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jidt/java/source/infodynamics/utils
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David Shorten dd215fdfbb spiking surrogates implemented 2021-08-11 09:20:35 +10:00
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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 spiking surrogates implemented 2021-08-11 09:20:35 +10:00
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 Tweak to method to print out an array of ints 2017-11-22 20:49:05 +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 Incorporated JL code from 21/11/2018 2018-12-10 20:22:15 +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 Rudimentary Javadocs completed for the utils package 2014-08-13 15:18:47 +00:00
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 Incorporated JL code from 21/11/2018 2018-12-10 20:22:15 +11:00
package-info.java Adding package-info.java files for Javadocs for the various packages 2014-08-13 15:36:10 +00:00