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895 Commits

Author SHA1 Message Date
jlizier ee3ce5dd51 Corrected function signature in loadxls2d for fish data loading 2022-09-07 09:17:51 +10:00
jlizier 8bc6d87d9b Adding scripts to create and start a python virtual environment with jpype1 etc installed 2022-09-06 10:27:38 +10:00
jlizier 348587ee59 Python demo 1 - removing deprecated type call in script 2022-09-06 10:27:08 +10:00
jlizier 65aa685d11 Fixing python demo 6, where the multivariate array conversion wasn't working for Python3 with Jpype. Fixed to use recommended array conversion as per UseInPython wiki. Addresses issue raised in PR #87 also. 2022-09-05 23:13:52 +10:00
jlizier 2b0a5cb943 Updated mixed-continiuous CMI KSG estimator, for the bias correction based on number of continuous variables. This was identified from testing, and aligns with testing so far. 2022-09-05 17:51:49 +10:00
jlizier 72024c7299 Updating demo PDFs and version number ahead of new v1.6 distribution 2022-09-05 17:43:14 +10:00
Joseph Lizier d750a737be
Removing what appears to be an old test file from the integrated Spiking TE code from David 2022-09-05 17:08:10 +10:00
jlizier 003a187a7a moving the demos using spiking TE estimator into different folder locations 2022-09-05 15:00:05 +10:00
Joseph Lizier fcfcca962b
Adding David Shorten to the authors list 2022-09-05 14:54:30 +10:00
Joseph Lizier 27f9cccf65
Don't need code for old way of doing spiking TE estimation 2022-09-05 14:45:50 +10:00
Joseph Lizier 47be5df74b
editing comment on how to implement dynamic correlation exclusions in spiking TE estimator 2022-09-05 14:43:18 +10:00
Joseph Lizier e747e8aa93
Merge pull request #93 from dpshorten/master 
Spike train TE estimation
 2022-09-05 14:38:21 +10:00
Joseph Lizier 8db0c12c37
Brief update to header comments on spiking TE example 2022-09-05 14:32:14 +10:00
jlizier 05248ef105 Extra fixing windows paths generated from AutoAnalyser to be properly escaped in data filename for Python/Matlab 2022-09-01 15:50:27 +10:00
jlizier c233485c90 Fixing windows paths generated from AutoAnalyser to be properly escaped 2022-09-01 15:28:28 +10:00
jlizier 9c2a25492f Clarifying where Econometrics Toolbox is required for Flocking demo 2022-08-30 12:38:10 +10:00
jlizier 5398785a67 Adding comment to Flocking demo that Econometrics Toolbox may be required 2022-08-30 12:37:03 +10:00
jlizier d250c6b24c Updating error comment in Flocking demo 2022-08-30 12:33:55 +10:00
dpshorten dc3874c72b
Update net_inf.py 
Comments to the net_inf.py file.
