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commonsmath3
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Adding new methods computePValueForGivenEstimate() and computeEstimateForGivenPValue to AnalyticMeasurementDistribution and implementing in ChiSquareMeasurementDistribution. Involves importing (and refactoring) a significantly larger chunk of commons.maths3 classes (and updating existing ones to latest 3.6.1 version for consistency). Also addresses issue #23 in changing the actual value of the ChiSquareMeasurementDistribution to be that of the information theoretic measurement rather than 2*N times it (which was the value that is actually chi squared distributed), which also necessitates changes to the Discrete and Gaussian calculators computeSignificance() methods.
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2017-06-14 11:09:01 +10:00 |
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AnalyticMeasurementDistribution.java
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Added utilities to convert between estimate values and p-values for an analytic null distribution in bulk (array calls)
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2017-08-30 16:24:17 +10:00 |
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AnalyticNullDistributionComputer.java
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Fixing javadoc reference in AnalyticNullDistributionComputer to correct class
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2017-08-18 13:48:03 +10:00 |
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ArrayFileReader.java
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Minor fixes to default values of TE calculator properties, and adding error messages for array file reading
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2015-07-09 14:38:23 +00:00 |
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ArrayFileWriter.java
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Rudimentary Javadocs completed for the utils package
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2014-08-13 15:18:47 +00:00 |
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ChiSquareMeasurementDistribution.java
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Added support for Chi^2 analytic distribution to support degrees of freedom 0 (this will handle e.g. where a source had no independent dimensions)
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2019-05-17 22:20:54 +10:00 |
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EmpiricalMeasurementDistribution.java
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Rudimentary Javadocs completed for the utils package
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2014-08-13 15:18:47 +00:00 |
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EmpiricalNullDistributionComputer.java
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Altering various continuous calculators to implement the EmpiricalNullDistributionComputer interface (where they're already implementing computeSignificance() etc.). Also altered the EmpiricalNullDistributionComputer methods to throw Exceptions, since the continuous calculators generally do this (and doesn't harm the discrete ones). Also involved implementing the methods in ConditionalMIMultiVariateCommon by selecting to permute the first variable by default.
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2017-08-18 15:31:27 +10:00 |
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EuclideanUtils.java
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Fixes issue 31 -- implementing fast nearest neighbour search for Kraskov MI using a k-d tree structure.
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2014-10-15 04:48:09 +00:00 |
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FirstIndexComparatorDouble.java
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Rudimentary Javadocs completed for the utils package
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2014-08-13 15:18:47 +00:00 |
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FirstIndexComparatorInteger.java
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Rudimentary Javadocs completed for the utils package
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2014-08-13 15:18:47 +00:00 |
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IntArrayWrapper.java
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Rudimentary Javadocs completed for the utils package
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2014-08-13 15:18:47 +00:00 |
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KdTree.java
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Nearest neighbour searchers now return number of points found for findPointsWithinR as well as marking them in input arrays. Also added new method sumDistanceAboveThresholdForPointsWithinRs() for the univariate searcher (to be used in spiking TE estimator under development)
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2018-11-24 21:16:36 +11:00 |
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MathsUtils.java
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Handling infinites in Chi square CDF function properly
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2019-05-17 22:24:54 +10:00 |
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MatrixUtils.java
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Added methods to MatrixUtils (plus unit tests) for adding/removing/swapping sample points into existing means and covariances
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2019-05-17 22:27:30 +10:00 |
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MeasurementDistribution.java
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Rudimentary Javadocs completed for the utils package
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2014-08-13 15:18:47 +00:00 |
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NativeUtils.java
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Added NativeUtils for native lib loading and included libKraskov.so in jar.
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2017-06-01 20:34:23 +10:00 |
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NearestNeighbourSearcher.java
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Nearest neighbour searchers now return number of points found for findPointsWithinR as well as marking them in input arrays. Also added new method sumDistanceAboveThresholdForPointsWithinRs() for the univariate searcher (to be used in spiking TE estimator under development)
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2018-11-24 21:16:36 +11:00 |
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NeighbourNodeData.java
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Adding fast nearest neighbour searcher for univariate data (uses only a sorted array rather than whole k-d tree). Adds an abstract nearest neighbour searcher so calling classes don't necessarily need to know whether they're dealing with uni or multi-variates. MI and conditional MI Kraskov altered to use this where possible.
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2014-10-30 04:04:16 +00:00 |
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NonPositiveDefiniteMatrixException.java
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Added methods to MatrixUtils to make a Cholesky decomposition of independent components only (useful for MI and conditional MI calculations), with a required update to the NonPositiveDefiniteMatrixException to include a field defining which row in the matrix was a problem. Also includes code to convert between native int[] arrays and ArrayList<Integers>, and new method signatures for column selection from matricies.
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2019-03-28 23:52:47 +11:00 |
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OctaveFileReader.java
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Rudimentary Javadocs completed for the utils package
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2014-08-13 15:18:47 +00:00 |
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OctaveFileWriter.java
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Rudimentary Javadocs completed for the utils package
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2014-08-13 15:18:47 +00:00 |
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OctaveMatrix.java
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Updating octave-java interface to use non-overloaded method signatures for int and boolean arrays (this seemed to have caused an issue on some versions with ints being converted to boolean first, thus losing all values except 0-1)
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2019-07-23 11:33:04 +10:00 |
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ParsedProperties.java
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Rudimentary Javadocs completed for the utils package
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2014-08-13 15:18:47 +00:00 |
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RandomGenerator.java
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Rudimentary Javadocs completed for the utils package
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2014-08-13 15:18:47 +00:00 |
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UnivariateNearestNeighbourSearcher.java
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Nearest neighbour searchers now return number of points found for findPointsWithinR as well as marking them in input arrays. Also added new method sumDistanceAboveThresholdForPointsWithinRs() for the univariate searcher (to be used in spiking TE estimator under development)
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2018-11-24 21:16:36 +11:00 |
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package-info.java
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Adding package-info.java files for Javadocs for the various packages
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2014-08-13 15:36:10 +00:00 |
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