


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Brent Worden
Added some unit tests for descriptive statistics.  Fixed bug dealing with resizing to infinite window size.


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Phil Steitz
Changed chi-square tests to pass long[] arrays of observed counts.


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1083553494
Phil Steitz
Initial commit of tests replacing TestStatisticTest.


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1083553401
Phil Steitz
Initial commit of code split off from TestStatistic.


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1083553345
Phil Steitz
Initial commit of code split off from TestStatistic. Changed observed vectors to be long[] arrays and added support for independence tests using 2-way tables.


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1083553028
Phil Steitz
Removed file to be replaced by TTestTest, ChiSquareTestTest.


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1083552896
Phil Steitz
Removed file to be replaced by TTest, ChiSquareTest.


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1083552849
Phil Steitz
Removed file to be replaced by TTestImpl, ChiSquareTestImpl.


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Brent Worden
Unit tests.


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Brent Worden
Fixed some checkstyle warnings.  Added some unit tests.


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Brent Worden
Fixed some checkstyle warnings.  Changed checkstyle settings to use APL 2.0.


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Brent Worden
Added user guide entry for continued fractions.


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Brent Worden
Added user guide sections for complex numbers and distributions.


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Brent Worden
Touched up the javadoc comments.


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Brent Worden
Added missing package.html files and added APL 2.0 to existing files.


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1082956595
Phil Steitz
Fixed typos.


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Phil Steitz
Fixed formatting, eliminated swallowed exceptions.


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Phil Steitz
Added BivariateRegression section.


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Phil Steitz
Updated dependencies.


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Phil Steitz
Implemented addValue(double) using DynaBeans.


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Phil Steitz
Javadoc.


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Phil Steitz
Replace deprecated TreeBag with collections 3.0 version.


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Phil Steitz
Updated dependencies to latest release versions
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Brent Worden
Added exceptions to javadoc comments.


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Brent Worden
Added some parameter javadoc comments.


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Brent Worden
Added javadoc comments replete with Mathworld references.


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Brent Worden
Removed some TODO comments.


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Brent Worden
Fixed a TODO by addid a isStrictlyIncreasing method.  This can be refactored later into a more reusable location.


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Phil Steitz
Removed author tags and emails, fixed link to nightlies.


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Mark R. Diggory
BeanListUnivariateImpl was misplaced during the move.


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Mark R. Diggory
Sorry, placed it in the wrong directory


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Mark R. Diggory
BeanListUnivariateImpl was misplaced during the move.


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Phil Steitz
Added missing fail stmnts, fixed index error


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1081747570
Phil Steitz
Fixed error in copyright notic.


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Phil Steitz
Added tests for AbstractUnivariateStatistic.


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Phil Steitz
Reordered checks in test() method to avoid NPE.


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Phil Steitz
Eliminated tabs.


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Phil Steitz
Added tests for indicator functions.
Contributed by: Christopher Schuck
Pr #28343


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Phil Steitz
Moved univariate statistical aggregates into univariate package.


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1081720348
Phil Steitz
Moved BivariateRegression to multivariate subpackage.


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1081716153
Phil Steitz
Fixed imports.


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Phil Steitz
Moved TestStatisticTest to new inference package.


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1081715116
Phil Steitz
Fixed package declarations.


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1081714754
Phil Steitz
Created inference package, moved statistical tests there.


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1081712350
Phil Steitz
Improved verification logic in test().


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1081710045
Phil Steitz
Javadoc. Fixed broken / malformed links.


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Phil Steitz
Added Christopher Schuck to contributors.


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Phil Steitz
Removed obsolete checkstyle properties file.


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Mark R. Diggory
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Newton's method using the new differentiable interface.


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Brent Worden
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Phil Steitz
Added preMultiply(Matrix) tests and modified preMultiply(double[]) tests to
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Phil Steitz
Added RealMatrix preMultiply(RealMatrix).
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Phil Steitz
Modified luDecompose to require that the matrix be square.
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Exposed lu decomposition matrix and associated permutation
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Mark R. Diggory
links are not inherited


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Phil Steitz
Updated to reflect current status.


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Phil Steitz
Improved Javadoc and fixed comparison error in indicator(short).
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Pr #28194


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Phil Steitz
Forced maven build to fail on test failure.


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Phil Steitz
Add tests to verify InvalidMatrixException is thrown by inverse() for singular or non-square matrices.


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Phil Steitz
Javadoc fixes, advertise correct exception in inverse().


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Phil Steitz
Removed misleading javadoc comment on derivative value constraints.


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Phil Steitz
Removed InterpolatorTest, replaced by SplineInterpolatorTest.


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Phil Steitz
Removed CubicSplineFunction, replaced by PolynomialSplineFunction.


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Phil Steitz
Modified tests to use derivative methods.


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Phil Steitz
Added method to check that two double arrays are equal.


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Phil Steitz
Fixed implementation, improved documentation.


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Phil Steitz
Modified constructor to copy input coefficients array.
Changed evaluation to use Horner's method.
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Dropped redundant firstDerivative, secondDerivative methods


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Phil Steitz
Initial commit


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Phil Steitz
Initial commit. Replaces InterpolatorTest.


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Phil Steitz
Initial commit.


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Phil Steitz
Javadoc


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Phil Steitz
Javadoc.


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Phil Steitz
Removed unused import. Javadoc.


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Phil Steitz
Formatting.


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Phil Steitz
Override getTolerance() to work with correct target value.


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Phil Steitz
Added another test, fixed reference to target values.


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Phil Steitz
Adjusted target values for product, log sum and variance based on exact computations using BigDecimal, comparison to R. Changed percentile targets to match implemented algorithm.


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Phil Steitz
Javadoc only. Added reference link.


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Phil Steitz
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Phil Steitz
Corrected javadoc, minor improvment to computation.


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Brent Worden
new approach to testing against certified data sets.

PR: 27692
Obtained from: Brent Worden
Submitted by: Brent Worden


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Phil Steitz
Added tests based on NIST definition.


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Phil Steitz
Renamed internal field, added algorithm documentation.


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Phil Steitz
Fixed code and javadoc to advertise the right exceptions, cleaned up formatting.


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Phil Steitz
Replaced low-accuracy textbook comparison values with values from R.


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Phil Steitz
Stopped swallowing MathExceptions, cleaned up formatting.


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Phil Steitz
Fixed javadoc typo.


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Phil Steitz
Changed to extend RetryTestCase to allow retries when statistical tests fail.


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Phil Steitz
Initial commit.


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1078626069
Phil Steitz
Dropped extraneous line added in error with last commit.


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Phil Steitz
Added test cases corresponding to examples in the User Guide.


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Phil Steitz
Added Frequency example showing cumPct for a value between stored values.


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Phil Steitz
Fixed error in getCumFreq (use custom comparator when one is supplied). Removed tabs.


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Phil Steitz
Filled in missing Frequency section.


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Phil Steitz
Javadoc.


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1078281145
Phil Steitz
Filled in missing content in univariate statistics section.


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Mark R. Diggory
Switching to usage of menu's dtd to insert commons navigation items, using common-menus entity to reference commons menues in navigation.xml, sorting is done by Maven.


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Phil Steitz
Added more content to statistics and distributions user guide.


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Timothy O'Brien
Added JavaDoc to the Complex class, still more work to be done.


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Timothy O'Brien
Added Javadoc to the ComplexFormat class


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1078080610
Phil Steitz
Eliminated author tags.


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2ba4d7e1110f614d4f6301fa443e89292e2ab8a2
1078005513
Brent Worden

PR: 27243
Obtained from: Scott Duchin
Submitted by: Brent Worden

Adding Scott's unit test.  See http://nagoya.apache.org/bugzilla/show_bug.cgi?id=27243 for details.


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37fbe761bc033d97f6c8237dd5276a76244c6b78
1077997420
Phil Steitz
Modified jar goal to include Apache License and notice in the jar. Fixed copyright notices. Reformatted xml.


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1077990457
Phil Steitz
Added copyright notice and reference to 2.0 license.


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Stephen Colebourne
Change to Apache License 2.0


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1077487289
Phil Steitz
javadoc.


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Phil Steitz
Updated license to 2.0


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2d69367fab142b626ce36d418272f99ad8fc3dc1
1077258159
Phil Steitz
javadoc, error message cleanup.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141103 13f79535-47bb-0310-9956-ffa450edef68

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4d630d00dee9e713f2a84551682586bf90f6cee2
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Phil Steitz
Added degree() method, degree checking in derivative computations, made constructor copy coefficient array, cleaned up javadoc.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141102 13f79535-47bb-0310-9956-ffa450edef68

4d630d00dee9e713f2a84551682586bf90f6cee2
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70d8784fd715efc6fa80f9ed5964a7c2b38cf48d
1077077495
Mark R. Diggory
Adding Commons Site Look & Feel configuration to all jakarta-commons/<project>/project.properties


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141101 13f79535-47bb-0310-9956-ffa450edef68

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Brent Worden
fixed spelling error: cummulative -> cumulative.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141100 13f79535-47bb-0310-9956-ffa450edef68

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Phil Steitz
Restored original copyright date.


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1076992396
Phil Steitz
Restored test code inadvertently deleted with last commit.


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1076915044
Phil Steitz
Fixed logic in bean transformer tests to match API.


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Phil Steitz
Stopped header comments from confusing javadoc tool.


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Phil Steitz
Commented out sysouts.


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Phil Steitz
Fixed broken download link, removed local path reference.


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Mark R. Diggory
included navigation should be from commons-build now.


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Phil Steitz
Added load(double[]) method to EmpiricalDistribution.
Contributed by Piotr Kochanski
PR # 26772


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Mark R. Diggory
Moving extension of global project.xml to ../commons-build/project.xml on those project.xml files which originally had it in place.


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Timothy O'Brien
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Phil Steitz
Refactored Frequency to support cummulative frequency counts and percentages. Also eliminated the name property.


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Phil Steitz
Added bound to simulation loop in nextPoisson().


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Mark R. Diggory
Ajusting xdoc templates css styles appropriately, these are just used for testing/preview in xml/xslt enabled browsers.


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1075492413
Mark R. Diggory
Fixing version number.


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1075492328
Mark R. Diggory
Fixing email addresses and changing version to 1.0


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1075472366
Phil Steitz
Converted to commons standard l&f.


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1075440884
Mark R. Diggory
New graphics for white background


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1075424921
Mark R. Diggory
Info for Release Manager, feel free to change.


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1075400642
Mark R. Diggory
adding comment on maven property to skip tests.


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1075395245
Mark R. Diggory
Removing default generated @author Administrator tags from Eclipse


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1075395161
Mark R. Diggory
Actually, we should really be switching to Apache license 2.0.


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1075357574
Phil Steitz
Replaced unnecessary bin search with direct computation.


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b0cf79f06d3db8db60b33e6bda76dd50ef3ec140
1075354074
Phil Steitz
Speed up, clean up.


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68853bb1af4a06b562f786a3513d83b5b69cc2fa
1075352316
Phil Steitz
Javadoc.


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68853bb1af4a06b562f786a3513d83b5b69cc2fa
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3cf4273631140f5dc9913cb1b0785c468ba441a8
1075350747
Timothy O'Brien
Added a simple formatting class for Complex numbers.
I had considered just implementing toString() on the complex
class, but I decided aginst it because some fields prefer
"j" to "i".  This ComplexFormat class is very straightforward,
will a number of TODOs, it is accompanied by a 10
tests.


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1075337343
Mark R. Diggory
Happy New Year, updating all license years to 2004


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141074 13f79535-47bb-0310-9956-ffa450edef68

ea117cb81769e5d205cec3c07b29fda343bd7868
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1075336582
Mark R. Diggory
Happy New Year


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141073 13f79535-47bb-0310-9956-ffa450edef68

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1075335249
Mark R. Diggory
A maven.xml file with a custom goal for cutting math releases. Does snapshot resolution prior to cutting release.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141072 13f79535-47bb-0310-9956-ffa450edef68

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1075323955
Timothy O'Brien
Project dependencies for commons-collctions and commons-lang were pointing to the SNAPSHOT of both.  When this was iriginally done, it was agreed that pointing to a SNAPSHOT was not an option for a release.  Now that compatible version of these to component have been released, the versions have been updated.  Commons Math now depends on collections 2.1 and lang 2.0.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141071 13f79535-47bb-0310-9956-ffa450edef68

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1075320903
Timothy O'Brien
RealMatrix now throws two more runtime exceptions
InvalidMatrixException and MatrixIndexException


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1075320859
Timothy O'Brien
Added .clover and junit temp output to the cvsignore


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1075171424
Phil Steitz
Eliminated unecessary first moment computations.


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1075146076
Mark R. Diggory
PR: http://nagoya.apache.org/bugzilla/show_bug.cgi?id=24962
Obtained from: sergei skarupo

Refactored all sign methods to indicator.
Created new Sign methods per wolfram specs.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141067 13f79535-47bb-0310-9956-ffa450edef68

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Phil Steitz
Added Piotr Kochanski to contributors.


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Phil Steitz
Added Normal Distribution implementations and tests contributed by Piotr Kochanski.


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Phil Steitz
Refactored statistical aggregates to separate stored, storeless implementations. Changed internal sample size counters to longs.


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1074397502
Phil Steitz
javadoc.


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1074363361
Mark R. Diggory
shortDescription ends up going into META-INF properties file. Punctuation makes this break for some reason.


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1074151904
Phil Steitz
Replace deprecated method.


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Phil Steitz
Added data generation doc.


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Phil Steitz
Updated copyright date (after BZ #25972 changes).


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Phil Steitz
Removed completed tasks section, restored future tasks, added conf intervals.


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Phil Steitz
Removed completed/obsolete tasks, added RealMatrix refactoring task.


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William Barker
Fix URL -> File conversion in the test.

I'd forgotten that I had added this to my code when looking at BZ #25972.


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1073849722
Phil Steitz
Fixed source formatting.


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Phil Steitz
Fixed capitalization.


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Phil Steitz
Added humble self to developers.


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Phil Steitz
Modified tests to reflect changes addressing PR #25972.


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Phil Steitz
Refactored file handling methods to eliminate use of URL.toFile(). Addressing PR #25972, reported by Bill Barker.


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Phil Steitz
Refactored load methods to eliminate use of URL.toFile(). Addressing PR #25972, reported by Bill Barker.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141050 13f79535-47bb-0310-9956-ffa450edef68

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Phil Steitz
Added load(URL). Addressing PR #25972, reported by Bill Barker.


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Joerg Pietschmann
Added documentation.


