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934 Commits

Author SHA1 Message Date
joseph.lizier 6761de7e02 Added debug prints to Kraskov Conditional MI calculators 2013-01-15 01:14:13 +00:00
joseph.lizier 40e7d4b211 Added common unit tests for conditional MI calculators, and added implementations of the tests for Kraskov and Gaussian conditional MI calculators 2013-01-14 12:57:01 +00:00
joseph.lizier f466012556 Made Kraskov Conditional MI calculator implement the common Conditional MI interface 2013-01-14 12:51:34 +00:00
joseph.lizier a06efba6e0 Added first python code example using JIDT 2013-01-14 12:49:16 +00:00
joseph.lizier 9b9abda733 Bug fix of computation of epsilon (box width) on conditional variable in Kraskov conditional MI calculator 2 2013-01-14 11:13:58 +00:00
joseph.lizier 3ff564237e Updating distribution version in ant file 2013-01-12 13:47:15 +00:00
joseph.lizier 3167944875 Adding interface for conditional mutual information (continuous) calculator, common methods for it, and implementation for Gaussian variables. 2013-01-12 13:43:43 +00:00
joseph.lizier 69b59403b4 Made the CellularAutomata demos compatible with Matlab 2013-01-12 13:37:34 +00:00
joseph.lizier fc8986d0ab Made the DetectingInteractionLags demos compatible with Matlab 2013-01-12 12:38:19 +00:00
joseph.lizier eb76d4a733 updated info about automatic Matlab matrix to java format conversion in this example's comments. 2013-01-12 11:15:31 +00:00
joseph.lizier b6aece6d51 Fixed main demo scripts to be compatible with Matlab (fixed printf -> printf, rows -> size(x, 1), and not specifically converting matlab arrays to java and back) 2013-01-12 10:57:11 +00:00
joseph.lizier 220f4a8857 Added data for unit test for covariance 2013-01-08 05:39:07 +00:00
joseph.lizier 74ba272f41 Added unit test for covariance 2013-01-08 05:38:22 +00:00
joseph.lizier 030a172d82 Patched covariance calculation, added utils, patched analytic computation of distribution of MI with linear Gaussians, altered comments 2013-01-08 05:37:48 +00:00
joseph.lizier ef6e426c36 Adding bit values to the outputs for our logistic maps example in the detecting interaction lags demo 2013-01-03 12:22:44 +00:00
joseph.lizier 8fe32003ab Adding more unit testing on Kraskov MI, including for dependent data sets 2012-12-20 13:23:52 +00:00
joseph.lizier d95f04ec70 Adding new sample data for more unit testing on Kraskov MI 2012-12-20 13:20:52 +00:00
joseph.lizier b0bc89dcb1 Made the unit tests for Kraskov MI more streamlined; added unit test for multivariate MI 2012-12-20 10:40:42 +00:00
joseph.lizier 617880f9f5 Making Kraskov MI and higher order calculators use MAX_NORM in the marginal spaces by default (previously this had to be supplied via a property - it was the standard choice made, but was not the default). This aligns with the default specified in the Kraskov paper. 2012-12-20 10:38:03 +00:00
joseph.lizier 87f7be56a5 Adding new test data set of 4 random columns 2012-12-18 11:32:55 +00:00
joseph.lizier 13816b9adc Making ant junit call avoid running the abstract Junit tests 2012-12-18 10:59:40 +00:00
joseph.lizier 90c0f5a105 Renaming abstract unit test classes inside java files (missed these in previous commit) 2012-12-18 10:57:44 +00:00
joseph.lizier 74ebf27fa0 Renaming abstract unit test classes inside java files 2012-12-18 10:53:03 +00:00
joseph.lizier 653b511c24 Renaming abstract unit test classes as first step to avoid ant file running them (next commit will update names inside java files) 2012-12-18 10:51:30 +00:00
joseph.lizier 4d4c021be9 Added data for unit testing of MI Kraskov calculator 2012-12-18 10:35:22 +00:00
joseph.lizier 23f7f84eaa Added common functionality for unit testing multivariate MI calculators into an abstract class. 
Added basic tester for Kraskov multivariate MI, including verifying against Kraskov MILCA tool
 2012-12-18 10:34:41 +00:00
joseph.lizier a6e09c7fc4 Pulled some common functionality for testing multivariate TE calculators into an abstract class. 
Added basic tester for Kraskov multivariate TE
 2012-12-13 14:50:33 +00:00
joseph.lizier e789acd4dc Adding various comments 
Patched bug in TECalculatorMultiVariateSingleObservationsKernel whereby only k*destDimensions dimensions of destPast were being considered (this is a problem where one wants to surreptitiously condition on extra variables).
 2012-12-13 14:42:40 +00:00
joseph.lizier b64b0c091d Adding unit tester for TECalculatorMultiVariateKernel 2012-12-13 12:27:42 +00:00
joseph.lizier faad3c82b2 Patched nats -> bits error as per Issue 12. 
Fixed comments in MI calculator header.

