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jidt/java/source/infodynamics/utils
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Joseph Lizier b1437452e4 Adding NORMALISE and NOISE_LEVEL_TO_ADD properties to all mutual information calculators for continuous-valued data (extends this capability from only KSG to Gaussian and kernel as well, the latter already had NORMALISE) 2019-04-02 12:38:17 +11:00
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commonsmath3 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. 2017-06-14 11:09:01 +10:00
AnalyticMeasurementDistribution.java Added utilities to convert between estimate values and p-values for an analytic null distribution in bulk (array calls) 2017-08-30 16:24:17 +10:00
AnalyticNullDistributionComputer.java Fixing javadoc reference in AnalyticNullDistributionComputer to correct class 2017-08-18 13:48:03 +10:00
ArrayFileReader.java Minor fixes to default values of TE calculator properties, and adding error messages for array file reading 2015-07-09 14:38:23 +00:00
ArrayFileWriter.java Rudimentary Javadocs completed for the utils package 2014-08-13 15:18:47 +00:00
ChiSquareMeasurementDistribution.java Added tracking of bias correction to ChiSquaredMeasurementDistribution, so the distribution is adjusted with bias correction. Should have been sent with previous commit for patch to CMI Gaussian bias correction 2018-08-27 00:29:59 +10:00
EmpiricalMeasurementDistribution.java Rudimentary Javadocs completed for the utils package 2014-08-13 15:18:47 +00:00
EmpiricalNullDistributionComputer.java 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. 2017-08-18 15:31:27 +10:00
EuclideanUtils.java Fixes issue 31 -- implementing fast nearest neighbour search for Kraskov MI using a k-d tree structure. 2014-10-15 04:48:09 +00:00
FirstIndexComparatorDouble.java Rudimentary Javadocs completed for the utils package 2014-08-13 15:18:47 +00:00
FirstIndexComparatorInteger.java Rudimentary Javadocs completed for the utils package 2014-08-13 15:18:47 +00:00
IntArrayWrapper.java Rudimentary Javadocs completed for the utils package 2014-08-13 15:18:47 +00:00
KdTree.java 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) 2018-11-24 21:16:36 +11:00
MathsUtils.java 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. 2017-06-14 11:09:01 +10:00
MatrixUtils.java Adding NORMALISE and NOISE_LEVEL_TO_ADD properties to all mutual information calculators for continuous-valued data (extends this capability from only KSG to Gaussian and kernel as well, the latter already had NORMALISE) 2019-04-02 12:38:17 +11:00
MeasurementDistribution.java Rudimentary Javadocs completed for the utils package 2014-08-13 15:18:47 +00:00
NativeUtils.java Added NativeUtils for native lib loading and included libKraskov.so in jar. 2017-06-01 20:34:23 +10:00
NearestNeighbourSearcher.java 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) 2018-11-24 21:16:36 +11:00
NeighbourNodeData.java 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. 2014-10-30 04:04:16 +00:00
NonPositiveDefiniteMatrixException.java 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. 2019-03-28 23:52:47 +11:00
OctaveFileReader.java Rudimentary Javadocs completed for the utils package 2014-08-13 15:18:47 +00:00
OctaveFileWriter.java Rudimentary Javadocs completed for the utils package 2014-08-13 15:18:47 +00:00
OctaveMatrix.java Rudimentary Javadocs completed for the utils package 2014-08-13 15:18:47 +00:00
ParsedProperties.java Rudimentary Javadocs completed for the utils package 2014-08-13 15:18:47 +00:00
RandomGenerator.java Rudimentary Javadocs completed for the utils package 2014-08-13 15:18:47 +00:00
UnivariateNearestNeighbourSearcher.java 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) 2018-11-24 21:16:36 +11:00
package-info.java Adding package-info.java files for Javadocs for the various packages 2014-08-13 15:36:10 +00:00