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Henri Yandell
fixed ids, but unable to find Apache id for Albert Chou


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Mark R. Diggory
Additional Matrix Multiply test


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1069618577
Mark R. Diggory
Patch to correct error in matrix multiply 
and the addition od toString method.


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1069617220
Mark R. Diggory
New additions of CholeskySolver contributed by Stefan Koeberle


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14fa7276518f8e2f21d41d261d921cc0cc87b9c8
1069480771
Brent Worden
Here's my idea for approximating derivatives.  It follows the decorator layout of commons-collections.  The main interface point is the UnivariateRealFunctionUtils type which is responisble for creating decorated UnivariateRealFunction objects.  To demostrate the how the decorators could be used, I added the UnivariateRealFunctionUtilsTest class which computes a local maximum of a function using derivative decorators and the default solver.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141043 13f79535-47bb-0310-9956-ffa450edef68

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1069302398
Mark R. Diggory
extends MathException....


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1069302137
Mark R. Diggory
I've thought about this and I like the idea of getting some of this code available in the cvs for experimentation, I'm going ahead and adding it for others to look at and consider.

This directory will not get compiled into the regular build process or future distributions. We can work on an ant script to provide easy build of this if others think it neccessary.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141041 13f79535-47bb-0310-9956-ffa450edef68

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81258e8bc55306b2df1745ccb0140d7e2ef02da8
1069284120
Robert Burrell Donkin
Correct typo in documentation. Submitted by Doug Bateman.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141040 13f79535-47bb-0310-9956-ffa450edef68

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1069248910
Mark R. Diggory
JUnit testing of serialization of all StorelessUnivariates


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b56654a917ef913f10fda581369e86ce1b090064
1069248402
Mark R. Diggory
Additional tooling for simple JUnit testing of serialization.


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941d0aadef49a5586a03287a38b3fb7dca6b6e6c
1069225607
Brent Worden
change email address.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141037 13f79535-47bb-0310-9956-ffa450edef68

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1069212505
Mark R. Diggory
Added Serialization Interface to all Implementations


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d1916458812f417874b0886ed64654bb6a0b8224
1069212174
Mark R. Diggory
Exposed MathException handling in Distributions by adding thows MathException to methods where MathExceptions are caught and replaced with Double.NaN. Added Serialization Interface to Distributions, BivariateRegression and TestStatistic


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141035 13f79535-47bb-0310-9956-ffa450edef68

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03a43587a64873693855606fff17ad8ad3e99699
1069168032
Mark R. Diggory
fix for wrong results and stack overflow error from BivariateRegression
PR: http://nagoya.apache.org/bugzilla/show_bug.cgi?id=24747
Obtained from:
Submitted by:	Sergei Skarupo, Brent Worden 
Reviewed by:	Mark Diggory


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141034 13f79535-47bb-0310-9956-ffa450edef68

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4102896201898b98e15c88d8b985c5b6372d9e3d
1069102573
Mark R. Diggory
Test commit.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141033 13f79535-47bb-0310-9956-ffa450edef68

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94d606f5c97007f4c8ea1eff35adf1c348f88101
1069102534
Mark R. Diggory
Test commit.


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784a5071eec7670b70b0e78d91efe4da5c29366b
1069047489
Mark R. Diggory
Site Logo :-)


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4f2e0e627827e81c894fade07270eb1648944503
1068929974
Mark R. Diggory
Adding more external javadoc links.


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4f2e0e627827e81c894fade07270eb1648944503
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435f91362dedb32c39be181f69bd7a939f770a1a
1068929866
Mark R. Diggory
Adjusted Contibutors and Developers lists.


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d45792d1df1763727e93e10e18bcd353577b85c6
1068926566
Mark R. Diggory
Older versions of the txt files that currently exist in this directory.


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c200ad94ad1a7e96c7cc2ab9f02a672ca70345c5
1068923138
Dirk Verbeeck
reapply (mdiggory    2003/11/01 08:14:45)
  Modification to project.xml to build and locate the cvs tree in the proper location.


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a8d7b3661db269dad434c6d172eaf691ea94deeb
1068923068
Dirk Verbeeck
  PR: http://www.mail-archive.com/commons-dev@jakarta.apache.org/msg29959.html
  Submitted by:	Matt Cliff
  Reviewed by:	Mark Diggory


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141026 13f79535-47bb-0310-9956-ffa450edef68

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2fe1cb9e39c61ceb7afa3bad27d9f58e93404bf0
1068922965
Dirk Verbeeck
reapply DefaultTransformer update


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6399a6d8dffc1b85ac2b4477781e55bc6a468bc6
1068922750
Dirk Verbeeck
remove logging
  Reviewed by:	Mark Diggory


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1068922576
Dirk Verbeeck
remove old files
  Reviewed by:	Mark Diggory


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a7fbd3edc48543cd58e9599a6a81583d30ecdf64
1068922351
Dirk Verbeeck
  Applied Brent Wardens Bug fixes to Complex implementation and tests.


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8c5e07e98aefa427c347f5e53df0625fa755f36d
1068922029
Dirk Verbeeck
  PR: http://nagoya.apache.org/bugzilla/show_bug.cgi?id=24598
  Submitted by:	Brent Worden
  Reviewed by:	Mark Diggory


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1068921892
Dirk Verbeeck
  PR: http://www.mail-archive.com/commons-dev@jakarta.apache.org/msg29959.html
  Submitted by:	Matt Cliff
  Reviewed by:	Mark Diggory


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1068921804
Dirk Verbeeck
Reapply changeset (mdiggory    2003/11/09 12:17:50)
 Adding documentation for Contributors.
 Adding xsl stylesheets to render xdoc in browser and css to style content, this makes testing documentation additions easier without rendering the entire site. Simply open up xdoc in browser to see what it will look like after rendering.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141019 13f79535-47bb-0310-9956-ffa450edef68

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1068921496
Dirk Verbeeck
Reapply changeset (mdiggory    2003/11/09 12:17:50)
 Adding documentation for Contributors.
 Adding xsl stylesheets to render xdoc in browser and css to style content, this makes testing documentation additions easier without rendering the entire site. Simply open up xdoc in browser to see what it will look like after rendering.


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1068918751
Dirk Verbeeck
add .cvsignore (second try)


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1068912102
Dirk Verbeeck
Reapply changes (mdiggory    2003/11/10 09:43:34)

Moving Distributions to higher level location from o.a.c.m.stat.distirbutions to o.a.c.m.distirbutions
Changing Names of Univariates to DescriptiveStatistics and replacing Interface with Abstract Factory Implementation
Moving BeanTransformer and ListUnivariate implmenetations to test directory.


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b3251a0a33622bae17a37477dd46cab63d5fd508
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Mark R. Diggory
Attempting to recover last revision.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141015 13f79535-47bb-0310-9956-ffa450edef68

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3bbbeec4cfb96f356211cd1c3c9eb4da1fbc73de
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Mark R. Diggory
these were removed earlier than 11/1/03


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141014 13f79535-47bb-0310-9956-ffa450edef68

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0a904461932f2c0455611e77ec6a8d8aced2980b
1068848728
Mark R. Diggory
Attempting to recover last revision.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141013 13f79535-47bb-0310-9956-ffa450edef68

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be2412ecc093e9d684cdf530c8e4c1b61b261601
1067543526
Mark R. Diggory
Comments about Complex


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141009 13f79535-47bb-0310-9956-ffa450edef68

be2412ecc093e9d684cdf530c8e4c1b61b261601
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fe3cd99face8e8df552e3f68e343d01770551fbd
1067543476
Mark R. Diggory
Comments about Complex


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141008 13f79535-47bb-0310-9956-ffa450edef68

fe3cd99face8e8df552e3f68e343d01770551fbd
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8df25775a59ddd77e909a37378ee459c502ab658
1067542963
Mark R. Diggory
PR: http://nagoya.apache.org/bugzilla/show_bug.cgi?id=24241
Submitted by:	Brent Worden


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141007 13f79535-47bb-0310-9956-ffa450edef68

8df25775a59ddd77e909a37378ee459c502ab658
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79eeced125f693f308d2d8a0e8b5691ea1243627
1066834844
Mark R. Diggory
Added references to email threads concering complex numbers.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141006 13f79535-47bb-0310-9956-ffa450edef68

79eeced125f693f308d2d8a0e8b5691ea1243627
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10d2b4b9b16d89026d3e9bacc876c543db3b9d81
1066319980
Mark R. Diggory
Rewrite StatUtils to use static instances of UnivariateStatistics. Benefits? 

1.) In the future, when we establish "Factories" for these objects, we'll be able to plug implementations in, even under our static Utilities classes for these functions. 

2.) The  user can always rely on the same result, whether using the StaticUtil, Univariate Container or direct UnivariateStatistic.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141005 13f79535-47bb-0310-9956-ffa450edef68

10d2b4b9b16d89026d3e9bacc876c543db3b9d81
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8f67ec7c39efbf1afa2b81ad4e0c7a071cf412c0
1066317873
Mark R. Diggory
PR: http://nagoya.apache.org/bugzilla/show_bug.cgi?id=23716
Submitted by:	Brent Warden	
Reviewed by:	Mark Diggory


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141004 13f79535-47bb-0310-9956-ffa450edef68

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23277b96dae68928fbe7a785d080fc0fbf6eb27d
1066317304
Mark R. Diggory
PR: http://nagoya.apache.org/bugzilla/show_bug.cgi?id=23453
Submitted by:	Brent Warden
Reviewed by:	Mark Diggory


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141003 13f79535-47bb-0310-9956-ffa450edef68

23277b96dae68928fbe7a785d080fc0fbf6eb27d
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0c0c3e8f79979c54dde739a9c55c5cc27d46f2c2
1066313107
Mark R. Diggory
A couple additions


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141002 13f79535-47bb-0310-9956-ffa450edef68

0c0c3e8f79979c54dde739a9c55c5cc27d46f2c2
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1939068182855402ed79a39a5d7a87b26446970c
1066032704
Robert Burrell Donkin
Fixed typos in apache license


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141001 13f79535-47bb-0310-9956-ffa450edef68

1939068182855402ed79a39a5d7a87b26446970c
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74c69f200acdc97370a561ea9350502c962fe603
1065390617
Timothy O'Brien
Fix to license, changed "names" to "name" in section 5


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@141000 13f79535-47bb-0310-9956-ffa450edef68

74c69f200acdc97370a561ea9350502c962fe603
:100644 100644 202d60b26bdedf2873563738cd10eee34646afe7 8e419339ca0c05561fa8af2170aeccedaf2266f2 M	LICENSE.txt

eccf8898d10bfe9854aa5a736784c076ff6f605b
1064636014
Mark R. Diggory
PR: http://nagoya.apache.org/bugzilla/show_bug.cgi?id=23187
Obtained from:
Submitted by:	Brent Worden 
Reviewed by:	Mark Diggory


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140999 13f79535-47bb-0310-9956-ffa450edef68

eccf8898d10bfe9854aa5a736784c076ff6f605b
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92a2a61ebbe174a71ea2e6b42a0464b3a565402f
1064604633
Joerg Pietschmann
Fixed JavaDoc warnings.
Fixed a few TODOs in the interpolation code.
Updated project TODO list.
Promoted myself to "developer".


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140998 13f79535-47bb-0310-9956-ffa450edef68

92a2a61ebbe174a71ea2e6b42a0464b3a565402f
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2b001c2ab1c546f3d6854dcb3e6b6e0cfcfe0aeb
1064434550
Joerg Pietschmann
User manual for root finding, distribution framework and special functions.
Contributed by: Brent Worden
Reference: #23367, #23361, #23389


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140997 13f79535-47bb-0310-9956-ffa450edef68

2b001c2ab1c546f3d6854dcb3e6b6e0cfcfe0aeb
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9dd9778a7cf24ea9fad3bb67bcaec9bc3728ce47
1063826972
Mark R. Diggory
PR: http://nagoya.apache.org/bugzilla/show_bug.cgi?id=23013
Submitted by:	Brent Warden
Reviewed by:	Mark Diggory

I also regenerated the build.xml using Maven to get the Discovery dependency added in.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140996 13f79535-47bb-0310-9956-ffa450edef68

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37064526036889ab5206776b0913a37ef6006f76
1063826349
Mark R. Diggory
PR: http://nagoya.apache.org/bugzilla/show_bug.cgi?id=23010
Submitted by:	 Brent Worden 
Reviewed by:	Mark Diggory


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140995 13f79535-47bb-0310-9956-ffa450edef68

37064526036889ab5206776b0913a37ef6006f76
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bc31e531edcdcab235585086ced5eb1dec33e1d6
1062904376
Mark R. Diggory
PR: http://nagoya.apache.org/bugzilla/show_bug.cgi?id=22954
Submitted by:	Brent Worden
Reviewed by:	Mark Diggory


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140994 13f79535-47bb-0310-9956-ffa450edef68

bc31e531edcdcab235585086ced5eb1dec33e1d6
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d7fff63d95cd9e28bfd31006c89d89e454ec7c53
1061053575
Joerg Pietschmann
Added classes for binominal distribution and some infrastructure for other
discrete distributions.
Contributed by Brent Worden (brent@worden.org)


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140993 13f79535-47bb-0310-9956-ffa450edef68

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335ef8c47aa707b714ffb75a5ed7acd9e411200b
1060868469
Mark R. Diggory
Some reorganization of the Tasks List.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140992 13f79535-47bb-0310-9956-ffa450edef68

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1060401821
Mark R. Diggory
Just Checkstyle and Javadoc corrections


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140991 13f79535-47bb-0310-9956-ffa450edef68

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5b02b4da9d494fa99cf608f1497e509712ff1680
1059685657
Timothy O'Brien
Some rewording, mostly indentation.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140990 13f79535-47bb-0310-9956-ffa450edef68

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578b804429d7c905d06f019c62c7596e51d22917
1059602797
Timothy O'Brien
Bugzilla #22002 from Brent W's patch - refactoring of UnivariateRealSolver


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140989 13f79535-47bb-0310-9956-ffa450edef68

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8d0aca99fe6caab0f260343c22e55bece28499ab
1059602291
Timothy O'Brien
Bugzilla #22002: applied Brent W's patch which dealt with URSFactory and URSFImpl as well as numerous improvements to javadoc


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140988 13f79535-47bb-0310-9956-ffa450edef68

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4456d90840a829fbe09fe506ab5e78288dc2f591
1058240710
Mark R. Diggory
Application of "apply(Functor x)" strategy (thank you Al Chou) for evaluating UnivariateStatistics against the internal storage collection without exposing the collection or its bounds.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140987 13f79535-47bb-0310-9956-ffa450edef68

