jlizier 1bb67f0840 Adding neighbour search utilities in preparation for attempting fast surrogate generation (performing multiple neighbour searches at once where we can); in particular adding a countPointsWithinR with a remapping of the point's indices. Unit test added as well for this.		2017-11-22 20:48:30 +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	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
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	Adding neighbour search utilities in preparation for attempting fast surrogate generation (performing multiple neighbour searches at once where we can); in particular adding a countPointsWithinR with a remapping of the point's indices. Unit test added as well for this.	2017-11-22 20:48:30 +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	Added several utilities for selecting columns to MatrixUtils	2017-03-23 14:31:38 +11:00
MeasurementDistribution.java	Rudimentary Javadocs completed for the utils package	2014-08-13 15:18:47 +00:00
NearestNeighbourSearcher.java	Adding neighbour search utilities in preparation for attempting fast surrogate generation (performing multiple neighbour searches at once where we can); in particular adding a countPointsWithinR with a remapping of the point's indices. Unit test added as well for this.	2017-11-22 20:48:30 +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	Adding neighbour search utilities in preparation for attempting fast surrogate generation (performing multiple neighbour searches at once where we can); in particular adding a countPointsWithinR with a remapping of the point's indices. Unit test added as well for this.	2017-11-22 20:48:30 +11:00
package-info.java	Adding package-info.java files for Javadocs for the various packages	2014-08-13 15:36:10 +00:00