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884 Commits

Author SHA1 Message Date
David Shorten 0e530cdceb history embeddings done 2021-07-23 17:26:18 +10:00
David Shorten deb9d97520 advancing previous indices throughout iteration 2021-07-22 19:06:53 +10:00
David Shorten fe0fb2ed49 positioning embeddings start point 2021-07-22 17:55:00 +10:00
David Shorten 56dacc5232 some progress towards PCB spiking estimator 2021-07-22 14:19:36 +10:00
David Shorten 4f889df786 added testing script 2021-07-21 10:15:08 +10:00
Joseph Lizier 70a7f5c33a Clarifying how to access an attribute (pValue) in the R demos 2021-04-19 11:32:23 +10:00
Pedro Mediano 07883af734 Updated printed messages with cross-platform newline character. 2021-02-09 10:23:30 +00:00
Pedro Mediano bc8c233e68 Added KSG implementation of various multivariate IT measures and unit tests. 2021-01-25 12:41:01 +00:00
Pedro Mediano a58a01fbfd Added discrete implementation of various multivariate IT measures and unit tests. 2021-01-24 22:13:15 +00:00
Pedro Mediano b3abd382aa Added abstract parent class for multivariate IT measures on discrete data. 2021-01-24 22:10:14 +00:00
Pedro Mediano f67e274819 Added Gaussian implementation of various multivariate IT measures and unit tests. 2021-01-24 22:06:39 +00:00
Pedro Mediano 403745800e Added abstract parent class for multivariate IT measures on continuous data. 2021-01-24 21:56:26 +00:00
Pedro Mediano 06cc6d649d Added `select*` methods for `int[][]` matrices. 2021-01-24 21:54:42 +00:00
Pedro Mediano b3192e225f Added convenience methods to multiply an array times a constant value. 2021-01-24 21:54:09 +00:00
Joseph Lizier 3222b5a629 Implementation and unit test for KSG MI calculation with new samples (both algorithms 1 and 2) 2020-10-30 16:21:10 +11:00
Joseph Lizier 0606f8ab39 Cleaning up CMI Kraskov for new samples, including fixing some comments, logic of not using GPU for this, and if no conditional counting all point as a conditional match 2020-10-30 16:19:31 +11:00
Joseph Lizier b5a6fa92c2 Fixing min and max of local CMI values 2020-10-29 13:45:25 +11:00
Joseph Lizier 44e53bc846 Updating error messages for kdTree 2020-10-29 13:39:40 +11:00
Joseph Lizier 8ecb512ce0 Updating flocking analysis to save AIS/TE from all parameters tested in an autoembedding process 2020-09-03 22:20:03 +10:00
Joseph Lizier 4c95b4ee86 Updating Flocking analysis demo to have more aggressive dynamic correlation exclusion. Also adding utility to plot the raw positions of the floc 2020-09-01 11:22:31 +10:00
Joseph Lizier 34161a2e6d Adding non-overloaded method signatures for multivariate arrays, so that the jpype python-java bridge can resolve which method signature to use more directly via these 2020-05-22 14:42:26 +10:00
Joseph Lizier bf207f866e Patched error in computing start and end times for valid observation sequences in conditional TE calculators (with validity booleans) 2020-05-21 00:57:34 +10:00
Joseph Lizier 820f700cb8 Fixed python write file utilities to work with unidimensional arrays 2020-05-21 00:19:16 +10:00
Joseph Lizier 471ea59bb2 Adding utilities for writing text files in python (can be done with numpy, but just making something quick my way) 2020-05-20 23:46:55 +10:00
Joseph Lizier d0a0fca40c Added non-overloaded method calls for conditionalTE continuous' addObservations() method calls with validity booleans - this is for JPype from Python which seems unable to resolve overloads of double[] and double[][], when more than one variable changes in this way 2020-05-16 12:18:57 +10:00
Joseph Lizier ccbccc6302 Merge branch 'master' of github.com:jlizier/JIDT 2020-05-15 17:37:32 +10:00
Joseph Lizier cbcca8d0ff fixing addedMoreThanOneObservationSet for the MultiInfoCalculator 2020-05-15 17:35:54 +10:00
Joseph Lizier 510f999d2e Adds addObservations calls with validity arrays for conditional transfer entropy 2020-05-15 17:34:00 +10:00
Pedro Mediano 64a7a80e30
Changed name of LDFLAGS to avoid potential conflicts 
Closes #80 .