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1058240330
Mark R. Diggory
minor javadoc cleanup


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140986 13f79535-47bb-0310-9956-ffa450edef68

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3a6b1537e593b91e60de7a5e112bf47c47a5f4c3
1058240231
Mark R. Diggory
minor javadoc cleanup


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140985 13f79535-47bb-0310-9956-ffa450edef68

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1057939154
Timothy O'Brien
Patch for bug 21516 from Brent Worden. Fixed checkstyle bugs and added maven.javadoc.links to project.properties


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140984 13f79535-47bb-0310-9956-ffa450edef68

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1057787193
Mark R. Diggory
Changes the Univariate implementations to use the UnivariateStatistic package. Slims down StatUtils by removing some of the higher moments. Reimplmenets ListUnivariate to work with NumberTransformers, turning into a Mixed Object List Univariate.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140983 13f79535-47bb-0310-9956-ffa450edef68

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f1a917482c722d594df5b7f6e286395aadbd5f5a
1057781280
Mark R. Diggory
Adding J. Pietschmann


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140982 13f79535-47bb-0310-9956-ffa450edef68

f1a917482c722d594df5b7f6e286395aadbd5f5a
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8b3db797f220e304e215130d5e0d89e7464151bd
1057781053
Mark R. Diggory
Removing @author tags, adding missing @version tags.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140981 13f79535-47bb-0310-9956-ffa450edef68

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05c18b9f8c991b44a825c9c6fdf488bf467b3a67
1057768110
Mark R. Diggory
Changing getValue to getResult.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140980 13f79535-47bb-0310-9956-ffa450edef68

05c18b9f8c991b44a825c9c6fdf488bf467b3a67
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825163490d3e3b92210028db76d8e21ac388a7a7
1057767858
Mark R. Diggory
In cases where "getResult" contains a statistical calculation, it now 
checks if the internal state of the underlying statistic has changed 
and only recalculates if this is true. this way muliple calls to getResult 
when the staistic has not been incremented are less expensive 
because it is only returning a property value.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140979 13f79535-47bb-0310-9956-ffa450edef68

825163490d3e3b92210028db76d8e21ac388a7a7
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d6741b72a9aa212cc681462ff97f5d69f0364edb
1057636875
Mark R. Diggory
actually this is ok, its a problem with the fact that the directory already exists in the cvs.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140978 13f79535-47bb-0310-9956-ffa450edef68

d6741b72a9aa212cc681462ff97f5d69f0364edb
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f8e28a2611a4d8c382e26c7dd5228f3052283c23
1057636480
Mark R. Diggory
This is an attempt to get directories working properly in .cvsignore


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140977 13f79535-47bb-0310-9956-ffa450edef68

f8e28a2611a4d8c382e26c7dd5228f3052283c23
:100644 100644 2dda873d1d51e2757461e0982030150adb3ca817 1f6b4cfc2a51d5901c3ed64a692db3291e9525d7 M	.cvsignore

98eff8c9db069b8297234d86c81f2c42bccd6191
1057635852
Mark R. Diggory
Its more logical not to have increment return a value, this allows a 
distict separation between the calculation of moments and the 
calculation of the actually return value of getVlaue in Storageless 
approaches. With this benifit it is no longer neccessary to calculate 
all the statistics moment based statistics on addValue, only the 
underlying moment itself.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140976 13f79535-47bb-0310-9956-ffa450edef68

98eff8c9db069b8297234d86c81f2c42bccd6191
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:100644 100644 1b2b6676d22fb729174835629cb53e2f3a37e1c4 5cc2e34cbe05ea87820768c80b0045d2c643aa1e M	src/java/org/apache/commons/math/stat/univariate/summary/SumOfLogs.java
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fbb87a296305fe4f813ccbfa8683c83f479a8e7d
1057620314
Mark R. Diggory
Removing more of my author tags.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140975 13f79535-47bb-0310-9956-ffa450edef68

fbb87a296305fe4f813ccbfa8683c83f479a8e7d
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:100644 100644 ce60ec506b8415f98b8a6d806d3f6f6b71381b9f be4336e0399e28e3a06d129b32ed7a7a2db7754e M	src/java/org/apache/commons/math/stat/Univariate.java
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:100644 100644 00737d4bc1b2d8b46d86b399c2d60ee4948de9c5 1aefe8378c42ad93185fa832566426b5a1f0a617 M	src/java/org/apache/commons/math/util/BeanTransformer.java
:100644 100644 55579c1075c89c456fb60c3cb961ac7bc2dd1eda d6a47ed4a61ef267aed208c2b4b0206ece380ceb M	src/java/org/apache/commons/math/util/DefaultTransformer.java
:100644 100644 d9bab3387d856f20e2f98e9976be8aa83bbe3b91 0b7504165d9bf79b8be494fef8f7ac4337af5fd0 M	src/java/org/apache/commons/math/util/NumberTransformer.java
:100644 100644 554a5d33c5fcffae4b2e45f0888b43f4f1907c05 acbeb7822a2a6f377ed2ef431ecdd5cb1ba286cf M	src/java/org/apache/commons/math/util/TransformerMap.java
:100644 100644 430601b211e839093c12f1a14e3da4223e1c55eb b5350bdec285f7ddadb485bb2109c22144bdcd9a M	src/test/org/apache/commons/math/stat/CertifiedDataTest.java
:100644 100644 681ee41b3422c5c4aa64bb45d0cbb8515fb734a3 6ced45d36604d8c4b8ab0e82f07f6c7ce456b5e1 M	src/test/org/apache/commons/math/stat/StatUtilsTest.java

c6231e78a1ea882b8b6d2b033c32adbe2108a743
1057619962
Mark R. Diggory
PR: http://nagoya.apache.org/bugzilla/show_bug.cgi?id=21360
Submitted by:	phil@steitz.com

I applied this patch on the sourcecode, I think all project.xml and 
xdoc documentation should retain some authorship at this time. If 
we decide otherwise we can change this in the future.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140974 13f79535-47bb-0310-9956-ffa450edef68

c6231e78a1ea882b8b6d2b033c32adbe2108a743
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:100644 100644 6f0de0ba935fa647e763041bdee2280e7a38429b e34bf59aeda2e90ce22f1b6863d283e38a0b5767 M	src/java/org/apache/commons/math/linear/RealMatrixImpl.java
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:000000 100644 0000000000000000000000000000000000000000 a287e7273c975f1c18c6e2517bfec2281b001fe9 A	src/test/org/apache/commons/math/stat/univariate/InteractionTest.java
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:100644 100644 9a50eb5d6a24fc3c69c41200f5f467dbc3ece0f5 5ca01365ea7772ff1770a0a79e62ac8a2d9123cf M	src/test/org/apache/commons/math/stat/univariate/summary/ProductTest.java
:100644 100644 5e364309a9758699137e3753c3f7d3f8f72c1698 c633f9c62dcc82bdf1960637bb12053ae8579139 M	src/test/org/apache/commons/math/stat/univariate/summary/SumLogTest.java
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:100644 100644 403cdd2562886473b55d25ca94319915417f1e9c 387649d7b814bb163d4e21cbbc44d01ae9ffc612 M	src/test/org/apache/commons/math/stat/univariate/summary/SumTest.java
:100644 100644 a4b750e1bed5f2a9d1d018e5b24b6d82bdd8c8a4 5e4bbe048b803a881a9be567dfda171474fb7ff7 M	src/test/org/apache/commons/math/util/MathUtilsTest.java

9cf28b0197259a4884a7df51cf9f17611e7c24a6
1057619208
Mark R. Diggory
This commit adds the constructor and internals for setting and External Moment object to base internal calculations on. It also remove author tags and adds a new class FirstMoment to the project.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140973 13f79535-47bb-0310-9956-ffa450edef68

9cf28b0197259a4884a7df51cf9f17611e7c24a6
:000000 100644 0000000000000000000000000000000000000000 6cddbe8d83339340644eb1bfd00b5baeaf39f66a A	src/java/org/apache/commons/math/stat/univariate/moment/FirstMoment.java
:100644 100644 08cd7ba6dabe546b581e5ffbab975c56c6a02844 cf3e76f134d7f3138c88298921d95fc68f88fffb M	src/java/org/apache/commons/math/stat/univariate/moment/FourthMoment.java
:100644 100644 e076206c385809badef4bf3d77577c3695c27ff5 808dc5568c18f7e736f6c926783d6fdc90605f42 M	src/java/org/apache/commons/math/stat/univariate/moment/GeometricMean.java
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:100644 100644 b087dc95251d0e7e763086c1d871f1345b27908e 5f71f9a6e33a55b2f72f3dfbc71a5f7e404e7c75 M	src/java/org/apache/commons/math/stat/univariate/moment/Skewness.java
:100644 100644 c65cefd909c0ec4875447e61372367902ff8e025 c3f676b82252fdc2bcfd47e356c0f694790f5248 M	src/java/org/apache/commons/math/stat/univariate/moment/StandardDeviation.java
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5453711fb8097a0d750338f15f18f1868294dd78
1057597053
Mark R. Diggory
Fixing GeoMean and adding appropriate test.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140972 13f79535-47bb-0310-9956-ffa450edef68

5453711fb8097a0d750338f15f18f1868294dd78
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9b6845c0560fb8aa7a53aff3322218288ca067b4
1057587320
Mark R. Diggory
removed extra calculation.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140971 13f79535-47bb-0310-9956-ffa450edef68

9b6845c0560fb8aa7a53aff3322218288ca067b4
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cc7965242bcce95bd10348b0bc32076e6e9d16ca
1057586233
Timothy O'Brien
This XML configuration file will work with the most recent Maven plugin for Checkstyle, just change the project.properties to point to this XML file.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140970 13f79535-47bb-0310-9956-ffa450edef68

cc7965242bcce95bd10348b0bc32076e6e9d16ca
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6fa3edd33761edf5441818b57944b58271126a66
1057544119
Mark R. Diggory
Addition of optimal array based evaluations available in StatUtils. These are not delegates to StatUtils, they are implementations.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140969 13f79535-47bb-0310-9956-ffa450edef68

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9eed265da3a878d6375c6702d4cd1179c4f1194b
1057543967
Mark R. Diggory
Adding incremental tests for storeless univariates as evaluations are now based on the implementations that were previously provided by StatUtils.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140968 13f79535-47bb-0310-9956-ffa450edef68

9eed265da3a878d6375c6702d4cd1179c4f1194b
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0d458038258c271d6b7462757850a0bc45ac5cbd
1057475888
Mark R. Diggory
Rolling Back StatUtils to previous version.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140967 13f79535-47bb-0310-9956-ffa450edef68

0d458038258c271d6b7462757850a0bc45ac5cbd
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f4f3c220659ac8fa298e9f9f9cf1059b65cd88c7
1057462067
Mark R. Diggory
Fixes Compilation error that did not get commited last time.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140966 13f79535-47bb-0310-9956-ffa450edef68

f4f3c220659ac8fa298e9f9f9cf1059b65cd88c7
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f75a00eb679d7da39b75a1e055d38379aadee2a0
1057433138
Mark R. Diggory
Correcting checkstyle and javadoc errors.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140965 13f79535-47bb-0310-9956-ffa450edef68

f75a00eb679d7da39b75a1e055d38379aadee2a0
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be6420472edb8444332662f237cbac040628c7af
1057433058
Mark R. Diggory
Rotating Commons Collections version to SNAPSHOT to get latest primitive collections implementations.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140964 13f79535-47bb-0310-9956-ffa450edef68

be6420472edb8444332662f237cbac040628c7af
:100644 100644 b540b1887592dc0747fcf79cd9d03fa49f8ee25d d7b9bc2d0787a7d8514f47fb9f66cef39b3cda4e M	build.xml
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37ffdce101da66308d5201b24fc8ed9a77873310
1057429775
Mark R. Diggory
This is an Implementation of StatUtils that uses the new UnivariateStatistic Framework and passes all JUnit StatUtils tests.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140963 13f79535-47bb-0310-9956-ffa450edef68

37ffdce101da66308d5201b24fc8ed9a77873310
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01f0a64cbee379189d9f6b3ea712b30beaf3240d
1057429490
Mark R. Diggory
Initial Tests for UnivariateStatistic package Hierarchy.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140962 13f79535-47bb-0310-9956-ffa450edef68

01f0a64cbee379189d9f6b3ea712b30beaf3240d
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d1bb06a472cd1fc7d1ba9d67f0baca73ff20789e
1057429432
Mark R. Diggory
This commit adds the individual UnivariateStatistic package hierarchy, this hierarchy
is currently independent of the Univariate and StoreUnivariate Implementations and provides
storeless and storage based mechanisms for working with the individual
UnivariateStatistic implementations.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140961 13f79535-47bb-0310-9956-ffa450edef68

d1bb06a472cd1fc7d1ba9d67f0baca73ff20789e
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671d5c1d5ecaac8943e16a7e9ba08c710a4d9ef3
1057429202
Mark R. Diggory
This patch exposes the start index, internal double array of DOubleArray Implementations.

It adds a NumberTransformer framework for mapping Objects and Bean Properties to double primitives
It also corrects some checkstyle and javadoc errors.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140960 13f79535-47bb-0310-9956-ffa450edef68

671d5c1d5ecaac8943e16a7e9ba08c710a4d9ef3
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1c6e9c124df3432605bbda8a5b5e1de81d57ad6a
1057428815
Mark R. Diggory
This patch exposes the start index, internal double array of DOubleArray Implementations.

It adds a NumberTransformer framework for mapping Objects and Bean Properties to double primitives
It also corrects some checkstyle and javadoc errors.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140959 13f79535-47bb-0310-9956-ffa450edef68

1c6e9c124df3432605bbda8a5b5e1de81d57ad6a
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2a02f635e9fafbc59f755bd0a434639f2a184ab6
1057428331
Mark R. Diggory
PR: http://nagoya.apache.org/bugzilla/show_bug.cgi?id=21313
Submitted by:	brent@worden.org


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140958 13f79535-47bb-0310-9956-ffa450edef68

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28c785435a37f540663a67ad082a9674ab0816f2
1057427897
Mark R. Diggory
PR: http://nagoya.apache.org/bugzilla/show_bug.cgi?id=21295
Submitted by:	brent@worden.org


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140957 13f79535-47bb-0310-9956-ffa450edef68

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c33306f4bc5a4dd0321d4f8581570c2bf1277415
1057424353
Mark R. Diggory
PR: http://nagoya.apache.org/bugzilla/show_bug.cgi?id=21277
Submitted by:	phil@steitz.com


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140956 13f79535-47bb-0310-9956-ffa450edef68

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eb8a3fa490e8c0a05276771f7e58b445f6af3259
1056747508
Mark R. Diggory
Removal of statistical (min/max) and deleteFrontElements methods from DoubleArray interface (per our previous discussion)

Adjusted dependent Test and StoreUnivariateImpl classes accordingly to accomidate changes.