Added log2 static value for TECommon to make code faster.
 2012-12-13 09:13:44 +00:00
joseph.lizier 29f183e91d Altered RandomGenerator.generateDistinctRandomInts() to return int[] instead of double[]. 
Added comments in CompleteTransferEntropyCalculator to clarify the meaning of offsets from other sources.
Added comments regarding entropy calculator
 2012-12-03 05:04:00 +00:00
joseph.lizier 635646997e Added info about DetectingInteractionLags demo to readme file 2012-11-19 03:55:58 +00:00
joseph.lizier 808ca04a6c Esuring that readme.txt file is overwritten by one with correct version 2012-11-19 03:50:41 +00:00
joseph.lizier c681c1184f Updated build version to 0.1.2 2012-11-19 03:44:40 +00:00
joseph.lizier 75067955f2 Adding demos for detecting correct interaction lags, as per our Wibral 2012 paper, contrasting with the momentary information transfer 2012-11-16 13:19:17 +00:00
joseph.lizier 5d63a6cb8b Fixed code to save images nicely 
Added script to reproduce results from moving frame of reference paper
 2012-11-12 00:18:45 +00:00
joseph.lizier 6557cd99c9 Fixed octave to java array and matrix conversions for size 1 arrays and matrices 2012-11-02 08:21:59 +00:00
joseph.lizier 734b2ac44a CA demos: added demos for entropy, entropy rate and excess entropy (even though EE calculator is not uploaded to the toolkit yet). 
Added capability for a moving frame of reference to the toolkit.

Sped up javaMatrixToOctave conversion for a sub-matrix.
 2012-11-01 12:09:02 +00:00
joseph.lizier 5ac7a20daa Patched new dependency specification in jardist target 2012-10-31 04:23:53 +00:00
joseph.lizier 13ddbba81c Fixed up clean target in ant. 
Added version template file.
 2012-10-31 04:21:46 +00:00
joseph.lizier 537327d0ea Finished ant build.xml file to make javadocs, jar and developer builds. 
Added readme-template.txt
 2012-10-31 04:07:10 +00:00
joseph.lizier 0521e71e9c fixed multiple dependencies in ant file 2012-10-30 06:43:41 +00:00
joseph.lizier b2d5d2b356 Adding ant build file 2012-10-30 06:41:42 +00:00
joseph.lizier 971c0f1760 Uploaded ConditionalMutualInformationCalculator after fixing the computeSignificance function. (untested so far however) 
Patched bad unicode character in comments for EntropyCalculatorMultivariateKozachenko
 2012-10-30 06:14:44 +00:00
joseph.lizier 2b67cede61 Patched scale for local info profiles in CA demos. 
Added complete transfer entropy and separable info.
Limited size of plots to 1000x1000 if they would be larger than this (would be a silly looking plot otherwise)
 2012-10-29 02:04:49 +00:00
joseph.lizier a75b1ebf07 Patched incorrect length measurement of hex string rule specifications for CA rules 2012-10-26 08:20:48 +00:00
joseph.lizier bb969f7d2c Adding basic Octave/Matlab demo scripts 2012-10-26 06:34:59 +00:00
joseph.lizier 7b770a9831 Adding demos directly, plus octave child directory, .m files for converting between octave and java arrays, and the CellularAutomata demo (just with active info storage for the moment). 2012-10-26 05:13:09 +00:00
joseph.lizier 731c17def1 Edited comments on MatrixUtils to talk about java-octave 2D matrix conversion issues 2012-10-25 14:08:27 +00:00
joseph.lizier 0332149b03 Addressing minor compile warning 2012-10-25 01:30:47 +00:00