 2022-08-25 16:12:35 +09:30
Joseph Lizier a040cde6da
Adding header comment to spk_to_pk.py and changing filename 2022-08-25 15:24:51 +10:00
jlizier 0935806338 Moving ant targets up to Java 7 instead of Java 6 (newer java versions are complaining now that 6 is too old to target) 2022-08-16 15:50:17 +10:00
David Shorten bcefd900c4 moved the location of the Python testing script 2022-08-04 16:06:25 +09:30
David Shorten a398c925a8 added python for spiking network inference 2022-08-04 16:03:12 +09:30
jlizier 9dfafda555 Merge branch 'master' of github.com:jlizier/jidt 2022-06-16 21:33:41 +10:00
jlizier 2714650cfa Amending Kraskov (KSG) MI estimators to have an experimental method to provide conditional entropy of the first variable given the second. Works by removing the Kozachenko Leonenko entropy of variable 1 from the MI, using the same kNN radii as the MI estimator. Includes Unit tests to provide some initial validation. 2022-06-16 21:29:29 +10:00
Joseph Lizier 2c72eb05f9
Specified AntScripts for quick build 2022-06-14 09:54:49 +10:00
jlizier 25159009ca updating max entropy discretisation to gracefully handle NaNs in the input (which shouldn't be there anyway) 2022-06-09 12:39:59 +10:00
Joseph Lizier e9fc39c4c2 Added simple Matlab script implementing the muiltivariate/iterative/greedy algorithm for effective network inference. Is a simplified version of the full algorithm in IDTxl, for demonstration purposes. Also includes calls to Oliver Cliff's toolkit for granger causality, which won't be functional for users who have not downloaded that; will be removed when the autocorrelation correction is added to JIDT for linear. 2022-04-08 10:49:57 +10:00
Joseph Lizier 899a5607f8 Merge branch 'master' of github.com:jlizier/JIDT 2022-03-31 12:16:21 +11:00
Joseph Lizier 41361417ae Updates to flocking demo including plotting local TEs per individual per time frame 2022-03-31 12:14:16 +11:00
David Shorten c068c8308d improving jittered surrogates 2022-02-25 18:49:12 +11:00
David Shorten 285c95947a integrating artemis changes 2022-02-22 14:39:15 +11:00
David Shorten b4e32727c9 merge 2022-02-22 11:55:09 +11:00
Joseph Lizier 0e33393cdc
Merge pull request #86 from pmediano/master 
Thanks Pedro, and sorry to take so long to attend to this
 2021-11-15 12:08:57 +11:00
Joseph Lizier b02760ddd3 Adding overloads on setObservations and addObservations for MI and TE calculators to handle one variable univariate and one variable multivariate 2021-11-15 10:58:59 +11:00
Joseph Lizier 8e55cf05d9 Merge branch 'master' of github.com:jlizier/JIDT 2021-11-02 23:13:59 +11:00
Joseph Lizier 7d7291fb9d Implementing Analytic null distributions for discrete conditional TE estimator 2021-11-02 23:11:45 +11:00
Joseph Lizier e5b223606c
Added YouTube image and link to Course to README 2021-10-11 23:12:39 +11:00
Joseph Lizier a65db51b78 Merge branch 'master' of github.com:jlizier/JIDT 2021-10-11 23:07:07 +11:00
Joseph Lizier 9c31807283 Adding image for the YouTube playlist 2021-10-11 23:05:53 +11:00
Joseph Lizier b4ab18f6c6
Adding link to Course to repo home page 2021-10-11 15:40:10 +11:00
Joseph Lizier 6f43dfb620 Altering the python-java jpype data conversion in AutoAnalyser to work properly with jpype 0.7 and upwards 2021-10-08 16:03:14 +11:00
Joseph Lizier f8eb84e183 Merge branch 'master' of github.com:jlizier/JIDT 2021-10-08 11:30:54 +11:00
Joseph Lizier 21ae0bdeaa Fixing logic error in printing whether GPU calculation was falling back to CPU 2021-10-08 11:28:37 +11:00
Joseph Lizier d101a9f2ff
Update README.md 2021-10-01 17:33:24 +10:00
Joseph Lizier ccf920d3a8
Added readme file to course folder 2021-10-01 17:32:21 +10:00
Joseph Lizier 898a04904c Added Matlab script to launch the AutoAnalyser - will be useful for Matlab users who don't have a separate JRE installed 2021-09-09 11:12:46 +10:00
Joseph Lizier 2caab8593e Adding option for generated CA cells to be stochastically altered in CA utility code 2021-09-06 12:51:14 +10:00
Joseph Lizier 5da70db3ae Updating readme pdfs for various demos from the JIDT wiki 2021-09-06 12:49:50 +10:00
Joseph Lizier 650159661d Patching conditional MI calculator to properly allow null or empty conditionals if dimension of conditionals is 0 2021-09-06 10:23:31 +10:00