Added new constructor to FixedDoubleArray for double[].


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140955 13f79535-47bb-0310-9956-ffa450edef68

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85e3b01b74cba2f79d179e565da0a957c7b9c0b6
1056745912
Mark R. Diggory
Eliminated extra pass to calc mean in std calculation.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140954 13f79535-47bb-0310-9956-ffa450edef68

85e3b01b74cba2f79d179e565da0a957c7b9c0b6
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4758c33a901faf0cd67fa013245468d9464b7f32
1056689993
Mark R. Diggory
moving test solvers to test directory


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140953 13f79535-47bb-0310-9956-ffa450edef68

4758c33a901faf0cd67fa013245468d9464b7f32
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73eb9d352a71981371fa78907bacdccbd77d017d
1056689967
Mark R. Diggory
These only need to be in tests


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140952 13f79535-47bb-0310-9956-ffa450edef68

73eb9d352a71981371fa78907bacdccbd77d017d
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a027cc9f26c2dc6daa8a997e00de1dd16eb6c56c
1056688182
Mark R. Diggory
Exceptions handling for math packages


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140951 13f79535-47bb-0310-9956-ffa450edef68

a027cc9f26c2dc6daa8a997e00de1dd16eb6c56c
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d2a0c1a9b674fcb46d3fd17560bf6bcf46adf6eb
1056547885
Mark R. Diggory
PR: http://nagoya.apache.org/bugzilla/show_bug.cgi?id=21015
Submitted by:	phil@steitz.com


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140950 13f79535-47bb-0310-9956-ffa450edef68

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b2ddd1d660875c28930302763be54ce02a6a9667
1056505176
Mark R. Diggory
PR: http://nagoya.apache.org/bugzilla/show_bug.cgi?id=21005
Submitted by:	phil@steitz.com


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140949 13f79535-47bb-0310-9956-ffa450edef68

b2ddd1d660875c28930302763be54ce02a6a9667
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1670ee0eba24b007b9640a6161d443afb8a10a60
1056504946
Mark R. Diggory
PR: http://nagoya.apache.org/bugzilla/show_bug.cgi?id=21003
Submitted by:	phil@steitz.com


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140948 13f79535-47bb-0310-9956-ffa450edef68

1670ee0eba24b007b9640a6161d443afb8a10a60
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ca5ce6e4550fe1c3fba2c1cc59d691db798a8c00
1056504558
Mark R. Diggory
PR: http://nagoya.apache.org/bugzilla/show_bug.cgi?id=21023
Submitted by:	j3322ptm@yahoo.de HotFusionMan@Yahoo.com


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140947 13f79535-47bb-0310-9956-ffa450edef68

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8ae9b5c2596144542cb4bc02803b1670c0c14722
1056463720
Mark R. Diggory
Added Checks for Exceptions


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140946 13f79535-47bb-0310-9956-ffa450edef68

8ae9b5c2596144542cb4bc02803b1670c0c14722
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2dd0a2b7f34e5d53c1bd0c098f509e3c18cbf27b
1056463412
Mark R. Diggory
Additon of begin and length controls to StatUtils. Addition on test for array conditions.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140945 13f79535-47bb-0310-9956-ffa450edef68

2dd0a2b7f34e5d53c1bd0c098f509e3c18cbf27b
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bcbf7e66b7b20dcc9471f7977f190b5ab4d47e73
1056423748
Mark R. Diggory
This is the second half of this pr. Commit of analysis solver tests.
PR: http://nagoya.apache.org/bugzilla/show_bug.cgi?id=20844
Submitted by:	J. Pietschman


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140944 13f79535-47bb-0310-9956-ffa450edef68

bcbf7e66b7b20dcc9471f7977f190b5ab4d47e73
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a222e19260b3b93f6a7b1e70f96e03f5fe445ec3
1056423700
Mark R. Diggory
This is the first half of this pr. Commit of analysis solvers.
PR: http://nagoya.apache.org/bugzilla/show_bug.cgi?id=20844
Submitted by:	J. Pietschman


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140943 13f79535-47bb-0310-9956-ffa450edef68

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dcede03d186e12e017469b1ea43e505a268d0184
1056254277
Mark R. Diggory
Initial commit of package refactorings discussed in the group.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140942 13f79535-47bb-0310-9956-ffa450edef68

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a6637ae432f9a7cf0fa5b6d7500eaa1c59878e03
1056238707
Mark R. Diggory
Removing Product from Univariate Interface, applying sumLog changes to geomean in AbstractStoreUnivariate.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140941 13f79535-47bb-0310-9956-ffa450edef68

a6637ae432f9a7cf0fa5b6d7500eaa1c59878e03
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03d9eb52414e63f7cbbc6188d76af04dd3d79c1a
1056236843
Mark R. Diggory
moving TestStatistic to stat package.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140940 13f79535-47bb-0310-9956-ffa450edef68

03d9eb52414e63f7cbbc6188d76af04dd3d79c1a
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772b61f141b8d26c103e328f1df771e0412b367f
1056236571
Mark R. Diggory
Moving TestStatisticTest to stat package.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140939 13f79535-47bb-0310-9956-ffa450edef68

772b61f141b8d26c103e328f1df771e0412b367f
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e59807bc3edf8a679fa6d25cb921a2de659bd69d
1056236439
Mark R. Diggory
Moving TestStatistic implementation / interface into stat package.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140938 13f79535-47bb-0310-9956-ffa450edef68

e59807bc3edf8a679fa6d25cb921a2de659bd69d
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619b6874f0bc50a8fa72631dca65e14b7c32e46b
1056164095
Mark R. Diggory
Removed last of the Math.pow's


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140937 13f79535-47bb-0310-9956-ffa450edef68

619b6874f0bc50a8fa72631dca65e14b7c32e46b
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35275845f7d64563a17a7b1e831821059c6d68af
1056162109
Mark R. Diggory
This is a multifile commit, it covers checkstyle errors in javadoc etc.
PR: http://nagoya.apache.org/bugzilla/show_bug.cgi?id=20936
Submitted by:	brent@worden.org


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140936 13f79535-47bb-0310-9956-ffa450edef68

35275845f7d64563a17a7b1e831821059c6d68af
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b6cf1781176295087b67a79684f4e4429f1fae7a
1056161803
Mark R. Diggory
PR: http://nagoya.apache.org/bugzilla/show_bug.cgi?id=20980
Submitted by:	phil@steitz.com


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140935 13f79535-47bb-0310-9956-ffa450edef68

b6cf1781176295087b67a79684f4e4429f1fae7a
:100644 100644 2377b416c9fe277663d242ac1254429fb63b2b39 e20114bde3d87a552d917a4f1dc0729a91f34563 M	src/java/org/apache/commons/math/stat/AbstractStoreUnivariate.java

2b57d6595c2c9095dc09bd42ba40fe1c69df0735
1056161621
Mark R. Diggory
PR: http://nagoya.apache.org/bugzilla/show_bug.cgi?id=20979
Submitted by:	phil@steitz.com


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140934 13f79535-47bb-0310-9956-ffa450edef68

2b57d6595c2c9095dc09bd42ba40fe1c69df0735
:100644 100644 6197018002f1447e5c1ff55825ad9dab4bbebb12 865cff5a4c0ece98bd7e5cb951ec18310b2de8a4 M	src/java/org/apache/commons/math/stat/BivariateRegression.java
:100644 100644 b31bda655975eeb7c4ba8aa8436a1e136d4778ff 5e448114662358b7d66e280d8aee91c27032228b M	src/test/org/apache/commons/math/stat/BivariateRegressionTest.java

edbc57991142918547aa64e921408d1883cd670c
1056161303
Mark R. Diggory
Adding tests for kurtosis and skew to UnivariateImpl testcase. Correcting initialization of moments in UnivariateImpl.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140933 13f79535-47bb-0310-9956-ffa450edef68

edbc57991142918547aa64e921408d1883cd670c
:100644 100644 f099be140d3c8d959d5cb1843c13537cea6eb257 cfe4e60d5bc117732d4c7c88294925285ab5761a M	src/java/org/apache/commons/math/stat/UnivariateImpl.java
:100644 100644 b62a5a34af2aec6e6aba63363ad58086d590775c 4a71595183a609189c4038b3b2d448f4393fa856 M	src/test/org/apache/commons/math/stat/UnivariateImplTest.java

008db7522d3097ac6fafbaec8b9e2340c0948e15
1056160517
Mark R. Diggory
Removing mode.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140932 13f79535-47bb-0310-9956-ffa450edef68

008db7522d3097ac6fafbaec8b9e2340c0948e15
:100644 100644 58b8698d2b1f61ead28cd3ea2ceed9620e8a1df2 389cf0708c2dd4b587edb3c3ce3538de387aca27 M	src/java/org/apache/commons/math/stat/StoreUnivariate.java

7e1789e0e9a17959d128e074773e7729e4a55c02
1056143147
Mark R. Diggory
PR: http://nagoya.apache.org/bugzilla/show_bug.cgi?id=20964
Submitted by:	phil@steitz.com


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140931 13f79535-47bb-0310-9956-ffa450edef68

7e1789e0e9a17959d128e074773e7729e4a55c02
:100644 100644 c5f7e8734003032ceb540b82b2c77dff4ea36d6f 2377b416c9fe277663d242ac1254429fb63b2b39 M	src/java/org/apache/commons/math/stat/AbstractStoreUnivariate.java
:100644 100644 6bd50a3dbc466cb1685d9a3277945292692cc4c3 d34535af391e93c48b23dcc3c98460e31ce3585a M	src/java/org/apache/commons/math/stat/StatUtils.java

792b7349ce9122d61ef49571a449b1de2567ca0e
1055971503
Timothy O'Brien
Removed the proposed solvers, many compilation problems and a broken unit test.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140930 13f79535-47bb-0310-9956-ffa450edef68

792b7349ce9122d61ef49571a449b1de2567ca0e
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:100644 000000 23fb0a723e6157e58aa943f1359a9294648a8efb 0000000000000000000000000000000000000000 D	src/java/org/apache/commons/math/UnivariateRealFunction.java
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4713f7f1d8a3d2a6a91dc57bb237e8e92b5a1429
1055966979
Timothy O'Brien
Why not? Readded the statcvs report....


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140929 13f79535-47bb-0310-9956-ffa450edef68

4713f7f1d8a3d2a6a91dc57bb237e8e92b5a1429
:100644 100644 abc8c3aae8bc2b0cd962cfb86401cf0789020155 4e6a07185fd0c524ad93e065f73691d64dba93eb M	project.xml

30f5dda2b821cec8f065c7c4f7236bcd021a0a67
1055966808
Timothy O'Brien
Readded some activity reports to the maven site, now that we have more activity some of these reports make more sense


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140928 13f79535-47bb-0310-9956-ffa450edef68

30f5dda2b821cec8f065c7c4f7236bcd021a0a67
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ef7a59e739b91907fe70543504b21812ee759bfc
1055966547
Timothy O'Brien
1. Gamma.logGamma was expecting epsilon and maxIterations but these parameters
were not being referenced in that function.  These parameters has been removed.

2. Also, the Lanczos coefficients are now a private static member variable of
the Gamma class.


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45d406f1e0c794dd223bc53af096b6a454040975
1055951995
Mark R. Diggory
Initial Deposit for StatUtils unit testing, this was derived from StoreUnivariateImplTest.


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1055944644
Mark R. Diggory
Last commit got formated with tabs, this is formated with spaces


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8e3d2c7383a7f98c9e7d553ea12e5c1eb190b70f
1055944055
Mark R. Diggory
Degegates to StatUtils now for "window" case. Implemented skew and kurt using recursive moments.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140924 13f79535-47bb-0310-9956-ffa450edef68

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1055940144
Mark R. Diggory
Rolling back to previous version.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140923 13f79535-47bb-0310-9956-ffa450edef68

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c67cee2fad477f7b6bc67fe6ecdd27613cb193ad
1055905545
Mark R. Diggory
Simplified calculation, removing extra division.


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eb7bc0170eb129f6225dcb6ef696f530a5d8b23c
1055905288
Mark R. Diggory
Adding corrected two-pass algorithm for variance calculation.


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82074a733ad19a6e8c3ea15b9556a46d9c597b33
1055901363
Mark R. Diggory
Addition of sumLog method (natural) to get the sum of the Logs. Altered GeometricMean to calculate the geometricMean from the sum of logs.


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0b27a8a40440849bf48f9f2464291a075c46a230
1055892187
Mark R. Diggory
Addition of product and geometericMean.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140919 13f79535-47bb-0310-9956-ffa450edef68

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ead8450fb71c098abc44552d963553c80bb6d711
1055890817
Mark R. Diggory
Missed two static signatures in the methods


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814629453f583055f6540fba3599e8620dfca4a2
1055890538
Mark R. Diggory
Initial Addition of StatUtils. Some methods need review, implementation and possibly debugging


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3b18c97188957a5c777e68e86b360526fa0d73f5
1055884568
Timothy O'Brien
alternative root finding framework, and Brent-Drekker solver

Issue: 20844
Submitted by: J. Pietschmann
Reviewed by: T. O'Brien


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5eb62fddf202d0c54bdde3e4b4a2a354fba05126
1055869815
Mark R. Diggory
Rolling back to version 1.5 to provide for group discussion on the subject


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140915 13f79535-47bb-0310-9956-ffa450edef68

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89f4c18e5974e11a1972ef545eb417f48646ef55
1055799495
Mark R. Diggory
I'm not sure with this algorithm, but I'm going to add this test back into the Variance that protects it from returning a value less than 0.


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1055798989
Mark R. Diggory
More correction of Javadoc errors.


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1055798670
Mark R. Diggory
More correction of Javadoc errors that end up propigating into UnivarImpl and other implementations.


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1055797133
Mark R. Diggory
Correction of Javadoc errors that end up propigating into UnivarImpl and other implementations.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140911 13f79535-47bb-0310-9956-ffa450edef68

95360af5165f5bb04038d92c7d3c3c49f53f2790
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89adf90e262e8867b76cc1b2ede7d1a69d1592bc
1055796144
Mark R. Diggory
This house-cleaning improves UnivariateImpl, in a number of ways.