 2020-05-02 14:37:27 +01:00
Joseph Lizier 1c2ccda1eb
Updated contributors list 2020-01-24 11:42:56 +11:00
Joseph Lizier edb8f997cb Added new loader file for 2D xls format to flocking analysis demo 2019-12-17 17:08:27 +11:00
Joseph Lizier 502f7ac22c Merge branch 'master' of github.com:jlizier/JIDT 2019-12-13 11:44:03 +11:00
Joseph Lizier 2c2d012e20 Sooraj Sekhar's addition to flocking analysis of allowing speed to be included in the information-theoretic calculations. Includes updated NetLogo demo where speed coherence is also added 2019-12-13 11:40:58 +11:00
Joseph Lizier f53ecba635
Added Emanuele Crosato to author's list for the flocking demo code 2019-09-01 22:06:27 +10:00
Joseph Lizier 4966fdabc2 Adding a code suite to run active information storage and transfer entropy analysis of positional / heading data from swarms/flocks/schools, including a demonstration of how to use the suite with a NetLogo example. Documentation on a wiki page to follow later ... 2019-08-29 23:08:16 +10:00
Joseph Lizier c22e37d1ab Adding new lecture slides for Module 0 Introduction to course 2019-08-09 17:20:12 +10:00
Joseph Lizier 61ae6fb40b Minor updates to AutoAnalyser to put fixtures in place for array conversion to Python with eventual handling of 2D arrays (code isn't really changed at the moment, but has methods to make this easy later) 2019-07-25 23:56:56 +10:00
Joseph Lizier 2ab3ac01bb Adding non-overloaded method signatures for adding 1D vs 2D observations for common class for continuous MI and CMI estimators, since JPype 0.7 does not seem able to resolve overloaded 1D vs 2D arrays any longer 2019-07-25 23:11:44 +10:00
Joseph Lizier 1667b9fe7a Added utility for subsampling rows from 2D matrix 2019-07-25 14:36:54 +10:00
Joseph Lizier 1dc2dc8b86 Updating all discrete calculators (except SeparableInfo, since it's outmoded) to have a default empty constructor, with an overloaded initialise method added that provides all relevant properties. Fixes #77, and provides a first step for #66. Also aligned PredictiveInfo and ConditionalTE calculators to use the appropriate super classes. 2019-07-25 14:29:51 +10:00
Joseph Lizier d545793bc5 Patching unit test on KSG MI with discrete which tested that result changed from K=2 to 4, but the threshold for change was too large. 2019-07-25 10:14:57 +10:00
Joseph Lizier 0dae162d82 Added new unit tests for TE with k=0 for Gaussian and KSG estimators 2019-07-23 11:43:55 +10:00
Joseph Lizier 17bf0e0be7 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) 2019-07-23 11:33:04 +10:00
Joseph Lizier fba941362d Adding further unit tests for Conditional TE (continuous-valued) to check different delays on conditional variables, and patching test of validity of calling univariate versus multivariate method signatures. 2019-07-12 14:45:23 +10:00
Joseph Lizier 1db8a2ac63 Making local computation for CMI Gaussian calculator store the lastAverage if it was called with the previous observations 2019-05-17 22:47:16 +10:00
Joseph Lizier 681c9196ee Added methods to MatrixUtils (plus unit tests) for adding/removing/swapping sample points into existing means and covariances 2019-05-17 22:27:30 +10:00
Joseph Lizier 9f9c79bc95 Handling infinites in Chi square CDF function properly 2019-05-17 22:24:54 +10:00
Joseph Lizier 8542d217ea 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) 2019-05-17 22:20:54 +10:00
Joseph Lizier fce1b34a5c Adding NORMALISE and NOISE_LEVEL_TO_ADD properties to all conditional mutual information calculators for continuous-valued data (extends this capability from only KSG to Gaussian as well) 2019-04-03 00:12:00 +11:00
Joseph Lizier d9db7a15ab Further clarifications for including NORMALISE and NOISE_LEVEL_TO_ADD properties to all mutual information calculators, and handling linear redundancy sub-cases 2019-04-03 00:07:05 +11:00