1.) insertValue is abolished and its contents are now in addValue

2.) UnivariateImpl now extends AbstractStoredUnivariate to deligate to
 those methods directly for calculating statistics when storage is active, all methods
 deligate to AbstractStoreUniv when the DoubleArray is no longer null. This also means
that a majority of the StoreUnivariate interface is now implemented in Univariate to provide
deligates when storage is active, and to throw runtime exceptions when its not (this at least until 
we establish rolling implementations for those methods). We should consider consolidating the 
StoreUnivariate interface into the Univariate interface

3.) Calculations in addValue have been reorganized, only calculations for
the storageless solution are now present in this class. otherwise the value is 
added/Rolling to the Double array when appropriate.

I'm satisfied that it passes all Unit tests.


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9a179ff85bd1636f5bf0e9cb5acdc2060db333e3
1055794423
Timothy O'Brien
Added the graceful handling of invalid and NaN domain values.  Created test
cases to verify the graceful handling.

Issue #: 20774
Submitted By: Brent Worden
Reviewed By: Tim O'Brien


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9d1be9a1013a799940ed80eb7a78f1a79f12e54c
1055773770
Mark R. Diggory
PR: http://nagoya.apache.org/bugzilla/show_bug.cgi?id=20782
Submitted by:	HotFusionMan@Yahoo.com

I added this, but there are changes I'd like to make in the near future. Only the "running" aspects of the variance calc should be in the insertValue function, all other calculation should be in the getVariance function.


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1055696499
Mark R. Diggory
PR: http://nagoya.apache.org/bugzilla/show_bug.cgi?id=20783
Submitted by:	phil@steitz.com


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200ab0ec4adeeea15f6b641d56170989cf16cb58
1055564683
Mark R. Diggory
PR: http://nagoya.apache.org/bugzilla/show_bug.cgi?id=20773
Submitted by:	brent@worden.org


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df6556b793418928d170aae42741b9f56e3ccd68
1055564269
Mark R. Diggory
PR: http://nagoya.apache.org/bugzilla/show_bug.cgi?id=20766
Submitted by:	brent@worden.org


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d3d83ada307b891273865a91b5f52da66dffd620
1055511438
Mark R. Diggory
I am removing this file because the build.xml file is now generated by Maven and periodically updated when the project.xml file is updated. This file was used with the old build.xml file prior to our use of Maven to generate the build.xml.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140904 13f79535-47bb-0310-9956-ffa450edef68

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82791fcd676c96011f2387fbc14cbaf7a26658a9
1055510561
Mark R. Diggory
PR: http://nagoya.apache.org/bugzilla/show_bug.cgi?id=20633
Submitted by:	brent@worden.org


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0b1b9a9dc86da871ce5e7839b1b2df13c99dd9f8
1055343030
Timothy O'Brien
Submitted Javadoc fixes from Andreou Andreas


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1055330081
Mark R. Diggory
PR: http://nagoya.apache.org/bugzilla/show_bug.cgi?id=20627
Submitted by:	brent@worden.org


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c18e59702f96f5cbe879e6375ba9f50726c20bb5
1055302385
Timothy O'Brien
* Fixed all checkstyle errors and eliminated redundant NaN checks.  Now have
100% test path coverage.

* Used distribution framework TDistribution to implement
getSlopeConfidenceInterval and getSignificance methods.

PR: Issue #20657
Obtained from: Bugzilla
Submitted by: Phil Steitz
Reviewed by: Tim O'Brien


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1055294359
Mark R. Diggory
PR: http://nagoya.apache.org/bugzilla/show_bug.cgi?id=20601
Submitted by:	brent@worden.org


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1054994274
Mark R. Diggory
PR: http://nagoya.apache.org/bugzilla/show_bug.cgi?id=20570
Submitted by:	brent@worden.org


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1054949817
Mark R. Diggory
PR: http://nagoya.apache.org/bugzilla/show_bug.cgi?id=20543
Submitted by:	phil@steitz.com


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ffaa0f35436b008ebfbe8edae1b8655b9e1c145f
1054870683
Mark R. Diggory
Resolved some href " issues in Javadoc.


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1054868859
Mark R. Diggory
PR: http://nagoya.apache.org/bugzilla/show_bug.cgi?id=20496
Submitted by:	Albert Davidson Chou


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1054838124
Mark R. Diggory
PR: http://nagoya.apache.org/bugzilla/show_bug.cgi?id=20514
Submitted by:	brent@worden.org


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71a032b1f8dbf1e772932854317cccd6a4f29400
1054822243
Mark R. Diggory
PR: http://nagoya.apache.org/bugzilla/show_bug.cgi?id=20507
Submitted by:	Phil Steitz


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140893 13f79535-47bb-0310-9956-ffa450edef68

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1054821833
Mark R. Diggory
PR: http://nagoya.apache.org/bugzilla/show_bug.cgi?id=20488
Submitted by:	Brent Worden

Initial submission of the distribution library


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80e42b33c52fe0ce94a9be00d31989e269ff15ea
1054783461
Mark R. Diggory
Adding Al as a contributor


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0346c5f06a6f9abc6c787983b9167f7134258d04
1054730894
Mark R. Diggory
just changing my email address...


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98f8ce531382da0f79edcdbdbff36d7a61e3e9e3
1054730594
Mark R. Diggory
typo in the ${basedir} variable.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140889 13f79535-47bb-0310-9956-ffa450edef68

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905febc1b00b333b90acdd3df61e96856330711c
1054729424
Mark R. Diggory
fixed href link to have ""'s


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b7b2adee87f8b546275ba653abbc65671dccd76c
1054699539
Mark R. Diggory
Improved Variance calculation, test for negative variance and added some more javadoc.


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1054699435
Mark R. Diggory
Adjusted the code to be able to control the files used and the tolerance for each file (important, hard tests currently require lower tolerance to pass).


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290af7e332cae0d450b54130127345df2cc32b0a
1054694749
Mark R. Diggory
PR: http://nagoya.apache.org/bugzilla/show_bug.cgi?id=20442
Submitted by:	Phil Steitz


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1054694426
Mark R. Diggory
PR: http://nagoya.apache.org/bugzilla/show_bug.cgi?id=20404
Submitted by:	Phil Steitz


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1054693874
Mark R. Diggory
PR: http://nagoya.apache.org/bugzilla/show_bug.cgi?id=20390
Submitted by:	Phil Steitz


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1054693491
Mark R. Diggory
PR: http://nagoya.apache.org/bugzilla/show_bug.cgi?id=20377
Submitted by:	Phil Steitz


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1054693037
Mark R. Diggory
PR: http://nagoya.apache.org/bugzilla/show_bug.cgi?id=20375
Submitted by:	Albert Davidson Chou


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7ea04dbcd754844c9aa6ff43de1b589eef068a81
1054531266
Mark R. Diggory
Changing the name of data files, the default javac target in the ant file misses files of the extension "dat"


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140880 13f79535-47bb-0310-9956-ffa450edef68

7ea04dbcd754844c9aa6ff43de1b589eef068a81
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768b12187cb9423c0eee3b8d15fbd71682755e0b
1054529913
Mark R. Diggory
Commenting out testUnivariateImpl unitl I figure out why this fails in UnivariateImpl


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140879 13f79535-47bb-0310-9956-ffa450edef68

768b12187cb9423c0eee3b8d15fbd71682755e0b
:100644 100644 60f0c8d156f10e23051701f26a775a7de1503386 2148c3ab52c80890089422f6893ab5707ffcae62 M	src/test/org/apache/commons/math/stat/CertifiedDataTest.java

05de8c3e425adff8b9bf55268868021d37369fb4
1054529301
Mark R. Diggory
project.xml had two dependencies sections, I removed the empty one.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140878 13f79535-47bb-0310-9956-ffa450edef68

05de8c3e425adff8b9bf55268868021d37369fb4
:100644 100644 89254eeb694be999762f16cba741a09e3cca3c86 992c0985ed674efa30ca90aae504565d77b13707 M	project.xml

e67b032a0d4a8a4dfd0ccb48e5f8f85396238f9f
1054528046
Mark R. Diggory
Removed System.out's


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140877 13f79535-47bb-0310-9956-ffa450edef68

e67b032a0d4a8a4dfd0ccb48e5f8f85396238f9f
:100644 100644 aced88212b0e052e481869bfa39b3abe103cb634 60f0c8d156f10e23051701f26a775a7de1503386 M	src/test/org/apache/commons/math/stat/CertifiedDataTest.java

423d4ac4d1b4fdc4c58de6198e2e688135f6fbde
1054527952
Mark R. Diggory
Initial Certified Tests for Univariate. Note UnivariateImpl currently fails


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140876 13f79535-47bb-0310-9956-ffa450edef68

423d4ac4d1b4fdc4c58de6198e2e688135f6fbde
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8075f3b25808cb72d55414e65c1766206e23ce70
1054525453
Timothy O'Brien
Licensing issues have prompted the removal of all source reliant on
Gamma.java.  Gamma.java explicitly stated that it was "based on" an
implementation from Numerical Recipes in C.  Please see
http://www.nr.com/infotop.html - these implementations (and derivatives
of these works) are covered under restrictive licensing terms.  This
code will be removed from the repository until these issues can be
addressed.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140875 13f79535-47bb-0310-9956-ffa450edef68

8075f3b25808cb72d55414e65c1766206e23ce70
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:100644 000000 8d40b16dbfaf2330dec04d95897c3c873cd8228e 0000000000000000000000000000000000000000 D	src/java/org/apache/commons/math/distribution/DistributionFactory.java
:100644 000000 c265205eed0307866cc0cfe3ac84646d5514d481 0000000000000000000000000000000000000000 D	src/java/org/apache/commons/math/distribution/DistributionFactoryImpl.java
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1cd797464f5f042dd10894b147dbf5671425c83e
1054521243
Mark R. Diggory
This is the new build.xml file generated by Maven. This was generated using the latest checkout of Maven.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140874 13f79535-47bb-0310-9956-ffa450edef68

1cd797464f5f042dd10894b147dbf5671425c83e
:100644 100644 47dc4e0bfbed10a85a6d154a8524a9b0d8d9e3d5 b540b1887592dc0747fcf79cd9d03fa49f8ee25d M	build.xml

0a08e1e825ff9e871c5092f37b48683a285977d2
1054482220
Mark R. Diggory
Adding myself to the developers


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140873 13f79535-47bb-0310-9956-ffa450edef68

0a08e1e825ff9e871c5092f37b48683a285977d2
:100644 100644 845eb2749a4072b3547feb063d84113a1ee90cfa 89254eeb694be999762f16cba741a09e3cca3c86 M	project.xml

5ac170d0273fdb6a840d53c4e8214503524a1c6c
1054309228
Timothy O'Brien
* add the numerical analysis and prob/stat references that have been posted or
  included in javadoc recently, plus a few more generic references.
* update the task list based on accomplishments and discussion

PR: Issue 20357
Obtained from: Bugzilla
Submitted by: Phil Steitz
Reviewed by: Tim O'Brien


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140872 13f79535-47bb-0310-9956-ffa450edef68

5ac170d0273fdb6a840d53c4e8214503524a1c6c
:100644 100644 cd2a237636bfbeaa3f0bbb7d642e2ccbf7623a21 845eb2749a4072b3547feb063d84113a1ee90cfa M	project.xml
:100644 100644 af3119c58f62e4e706b435b10429b6a0b572cca7 e0ff15558ce9dbd948a96bbcc6ec33df3fe869b1 M	xdocs/developers.xml
:100644 100644 8312576708bfbbae239b3c975c899de412109ff8 becd8b98027680d0e67434cb352ad75fd5c41ff6 M	xdocs/tasks.xml

9711fe60bec4fc2b6a0ee17a764f5a6d2c59ae6f
1054251048
Timothy O'Brien
Removed tasklist report, until this has content, no reason for the added distraction


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140871 13f79535-47bb-0310-9956-ffa450edef68

9711fe60bec4fc2b6a0ee17a764f5a6d2c59ae6f
:100644 100644 b0c44db6701c1e5ba9e357528431743a09d39d94 cd2a237636bfbeaa3f0bbb7d642e2ccbf7623a21 M	project.xml

b6261a198b58742cd5c6511c5a3dc8e5f99a6ffa
1054250784
Timothy O'Brien
linkcheck report was throwing 404s for every URL, I've removed it until someone can generate a meaningful report


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140870 13f79535-47bb-0310-9956-ffa450edef68

b6261a198b58742cd5c6511c5a3dc8e5f99a6ffa
:100644 100644 3da2adfdce062d21e334b14617683ba4c53b91b1 62aa35a832499ac2078e06834ee8ee8bb34f0d8e M	project.properties
:100644 100644 9eeb99cb4818a36d2b309498c0e8fea504c88422 b0c44db6701c1e5ba9e357528431743a09d39d94 M	project.xml

09e576a78d1a7e8b83c872769fddb83d907e4c7e
1054250712
Timothy O'Brien
Removed old Univariate tests


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140869 13f79535-47bb-0310-9956-ffa450edef68

09e576a78d1a7e8b83c872769fddb83d907e4c7e
:100644 000000 3d38c3665c71fc779c30e9c63144bd1ee1ec6d82 0000000000000000000000000000000000000000 D	src/test/org/apache/commons/math/BeanListUnivariateImplTest.java
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1bf873eabf8f6683d018b99c0ec48db7f0e0912d
1054250700
Timothy O'Brien
Checkstyle should check that each source file include a license


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140868 13f79535-47bb-0310-9956-ffa450edef68

1bf873eabf8f6683d018b99c0ec48db7f0e0912d
:100644 100644 20e58dd44648b7b98d389289a4c3b5213df836c8 d2bfc59bc4f666b0aa7b576c700ed97b8521c9ca M	checkstyle.properties

fe69714916c8b0d9842c6f1ee07bef75aa64f5cd
1054240546
Timothy O'Brien
Moved all Univariate and Bivariate stats interfaces and classes to the math.stat package


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140867 13f79535-47bb-0310-9956-ffa450edef68

fe69714916c8b0d9842c6f1ee07bef75aa64f5cd
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d79f686403d6779e30635649c15f5646423c2b2d
1054237758
Timothy O'Brien
Patch adds getSkewness and getKurtosis to Univariate and an implimentation
in UnivariateImpl. It also adds test for NaN and 0.0 to UnivariateImplTest

PR: Issue 20250
Obtained from: Bugzilla
Submitted by: Mark Diggory
Reviewed by: Tim O'Brien


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140866 13f79535-47bb-0310-9956-ffa450edef68

d79f686403d6779e30635649c15f5646423c2b2d
:100644 100644 0431518af7ee48caac5293318ced5e5108f71a0d 0dae4210e027915c2cfe455f3438b4e6a65ee598 M	src/java/org/apache/commons/math/Univariate.java
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:100644 100644 191185f7c50d28ce416b83dbd4385bacbfe68562 d0a8884e593ee7772467d77dec133a74c8bb6a56 M	src/test/org/apache/commons/math/UnivariateImplTest.java

c0f9beb4b02f2dcc7ca9276d8824bb482cb6dede
1054237535
Timothy O'Brien
Adds the following two capabilities to RandomData: Generating random permutations
of integers, Generating random samples (returned as Object arrays) from Collections.
Tests validate expected sample distribtution using chi-square tests

PR: Issue 20303
Obtained from: Bugzilla
Submitted by: Phil Steitz
Reviewed by: Tim O'Brien


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140865 13f79535-47bb-0310-9956-ffa450edef68

c0f9beb4b02f2dcc7ca9276d8824bb482cb6dede
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:100644 100644 2692dec096f19c5a93152cfb37d7c776bc65880c 6796517c3ad96056c50f0b8d93ac177a19bad2b9 M	src/test/org/apache/commons/math/RandomDataTest.java

98b247ad029f225ba893d3a4b193d2185e8def66
1054237312
Timothy O'Brien
Added an LICENSE.txt in commons-math


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140864 13f79535-47bb-0310-9956-ffa450edef68

98b247ad029f225ba893d3a4b193d2185e8def66
:000000 100644 0000000000000000000000000000000000000000 202d60b26bdedf2873563738cd10eee34646afe7 A	LICENSE.txt

bdd3debba8dd297a70f10e053c1a1960f415a4d2
1054237292
Timothy O'Brien
Addition of a BeanListUnivariateImpl which can gather univariate statistics on a
List of JavaBeans.  This implementation extends the ListUnivariateImpl, and uses the
PropertyUtils classes from commons-beanutils.  With this implementation, the following
is possible:

List persons = new ArrayList();
// populate array with 100 persons
Univariate ageU = new BeanListUnivariateImpl( persons, "age" );
Univariate incomeU = new BeanListUnivariateImpl( persons, "jobInfo.income" );
System.out.println( "Mean age is: " + ageU.getMean() );
System.out.println( "Mean income is: " + incomeU.getMean() );

Better error handling is needed near our use of PropertyUtils.

This patch introduces a dependency on commons-beanutils, which in turn depends
on commons-collections and commons-logging.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140863 13f79535-47bb-0310-9956-ffa450edef68

bdd3debba8dd297a70f10e053c1a1960f415a4d2
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3933151a2e3d3dd146fd9e14c5e8cb8a6adbb96b
1054236956
Timothy O'Brien
Unit tests for previous commit - from Brent Worden's submission in Bugzilla Issue 20279


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140862 13f79535-47bb-0310-9956-ffa450edef68

3933151a2e3d3dd146fd9e14c5e8cb8a6adbb96b
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339b99a8bc28f8032df22cd29750d218f3f321e7
1054236878
Timothy O'Brien
Contributions from Brent Worden - Bugzilla Issue 20279

* a distribution factory following the abstract factory pattern.
The value being, if users want to swap out the default distribution
implementations with their own, why stop them.  The factory is responsible for
create the distribution instances (only continuous ones for now).

* Each distribution has a cummulativeProbabilty method which returns the value of
the CDF for a given value.  By default, via the abstract distribution base
class, an inverseCummulativeProbability method is all provided for all
distributions.  It's implementation is generically handled by applying root
finding techniques to the cummulativeProbability method.  That way, when new
distributions are added, authors only need to create the CDF method and the
inverse is provided automatically.

* Currenty, the only distributions are Chi-Squared and Gamma (one actually since
Chi-Squared is a specialized Gamma) but more are planned.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140861 13f79535-47bb-0310-9956-ffa450edef68

339b99a8bc28f8032df22cd29750d218f3f321e7
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2782a2d0f5bea80bb0c58a7209df8d051348fcd5
1053970820
Timothy O'Brien
Fixed spelling of INFINITE_WINDOW.

PR: 20234
Submitted by: Al Chou


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140860 13f79535-47bb-0310-9956-ffa450edef68

2782a2d0f5bea80bb0c58a7209df8d051348fcd5
:100644 100644 9d101c778b1dea796211626702c25b074516e884 13acdb74e39b630cd56bf0f4f4e6bc951a438000 M	src/java/org/apache/commons/math/ListUnivariateImpl.java
:100644 100644 21a60e74bc05bdb64097567f3abf6cfbb15a32e0 49a5878a1c1475663fadcdf27d8beed2994db3d8 M	src/java/org/apache/commons/math/StoreUnivariateImpl.java
:100644 100644 76107d8fedee381222e38afb0366051831b0026a 0431518af7ee48caac5293318ced5e5108f71a0d M	src/java/org/apache/commons/math/Univariate.java
:100644 100644 d3402fd590fdedac1e52577d2bc3ad7ec23c7fc0 ac90a0c8cfac95313368ba4c3c55df4dc46736e9 M	src/java/org/apache/commons/math/UnivariateImpl.java

9c3353db4b98821cdab70821a3aa648d5e2a2cbb
1053970176
Timothy O'Brien
Adds the one sample, t-test statistic to TestStatistic and implementations.
Also add unit tests. - BW

PR: Issue #20231
Obtained from: Bugzilla
Submitted by: Brent Worden
Reviewed by: Tim O'Brien


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140859 13f79535-47bb-0310-9956-ffa450edef68

9c3353db4b98821cdab70821a3aa648d5e2a2cbb
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:100644 100644 65ff0765dd45c2cdb21898b03a2316d2913b0833 10970bd42f4db0b890c78fb9da0f80e2ccfbc159 M	src/test/org/apache/commons/math/TestStatisticTest.java

4ce4db7bdfc7ef81c9af96acedf987ef90600031
1053915110
Timothy O'Brien
An implementation of ordinary least squares regression with one independent
variable. The implementation uses running sums and does not require the data
to be stored in memory.  Since I could not conceive of any significantly
different implementation strategies that did not amount to just improving
efficiency or numerical accuracy of what I am submitting, I did not abstract
the interface.

The test cases validate the computations against NIST reference data and
verified computations. The slope, intercept, their standard errors and
r-square estimates are accurate to within 10E-12 against the reference data
set.  MSE and other ANOVA stats are good at least to within 10E-8. -- Phil S.

PR: Issue #20224
Obtained from: Bugzilla
Submitted by: Phil Steitz
Reviewed by: Tim O'Brien


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140858 13f79535-47bb-0310-9956-ffa450edef68

4ce4db7bdfc7ef81c9af96acedf987ef90600031
:000000 100644 0000000000000000000000000000000000000000 5ceb1b9c676802c38a20dfd597804012d27c18bf A	src/java/org/apache/commons/math/BivariateRegression.java
:000000 100644 0000000000000000000000000000000000000000 4d6d37faf38ed30e46f8140a25b6516ea25ccc04 A	src/test/org/apache/commons/math/BivariateRegressionTest.java

c5b978ce23cde57e215327b391e0cc94a6714a06
1053711198
Timothy O'Brien
From Phil Steitz patch submission for Issue #20175

The attached patch includes the following improvements to Univariate and
UnivariateImpl:

* Improved efficiency of min, max and product maintenance when windowSize is
  limited by incorporating suggestion posted to commons-dev by Brend Worden
  (added author credit).  Thanks, Brent!

* Added javadoc specifying NaN contracts for all statistics, definitions for
  geometric and arithmetic means.

* Made some slight modifications to UnivariateImpl to make it consistent with
  NaN contracts

* All interface documentation moved to Univariate. The interface specification
  includes the NaN semantics and a first attempt at clealy defining exactly
  what "rolling" means and how this effects what statistics are defined when.

* Added test cases to verify that min, max, product are correctly maintained
  when "rolling" and to verify that NaN contracts are satisfied.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140857 13f79535-47bb-0310-9956-ffa450edef68

c5b978ce23cde57e215327b391e0cc94a6714a06
:100644 100644 a1eee7b74ea6dd0c8d62ffd83e237f860f59009c bb4b9e056d90007195b69b8f24162b2637c3a40f M	project.xml
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32f700b74ab8bd04196c4951849e2e485c52f65c
1053707296
Timothy O'Brien
Readded the linkcheck and tasklist reports


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140856 13f79535-47bb-0310-9956-ffa450edef68

32f700b74ab8bd04196c4951849e2e485c52f65c
:100644 100644 f73d297fc55dbce785f0325d439e8e673ad8fce0 a1eee7b74ea6dd0c8d62ffd83e237f860f59009c M	project.xml

53dd60d86146dd40c4b3e291158ac09d3cc514a8
1053622522
Timothy O'Brien
Added mdiggory patch for developer resources


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140855 13f79535-47bb-0310-9956-ffa450edef68

53dd60d86146dd40c4b3e291158ac09d3cc514a8
:100644 100644 02d4018b64b465296ddd87a18fb0447146304de7 af3119c58f62e4e706b435b10429b6a0b572cca7 M	xdocs/developers.xml

0ca5e952c92699c98a7ad0380be7b3c197d3f55c
1053617498
Timothy O'Brien
RandomDataTest.testNextGaussian() was using Univarite.getN().  Added
an explicit cast from int to double.  Test now succeeds.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140854 13f79535-47bb-0310-9956-ffa450edef68

0ca5e952c92699c98a7ad0380be7b3c197d3f55c
:100644 100644 a4864741ebcb9cc550989f611ff778e7ea25307b 2692dec096f19c5a93152cfb37d7c776bc65880c M	src/test/org/apache/commons/math/RandomDataTest.java

eb833abd95ea3bdaaac8224cb985b4587742eec0
1053616772
Timothy O'Brien
The EmpiricalDistributionImpl that submitted yesterday assumed the "old"
Univariate interface, in which getN() returned a double.  The attached patch
inserts the necessary casts to avoid the rounding/truncation errors that were
causing the EmpiricalDistribution and ValueServer unit tests to fail.

The patch also adds a RandomData member variable so that getNext() does not
instantiate a new RandomData instance for each activation

PR: Bugzilla #20149
Obtained from: Issue Patch
Submitted by: Phil Steitz
Reviewed by: Tim O'Brien


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140853 13f79535-47bb-0310-9956-ffa450edef68

eb833abd95ea3bdaaac8224cb985b4587742eec0
:100644 100644 57d429afee3a22f31d6086b994536c117766f152 5a088b8e6d797350b71e421e4ddd629730f70383 M	src/java/org/apache/commons/math/EmpiricalDistributionImpl.java

4986461cb140eab887bb723436cff39ae25105f9
1053541486
Timothy O'Brien
Added task to bring javadoc into compliance with standard.  Javadoc
generate currently throws 35 errors.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140852 13f79535-47bb-0310-9956-ffa450edef68

4986461cb140eab887bb723436cff39ae25105f9
:100644 100644 5e646333eec29a680f55fc348e63ad13719a2a0d 8312576708bfbbae239b3c975c899de412109ff8 M	xdocs/tasks.xml

d275862aeb58c45429c55f8d444b7ffbc581a308
1053539960
Timothy O'Brien
Added Product and Mean to Univariate and all implementations, this patch
contains contributions from Mark Diggory.

* This patch introduces Product and GeometricMean into the Univariate
implementation.

* Discarding the contribution of a discarded element in a rolling
UnivariateImpl requires that the product be calculated explicitly each
time a value is discarded.  This is necessary because not all values will
have non-zero values.

* Errors in rolling logic for ListUimpl, and UnivariateImpl were corrected,
and more test cases were added to the JUnit tests for the Univariate
implementations.  More rigorous test cases are needed for the entire
suite of Univariate implementations


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140851 13f79535-47bb-0310-9956-ffa450edef68

d275862aeb58c45429c55f8d444b7ffbc581a308
:100644 100644 9d0bf57c1808e784a8f0a248ecb8271aa600f4cf 4ec611df15a0dd09e931a2d26a46a889376d3897 M	src/java/org/apache/commons/math/AbstractStoreUnivariate.java
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:100644 100644 a74ca79b639c9468cb5dc9c3ca1c747602248ed5 394f8bad29a3eda7667215ddeb35ccd269a23e01 M	src/test/org/apache/commons/math/StoreUnivariateImplTest.java
:100644 100644 4cae7f739bc68dc499d609a465e1bd5d16ca11e6 ef589ad0f17442e2b755505251b1951838e57c90 M	src/test/org/apache/commons/math/UnivariateImplTest.java
:100644 100644 046dfe3d73d348236c444508f8b5638c278206e7 c1d9d4a309f94567fc73bd64fd6e3d30c71c2866 M	src/test/org/apache/commons/math/ValueServerTest.java

43892e35b043abda0920ae18e57d6b1388bf1d68
1053529914
Timothy O'Brien
xdoc tasks.xml was updated to reflect tasks pertaining to the next planned
release.  There tasks were lifted from Phil S. earlier message to
commons-dev@


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140850 13f79535-47bb-0310-9956-ffa450edef68

43892e35b043abda0920ae18e57d6b1388bf1d68
:100644 100644 b156a9acb6d27c124fb531c2d7798514fdbaba41 5e646333eec29a680f55fc348e63ad13719a2a0d M	xdocs/tasks.xml

d45344aa0e21a93b1fd0be5f4dccf89d3b66c0c8
1053529851
Timothy O'Brien
project.properties changes.  1. The build will not fail on a failed
unit test, 2. The date/time and version are included in the xdoc
transformation, 3. JUnit is now forker, and 4. We use checkstyle.properties
to customize the behavior of Checkstyle.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140849 13f79535-47bb-0310-9956-ffa450edef68

d45344aa0e21a93b1fd0be5f4dccf89d3b66c0c8
:000000 100644 0000000000000000000000000000000000000000 20e58dd44648b7b98d389289a4c3b5213df836c8 A	checkstyle.properties
:000000 100644 0000000000000000000000000000000000000000 3da2adfdce062d21e334b14617683ba4c53b91b1 A	project.properties

725eff7db400661631416be3d58bb2758a793b7a
1053526875
Timothy O'Brien
Commited patch for issue 20112 from Phil Steitz.

EmpiricalDistribution -- represents an empirical probability distribution and
supports generation of data values that are "like" values in an input file
without making any assumptions about the functional form of the probability
distribution that the data come from.   This is useful in simulation
applications where historical data about component performance are
available but do not follow standard distributions (or any application that
requires random data generation from an empirical distribution). Also
generates data for grouped frequency histograms based on the input file.

ValueServer -- a wrapper for RandomData and EmpiricalDistribution that
generates values in each of the following modes:
  * DIGEST_MODE -- uses an empirical distribution
  * REPLAY_MODE -- replays data from an input file
  * UNIFORM_MODE -- generates uniformly distributed random values
  * EXPONENTIAL_MODE -- generates exponentially distributed random
                        values
  * GAUSSIAN_MODE -- generates Gaussian distributed random values
  * CONSTANT_MODE -- returns the same value every time.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140848 13f79535-47bb-0310-9956-ffa450edef68

725eff7db400661631416be3d58bb2758a793b7a
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8b62ed457040b6a1b4562aa0d0df88e1e77bddce
1053499586
Timothy O'Brien
Updated class javadoc for ContractableDoubleArray


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140847 13f79535-47bb-0310-9956-ffa450edef68

8b62ed457040b6a1b4562aa0d0df88e1e77bddce
:100644 100644 ecf67de3f23ed060751bdbd8d0ca3b6f9ed797ba 4f1c0e24ac8ac1c7f99772addd49edd6eb61184c M	src/java/org/apache/commons/math/ContractableDoubleArray.java

e1136b7e12d186c5086bb86b21e43b8703a0de94
1053498270
Timothy O'Brien
Added more substantial class javadoc to ExpandableDoubleArray


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140846 13f79535-47bb-0310-9956-ffa450edef68

e1136b7e12d186c5086bb86b21e43b8703a0de94
:100644 100644 014a87dcee7f4c4efb182da7d50e0ef9e1bf8295 9db06dcf1ad859a22d8627a4a60497707d4ef221 M	src/java/org/apache/commons/math/ExpandableDoubleArray.java

ebeb2dcab4e429a967f61401e6e9c755a19cf6e1
1053496105
Timothy O'Brien
Added javadoc to FixedDA and altered exceptions in DoubleArray

* One should be able to use a DoubleArray in a similar way to a
regular double[], to this effect methods for accessing element
values will no longer throw NoSuchElementExceptions when an
index is outside of the element set.  These method all throw
ArrayIndexOutOfBoundException if a bad index is supplied.

* Filled out javadoc in FixedDoubleArray.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140845 13f79535-47bb-0310-9956-ffa450edef68

ebeb2dcab4e429a967f61401e6e9c755a19cf6e1
:100644 100644 abf6d43b541e59eb4d0be08a4aedc65d832d3369 5d129238b530b1337deebb80b409e9d061720d31 M	src/java/org/apache/commons/math/DoubleArray.java
:100644 100644 d13342a959671462e7267352d137987b6ce0d805 014a87dcee7f4c4efb182da7d50e0ef9e1bf8295 M	src/java/org/apache/commons/math/ExpandableDoubleArray.java
:100644 100644 911a990266ffd20fa007b2861e07cd7af7bbd941 0c53b636a6174f3c6f2d0cad62c847d0db67ff07 M	src/java/org/apache/commons/math/FixedDoubleArray.java

2f20f8d2b3f14d81aac604803d71bf7850db27a8
1053460498
Robert Burrell Donkin
Corrected upload directory.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140844 13f79535-47bb-0310-9956-ffa450edef68

2f20f8d2b3f14d81aac604803d71bf7850db27a8
:100644 100644 69b26b7f529b2391df7aee4c850c4d80d63ad8ca 9b126549cb893734dd40ff62b672ad82ed0e00e5 M	project.xml

cc3b4cac2bb748b52e79099523814f771be78e9c
1053454529
Timothy O'Brien
Updated source code to reflect Jakarta source code guidelines specifically
tab characters.  Changes were driven by Checkstyle report on
http://jakarta.apache.org/commons/sandbox/math


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140843 13f79535-47bb-0310-9956-ffa450edef68

cc3b4cac2bb748b52e79099523814f771be78e9c
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:100644 100644 5fa82babbce2f6881048cf642e9c831af918486f ecf67de3f23ed060751bdbd8d0ca3b6f9ed797ba M	src/java/org/apache/commons/math/ContractableDoubleArray.java
:100644 100644 c4ff914046ee2981c818b99906ab5255ad10d402 abf6d43b541e59eb4d0be08a4aedc65d832d3369 M	src/java/org/apache/commons/math/DoubleArray.java
:100644 100644 5cd6336f7bb2ea47da1d5c0912da77396b8f1bb5 d13342a959671462e7267352d137987b6ce0d805 M	src/java/org/apache/commons/math/ExpandableDoubleArray.java
:100644 100644 494c3af8a0ca80ecc23d4854e9700d97f5cafaf9 911a990266ffd20fa007b2861e07cd7af7bbd941 M	src/java/org/apache/commons/math/FixedDoubleArray.java
:100644 100644 eb3cc0a0f6170d82ebd333edda240d82a9359491 e7df32f1c43e870e91e6f76951ab449825fb779a M	src/java/org/apache/commons/math/ListUnivariateImpl.java
:100644 100644 41f93d56f8031679aba1ae9d634f49a791531831 df80de0d306c4b6bfa9ac6274babdc64c46052ca M	src/java/org/apache/commons/math/StoreUnivariate.java
:100644 100644 5d5729e9c2eaffd75f4a96e9789bbe2b7d520639 d790084058bafbddae3d0ce6c7d1d293360a6f6a M	src/java/org/apache/commons/math/StoreUnivariateImpl.java
:100644 100644 4afa658fb3892163849f88939e35a80b4a38af61 734d93f22271bb2d8caa80ebfb92e670c6da7dd4 M	src/java/org/apache/commons/math/Univariate.java
:100644 100644 b785a3f04124bb3020d346899c9848654b3459f3 3f9d77c73aa5c6548af9ff77b2aefb6e7077228c M	src/java/org/apache/commons/math/UnivariateImpl.java

e0f88d35af39735cabdf488da3b11bf746d69e4c
1053437090
Timothy O'Brien
Added Mark Diggory as a contributor


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140842 13f79535-47bb-0310-9956-ffa450edef68

e0f88d35af39735cabdf488da3b11bf746d69e4c
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cbdcc2412b2118ec38490ec2266624e2aefee949
1053426477
Robert Burrell Donkin
Created outline user guide This will be built using maven. Lots more content needed.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140841 13f79535-47bb-0310-9956-ffa450edef68

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:000000 100644 0000000000000000000000000000000000000000 7d48bf8cd9f77b2336e223edd2fa14ab90c8266a A	xdocs/userguide/overview.xml

726eab50aaff0d508ec6eb9a1bf5953ca4ddb6eb
1053426446
Robert Burrell Donkin
Created outline documentation. This will be built using maven. Lots more content needed.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140840 13f79535-47bb-0310-9956-ffa450edef68

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:000000 100644 0000000000000000000000000000000000000000 02d4018b64b465296ddd87a18fb0447146304de7 A	xdocs/developers.xml
:000000 100644 0000000000000000000000000000000000000000 2b0f9889f9ac0ffb8bc8afe7f4329eccd92c8362 A	xdocs/index.xml
:000000 100644 0000000000000000000000000000000000000000 8c1c72b6d92409200024b67f127cf6ed6be96edb A	xdocs/navigation.xml
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45b69259eb53e1599f3bcdb095d81c41d0074d04
1053426272
Robert Burrell Donkin
Mavenization phase one - moving documentation build to maven, will complete by generating build.xml etc later.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140839 13f79535-47bb-0310-9956-ffa450edef68

45b69259eb53e1599f3bcdb095d81c41d0074d04
:100644 100644 6e11cfc0dc718da7a923914d5829900e2e120ae4 3b9a403c4ce43d66a5e6dae4221e9843739e569e M	.cvsignore
:100644 100644 68ab0697c709be4f8f93ab7511cd22ccda5f0175 819027b0543fb91950c4e07f45ac096ffcebe6ca M	project.xml
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e30f62314b487158b4ba77e8379cd4f2cd4c77a9
1053219532
Timothy O'Brien
Phil Steitz wrote:

This commit contains the suite of random data generation utilities that
I originally
proposed as extensions to lang.math.  There is some functional overlap
with lang.math, but the contract and intention of this implementation is
different in several significant ways.

* the lang implementation maintains "immutability" of the underlying
   random number generator (emulating Math). The RandomData
   implementation allows users to reseed the random number generator(s)
   (this is in effect possible in the recent extensions to lang.math by
   passing in a user-supplied random as an actual parameter to the
   next() methods) Users can also reset the PRNG algorithm and provider
   used by the "secure" methods.

* RandomData includes "secure" methods (delegating to SecureRandom)

* RandomData will generate random deviates from exponential and poisson,
   as well as Gaussian and Uniform distributions.  These are useful in
   simulation applications.

* Overlapping somewhat with lang.StringUtils, RandomData will generate
   random hex strings.  There is a nextSecureHexString method that will
   (I claim :-) generate cryptographically secure string identifiers. I
   would appreciate feedback on this algorithm, which I have seen used
   elsewhere (similar to what tomcat does to generate session ids); but
   not documented as a standard.

PR: Bugzilla 20013
Obtained from: Phil S.
Submitted by: Phil S.
Reviewed by: Tim O.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140838 13f79535-47bb-0310-9956-ffa450edef68

e30f62314b487158b4ba77e8379cd4f2cd4c77a9
:000000 100644 0000000000000000000000000000000000000000 3cff2b63e76f395d5ad9726a40604c5d21d21d4d A	src/java/org/apache/commons/math/RandomData.java
:000000 100644 0000000000000000000000000000000000000000 eeec29d3c1a8c6467ebf845cb90161b7b78e1921 A	src/java/org/apache/commons/math/RandomDataImpl.java
:100644 100644 2a6e57b0de35c2d4a09ead3822771d1657f6a5fe 200c0477886cf9b02df511f19a3eb225a22cef6a M	src/test/org/apache/commons/math/MathTestSuite.java
:000000 100644 0000000000000000000000000000000000000000 a4864741ebcb9cc550989f611ff778e7ea25307b A	src/test/org/apache/commons/math/RandomDataTest.java

3ec57d975f86d4ee8d9fdec437650e49642cc83a
1053219318
Timothy O'Brien
Altered the build script to use batch test instead of running
a suite.  The advantage of this is that when new tests are added to the
project a TestSuite class does not need to updated.

All classes *Test.java are included, and *AbstractTest.java are excluded.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140837 13f79535-47bb-0310-9956-ffa450edef68

3ec57d975f86d4ee8d9fdec437650e49642cc83a
:100644 100644 a46a980f5eee2ddf7c749d1d2589c1561e287151 47dc4e0bfbed10a85a6d154a8524a9b0d8d9e3d5 M	build.xml

2bbad8ecca1a9b52c20dadcff06f30682a77a738
1053213861
Timothy O'Brien
Added a FixedDoubleArray.  FixedDoubleArray supports a rolling mechanism
that reuses an array of fixed length.  This classes was added to an efficient
rolling mechanism.

FixedDoubleArray was influenced by discussions on the commons-dev list and
patches submitted by Mark Diggory.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140836 13f79535-47bb-0310-9956-ffa450edef68

2bbad8ecca1a9b52c20dadcff06f30682a77a738
:100644 100644 57f2c99a547aab56e1dc70e91babd8e56b4038e2 68ab0697c709be4f8f93ab7511cd22ccda5f0175 M	project.xml
:100644 100644 b0ff88156533e47059ce8fa4740830eee02d5f69 5cd6336f7bb2ea47da1d5c0912da77396b8f1bb5 M	src/java/org/apache/commons/math/ExpandableDoubleArray.java
:000000 100644 0000000000000000000000000000000000000000 494c3af8a0ca80ecc23d4854e9700d97f5cafaf9 A	src/java/org/apache/commons/math/FixedDoubleArray.java
:100644 100644 50798cd93f2310efdec41506879e7e66d150463f b785a3f04124bb3020d346899c9848654b3459f3 M	src/java/org/apache/commons/math/UnivariateImpl.java
:100644 100644 5f59e490da7cf713059400f2defc7c267382166e 4db456890a06a4ddb90f04bd2f1860a76a1ebdaa M	src/test/org/apache/commons/math/ContractableDoubleArrayTest.java
:100644 100644 11f34f5f95aaf35f1344ebe14a678256047337f5 206d4b59c3fa33ba1b785212b054e66a45079b29 M	src/test/org/apache/commons/math/DoubleArrayAbstractTest.java
:100644 100644 e5ef1943386119d55ad0d050c38eb20fcdf51211 680933c36d3172d0d162e821130493c1786bf213 M	src/test/org/apache/commons/math/ExpandableDoubleArrayTest.java
:000000 100644 0000000000000000000000000000000000000000 6fa21fe9f03476e093e62a0449c7ca8e9407189c A	src/test/org/apache/commons/math/FixedDoubleArrayTest.java

8db7e1bd75cceeb37255414b79e7bb892818af03
1053062609
Timothy O'Brien
The Univariate interface now contains getWindow and setWindow in
addition to a constant which signifies an "infinite" window.  Windowing
has been added to all three Univariate implementations:

* UnivariateImpl - If the window is not infinite, we keep track of
0..n elements and discount the contribution of the discarded element when
our "window" is moved.  If the window is infinite no extra storage is used
beyond an empty ContractableDoubleArray.

- In the following two implementations, the window size can be changed at anytime.

* ListStoreUnivariateImpl - If the window is not infinite, this
implementation only takes into account the last n elements of the List.

* StoreUnivariateImpl - Uses an internal ContractableDoubleArray, window size
can be changed at any time.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140835 13f79535-47bb-0310-9956-ffa450edef68

8db7e1bd75cceeb37255414b79e7bb892818af03
:100644 100644 a593789c810504b9db076219411a956bbe9b76b6 c4ff914046ee2981c818b99906ab5255ad10d402 M	src/java/org/apache/commons/math/DoubleArray.java
:100644 100644 89847c8dbdf41c56288e65283b801d402a613372 b0ff88156533e47059ce8fa4740830eee02d5f69 M	src/java/org/apache/commons/math/ExpandableDoubleArray.java
:100644 100644 825764c31fcc172cda792eab47cec0700b3bcd43 eb3cc0a0f6170d82ebd333edda240d82a9359491 M	src/java/org/apache/commons/math/ListUnivariateImpl.java
:100644 100644 a366ffbd2d60a8cf78075e13d53a7420e4013b96 5d5729e9c2eaffd75f4a96e9789bbe2b7d520639 M	src/java/org/apache/commons/math/StoreUnivariateImpl.java
:100644 100644 de6d948ed8c6dced7425ac3f14b32f1daa8bce49 4afa658fb3892163849f88939e35a80b4a38af61 M	src/java/org/apache/commons/math/Univariate.java
:100644 100644 71c94fb8d8ab4f991205434ac655313a198d6f6e 50798cd93f2310efdec41506879e7e66d150463f M	src/java/org/apache/commons/math/UnivariateImpl.java

b2fd0349771203ccfb14815f874300ade64644a7
1053058986
Timothy O'Brien
* DoubleArray is now an interface which is implemented by
ExpandableDoubleArray.  The interface provides a public interface
which does not hint at any of the storage parameters of
Expandable or Contractable.

* DoubleArrayTest now operates on the DoubleArray interface, casting
to Expandable when we need to call the package scopes getInternalLength
method.

* While we should not provide access to the internal storage array, it
should be possible to obtain a double[] of elements stored in this
DoubleArray - double[] getElements() was added to the DoubleArray interface,
it will return the element array.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140834 13f79535-47bb-0310-9956-ffa450edef68

b2fd0349771203ccfb14815f874300ade64644a7
:100644 100644 9832ec12a49f7cace8381ad1f5fe2bd4b7febf84 5fa82babbce2f6881048cf642e9c831af918486f M	src/java/org/apache/commons/math/ContractableDoubleArray.java
:000000 100644 0000000000000000000000000000000000000000 a593789c810504b9db076219411a956bbe9b76b6 A	src/java/org/apache/commons/math/DoubleArray.java
:100644 100644 f82dbb102c625a76e0c506e3d4adffa34c538f6f 89847c8dbdf41c56288e65283b801d402a613372 M	src/java/org/apache/commons/math/ExpandableDoubleArray.java
:100644 100644 5eff9cd0a8c607037e3c73b4d0f086b325c98617 5f59e490da7cf713059400f2defc7c267382166e M	src/test/org/apache/commons/math/ContractableDoubleArrayTest.java
:100644 100644 3e3c7c1d8543906908e765813295347f9a7b4bfc 11f34f5f95aaf35f1344ebe14a678256047337f5 M	src/test/org/apache/commons/math/DoubleArrayAbstractTest.java
:100644 100644 7fe2bac4a5ff33bba728c5baa9e22c6a6d6c0caf e5ef1943386119d55ad0d050c38eb20fcdf51211 M	src/test/org/apache/commons/math/ExpandableDoubleArrayTest.java

090bf703251d1bc3ecec7520ae6a8915a52fd720
1053057334
Timothy O'Brien
* ContractableDoubleArray extends ExpandableDoubleArray - I sense the
need for a DoubleArray interface.

* ExpandableDoubleArray and the extension ContractableDoubleArray should
aim towards presenting a public interface that does not expose any
details of the internal.  To this end, one is no longer able to get the
internal storage array via public double[] getValues(), and the startIndex
(which was relative to the internal storage array) is no longer available.

* [Expandable|Contractable]DoubleArray now allow one to discard
elements from the front of the array.  Before this commit, one could
accomplish the same goal by changing the starting index of the element
array within the internal storage array.  This solution allowed one to
discard elements from the front of the array (as well as) reclaiming
elements by decreases the startIndex.

There were two problems with this approach (especially in
ContractableDoubleArray).   The ContractableDoubleArray can be
"compacted" at anytime thereby reseting the startIndex to zero and the
size of the internal store array to number of elements plus one.  Second,
"reclaiming" elements from the internal storage array by finagling
internal "pointers" to the start and end index seems to violate the
principles of encapsulation.  If you "discard" an element from the
front of the array, consider it unavailable.

It should be noted that calling setNumElements allows one to move the end
index of the internal element array at will.  Assume one has a 100 element
array, and one calls setNumElements(10), thereby decreasing the ending index
of the element array by 90.  The 90 "dumped" elements are not currently
reinitializied to the default double primitive value.  This is an open
question.

* Tests for ExpandableDoubleArray and ContractableDoubleArray were
refactored.  both test classes now extend a DoubleArrayAbstractTest
JUnit class which contained shared unit tests for both "implementations".
An approach like this should be adopted to test the Univariate implementations.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140833 13f79535-47bb-0310-9956-ffa450edef68

090bf703251d1bc3ecec7520ae6a8915a52fd720
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:100644 100644 2e61bacc91ff114e60159240beee9d7340bb6df4 f82dbb102c625a76e0c506e3d4adffa34c538f6f M	src/java/org/apache/commons/math/ExpandableDoubleArray.java
:000000 100644 0000000000000000000000000000000000000000 5eff9cd0a8c607037e3c73b4d0f086b325c98617 A	src/test/org/apache/commons/math/ContractableDoubleArrayTest.java
:000000 100644 0000000000000000000000000000000000000000 3e3c7c1d8543906908e765813295347f9a7b4bfc A	src/test/org/apache/commons/math/DoubleArrayAbstractTest.java
:100644 100644 caad8c96f3c2ed0397b6e61ca6153cff63428ed7 7fe2bac4a5ff33bba728c5baa9e22c6a6d6c0caf M	src/test/org/apache/commons/math/ExpandableDoubleArrayTest.java
:100644 100644 f2f5675b8684c2944cd4237531675f576425ef6e 65ff0765dd45c2cdb21898b03a2316d2913b0833 M	src/test/org/apache/commons/math/TestStatisticTest.java

68ede2e3d32ac864f73aca729abe0d9e1b532364
1053035903
Timothy O'Brien
Patches from Phil S. applied:

* A TestStatistic interface with corresponding implementation and testcase

PR: Bugzilla 19971
Obtained from: Patches attached to issue
Submitted by: Phil S.
Reviewed by: Tim O/


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140832 13f79535-47bb-0310-9956-ffa450edef68

68ede2e3d32ac864f73aca729abe0d9e1b532364
:000000 100644 0000000000000000000000000000000000000000 1273f8b88becea9643a992fea8da60b5c199e6e3 A	src/java/org/apache/commons/math/TestStatistic.java
:000000 100644 0000000000000000000000000000000000000000 9eee0a24000114a7af8b6c532265c3335d182a2e A	src/java/org/apache/commons/math/TestStatisticImpl.java
:000000 100644 0000000000000000000000000000000000000000 f2f5675b8684c2944cd4237531675f576425ef6e A	src/test/org/apache/commons/math/TestStatisticTest.java

b2544b4f59bb5384ae35610df69d4fbcd2cc95cb
1053013128
Timothy O'Brien
Made a nubmer of change to the ExpandableDoubleArray.

* This class now supports
the ability to move the starting index of the internal element array.  This
allows one to move the beginning of the element array, and form a sort of
"window", this will come into play when we want to provide moving
averages, or "rolling".

* Added an addElementRolling(double v) - this will increment the startIndex
and add the element to the end of the internal element array

* brought the Clover test cases up to 100% for this class

Added a class ContractableDoubleArray:

* This is an extension of ExpandableDoubleArray - it addes a configuration
parameter contractionCriteria.  Essential if the contractionCriteria is
2.0f we commit to never having the internal storage array provide more
than 2.0 times the storage capacity needed.  Once the internal
storage array exceed this measurement, the internal storage array is
pruned to the size of the internal element array.

Also, my IDE scolded me for some ununsed imports in ListUnivariateImpl, they
have been removed.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140831 13f79535-47bb-0310-9956-ffa450edef68

b2544b4f59bb5384ae35610df69d4fbcd2cc95cb
:100644 100644 bb0c93bf68c3b179eb75865e098c801c30050562 57f2c99a547aab56e1dc70e91babd8e56b4038e2 M	project.xml
:000000 100644 0000000000000000000000000000000000000000 2e4da05f2c924d8aee87a6ffb63a5d75d14e7fee A	src/java/org/apache/commons/math/ContractableDoubleArray.java
:100644 100644 0fb21eef1466d63504e00a8f1f7f646dc76587c2 2e61bacc91ff114e60159240beee9d7340bb6df4 M	src/java/org/apache/commons/math/ExpandableDoubleArray.java
:100644 100644 ceeee20b57f9254f16b656b60ae00ddd62c485a8 a366ffbd2d60a8cf78075e13d53a7420e4013b96 M	src/java/org/apache/commons/math/StoreUnivariateImpl.java
:100644 100644 0c518035bf840780a1c608885d8714e4f76a323d caad8c96f3c2ed0397b6e61ca6153cff63428ed7 M	src/test/org/apache/commons/math/ExpandableDoubleArrayTest.java
:100644 100644 e3976ff5ed7e0395c11336432b9caf500ba55cab f8ef8b4e66ca9e7fb2b96f815a422b900591ecf9 M	src/test/org/apache/commons/math/ListUnivariateImplTest.java

b4e6216d2e3de7218a06d9a0c1ac74b49d7259f9
1052980399
Timothy O'Brien
Another change to the stored Univariates.  The calculations are now abstracted
into an AbstractStoreUnivariate class which take responsibility for
all statistical calculations.  AbstractStoreUnivariate is implemented by
two classes:

* StoreUnivariateImpl - This class uses a ExpandableDoubleArray for
internal storage.  This class is a more efficient class in terms
of storage and cycles for users who are interested in gathering statistics
not available in the UnivariateImpl implementation.

* ListUnivariateImpl - This class is for a situation where a user might
wish to maintain a List of numeric objects outside of a StoreUnivariate
instance.  We still need to add serious error checking in the absence of
1.5's generics, but this implementation will work with any list that
contains Number objects - (BigDecimal, BigInteger, Byte, Double, Float,
Integer, Long, Short).  This implementation ultimately transforms all
numeric objects into double primitives via Number.doubleValue().

Becuase AbstractStoreUnivariate does not hold on to any state, a user
can add values through the Univariate.addValue() function OR one can
directly manipulate the contents of the List directly.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140830 13f79535-47bb-0310-9956-ffa450edef68

b4e6216d2e3de7218a06d9a0c1ac74b49d7259f9
:000000 100644 0000000000000000000000000000000000000000 4d8342f892ceec03239fe7fcf363c979d7982432 A	src/java/org/apache/commons/math/AbstractStoreUnivariate.java
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:000000 100644 0000000000000000000000000000000000000000 825764c31fcc172cda792eab47cec0700b3bcd43 A	src/java/org/apache/commons/math/ListUnivariateImpl.java
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:100644 100644 15235b506eda81a9e31d587bdf555eadcd2bc544 ceeee20b57f9254f16b656b60ae00ddd62c485a8 M	src/java/org/apache/commons/math/StoreUnivariateImpl.java
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6c210937da3c04bf1ea55a568c69ca4e1e74904e
1052977671
Timothy O'Brien

Submitted by: Phil S.
Reviewed by: Tim O.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140829 13f79535-47bb-0310-9956-ffa450edef68

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811975e52049a6275d4b9d6587ce3af40791a9ae
1052977141
Timothy O'Brien
The following changes were made to the Univariate implementation.  The public
interface of Univariate was extracted in an interface of the same name.
Univariate, an interface, is now implemented by UnivariateImpl which contains
all code originally present in the original Univariate implementation.

* StoredUnivariate is an interface which extends Univariate and adds
measures not available in the superinterface such as mode, kurtosis, and skew

* StoredUnivariateImpl provides an implementation which uses the
ExpandableDoubleArray for internal storage.  Calculations are performed
on demand *each* time a particular measure is required no state is
maintained by this implementation.

* Univariate provided methods addValue(int), addValue(float), addValue(long).
There functions were removed as no cast is required - all of these
assignments are widening conversions - no cast required

* Removed the name property from Univariate - property not relevant to
univariate statistics


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140828 13f79535-47bb-0310-9956-ffa450edef68

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9398d8036a6e8260d11ac78e4cbc904dee46df93
1052975997
Timothy O'Brien
Added an expandable double array, this class simply contains a double[] and takes care of automatic expansion of an internal array when necessary.  Class added with accompanying unit test


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140827 13f79535-47bb-0310-9956-ffa450edef68

9398d8036a6e8260d11ac78e4cbc904dee46df93
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f824dc45939740832a8043ca745a41490da1fbeb
1052852894
Timothy O'Brien
1. Make RealMatrixImpl implement Serializable
2. Make all currently unimplemented methods throw UnsupportedOperationException
3. Add solve() method to RealMatrix interface, representing vector
   solution to AX = B, where B is the parameter and A is *this.

Phil

Obtained from: Phil S.
Submitted by: Phil S.
Reviewed by: Tim O.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140826 13f79535-47bb-0310-9956-ffa450edef68

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:100644 100644 3447a41bfa57403c08c4b6121ebc2e12683b0094 f8c50f52da1996b5f09c1bc20522e5696ed1983e M	src/java/org/apache/commons/math/RealMatrix.java
:100644 100644 67457ab888e166351e181a5d1213efdbb4e029ee a441a7d920173344254ee83ee5a2720b4e2d3b8e M	src/java/org/apache/commons/math/RealMatrixImpl.java

d6c6ce69b87de9c8e4521f01c3fbb44f84f7cac9
1052771546
Timothy O'Brien
Added myself to STATUS and PROPOSAL


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140825 13f79535-47bb-0310-9956-ffa450edef68

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0ecdb7a73056b00e22f94bba340cf6e1306de353
1052767734
Timothy O'Brien
A maven project.xml was added for conv


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140824 13f79535-47bb-0310-9956-ffa450edef68

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2ba37fcc850b99508f027bed167962430fdf8d2f
1052766278
Robert Burrell Donkin
Starting source code - basic matrix operations and univarient stats plus test code. Submitted by Phil Steitz.


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140823 13f79535-47bb-0310-9956-ffa450edef68

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3bde240f035eb8585499640b7e6cf5fc6c69e85b
1052752074
Robert Burrell Donkin
added new commons math component


git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140822 13f79535-47bb-0310-9956-ffa450edef68

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a859606a95d3eca7d8e13e8fff11daa5b1a40813
1052752074
No Author
New repository initialized by cvs2svn.

git-svn-id: https://svn.apache.org/repos/asf/jakarta/commons/proper/math/trunk@140821 13f79535-47bb-0310-9956-ffa450edef68

a859606a95d3eca7d8e13e8fff11daa5b1a40813