mirror of https://github.com/jlizier/jidt
Updating readme information and release notes ready for release
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Java Information Dynamics Toolkit (JIDT)
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Copyright (C) 2012-2014 Joseph T. Lizier
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Copyright (C) 2014-2015 Joseph T. Lizier and Ipek Özdemir
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Copyright (C) 2014-2016 Joseph T. Lizier and Ipek Özdemir
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Version @VERSION@ (see release notes below)
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@ -31,22 +31,23 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
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Website
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=============
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Full information on the JIDT (usage, etc) is provided at the project page and wiki on google code:
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Full information on the JIDT (usage, etc) is provided at the project page and wiki on github:
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http://code.google.com/p/information-dynamics-toolkit/
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https://github.com/jlizier/jidt/
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https://github.com/jlizier/jidt/wiki
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=============
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Installation
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=============
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"Full" description of any required installation is at: http://code.google.com/p/information-dynamics-toolkit/wiki/Installation
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"Full" description of any required installation is at: https://github.com/jlizier/jidt/wiki/Installation
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However, if you are reading this file, you've downloaded a distribution and you're halfway there!
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There are no dependencies to download; unless:
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a. You don't have java installed - download it from http://www.java.com/
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b. You wish to build the project using the build.xml script - this requires ant: http://ant.apache.org/
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c. You wish to run the JUnit test cases - this requires JUnit: http://www.junit.org/ - for how to run JUnit with our ant script see http://code.google.com/p/information-dynamics-toolkit/wiki/JUnitTestCases
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c. You wish to run the JUnit test cases - this requires JUnit: http://www.junit.org/ - for how to run JUnit with our ant script see https://github.com/jlizier/jidt/wiki/JUnitTestCases
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Then just put the jar in a relevant location in your file structure.
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@ -61,10 +62,10 @@ A research paper describing the toolkit is included in the top level directory -
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A tutorial, providing background to the information-theoretic measures, various estimators, and then to the JIDT toolkit itself is included in the tutorial folder (see "JIDT-TutorialSlides.pdf" for the tutorial slides, and "README-TutorialAndExercise.pdf" for further description of the tutorial exercises).
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Javadocs for the toolkit are included in the full distribution at javadocs.
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They can also be generated using "ant javadocs" (useful if you are on an SVN view).
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Further, they will soon be posted on the web.
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They can also be generated using "ant javadocs" (useful if you are on a git clone).
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Further, they will are posted on the web via links at https://github.com/jlizier/jidt/wiki/Documentation
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The project wiki also contains further information on various aspects; see http://code.google.com/p/information-dynamics-toolkit/ to start.
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The project wiki also contains further information on various aspects; see https://github.com/jlizier/jidt/wiki to start.
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Further documentation is provided by the Usage demo examples below.
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@ -76,33 +77,33 @@ You can also join our email discussion group jidt-discuss at http://groups.googl
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Several sets of demonstration code are distributed with the toolkit:
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a. demos/AutoAnalyser -- a GUI tool to compute transfer entropy on a chosen data set with the toolkit, and also automatically generate code in Java, Python and Matlab to show how to do this calculation with the toolkit. See description at https://code.google.com/p/information-dynamics-toolkit/wiki/AutoAnalyser
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a. demos/AutoAnalyser -- a GUI tool to compute transfer entropy on a chosen data set with the toolkit, and also automatically generate code in Java, Python and Matlab to show how to do this calculation with the toolkit. See description at https://github.com/jlizier/jidt/wiki/AutoAnalyser
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b. demos/java -- basic examples on easily using the Java toolkit -- run these from the shell scripts in this directory -- see description at http://code.google.com/p/information-dynamics-toolkit/wiki/SimpleJavaExamples
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b. demos/java -- basic examples on easily using the Java toolkit -- run these from the shell scripts in this directory -- see description at https://github.com/jlizier/jidt/wiki/SimpleJavaExamples
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c. Several demo sets mirror the SimpleJavaExamples to demonstrate the use of the toolkit in non-Java environments:
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i. demos/octave -- basic examples on easily using the Java toolkit from Octave or Matlab environments -- see description at http://code.google.com/p/information-dynamics-toolkit/wiki/OctaveMatlabExamples
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i. demos/octave -- basic examples on easily using the Java toolkit from Octave or Matlab environments -- see description at https://github.com/jlizier/jidt/wiki/OctaveMatlabExamples
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ii. demos/python -- basic examples on easily using the Java toolkit from Python -- see description at http://code.google.com/p/information-dynamics-toolkit/wiki/PythonExamples
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ii. demos/python -- basic examples on easily using the Java toolkit from Python -- see description at https://github.com/jlizier/jidt/wiki/PythonExamples
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iii. demos/r -- basic examples on easily using the Java toolkit from R -- see description at http://code.google.com/p/information-dynamics-toolkit/wiki/R_Examples
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iii. demos/r -- basic examples on easily using the Java toolkit from R -- see description at https://github.com/jlizier/jidt/wiki/R_Examples
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iv. demos/julia -- basic examples on easily using the Java toolkit from Julia -- see description at http://code.google.com/p/information-dynamics-toolkit/wiki/JuliaExamples
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iv. demos/julia -- basic examples on easily using the Java toolkit from Julia -- see description at https://github.com/jlizier/jidt/wiki/JuliaExamples
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v. demos/clojure -- basic examples on easily using the Java toolkit from Clojure -- see description at http://code.google.com/p/information-dynamics-toolkit/wiki/Clojure_Examples
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v. demos/clojure -- basic examples on easily using the Java toolkit from Clojure -- see description at https://github.com/jlizier/jidt/wiki/Clojure_Examples
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d. demos/octave/CellularAutomata -- using the Java toolkit to plot local information dynamics profiles in cellular automata; the toolkit is run under Octave or Matlab -- see description at http://code.google.com/p/information-dynamics-toolkit/wiki/CellularAutomataDemos
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d. demos/octave/CellularAutomata -- using the Java toolkit to plot local information dynamics profiles in cellular automata; the toolkit is run under Octave or Matlab -- see description at https://github.com/jlizier/jidt/wiki/CellularAutomataDemos
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e. demos/octave/SchreiberTransferEntropyExamples -- recreates the transfer entropy examples in Schreiber's original paper presenting this measure; shows the correct parameter settings to reproduce these results -- see description at http://code.google.com/p/information-dynamics-toolkit/wiki/SchreiberTeDemos
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e. demos/octave/SchreiberTransferEntropyExamples -- recreates the transfer entropy examples in Schreiber's original paper presenting this measure; shows the correct parameter settings to reproduce these results -- see description at https://github.com/jlizier/jidt/wiki/SchreiberTeDemos
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f. demos/octave/DetectingInteractionLags -- demonstration of using the transfer entropy with source-destination lags; the demo is run under Octave or Matlab -- see description at http://code.google.com/p/information-dynamics-toolkit/wiki/DetectingInteractionLags
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f. demos/octave/DetectingInteractionLags -- demonstration of using the transfer entropy with source-destination lags; the demo is run under Octave or Matlab -- see description at https://github.com/jlizier/jidt/wiki/DetectingInteractionLags
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g. demos/java/InterregionalTransfer -- higher level example using collective transfer entropy to infer effective connections between "regions" of data -- see description at http://code.google.com/p/information-dynamics-toolkit/wiki/InterregionalTransfer
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g. demos/java/InterregionalTransfer -- higher level example using collective transfer entropy to infer effective connections between "regions" of data -- see description at https://github.com/jlizier/jidt/wiki/InterregionalTransfer
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h. demos/octave/NullDistributions -- investigating the correspondence between analytic and bootstrapped distributions for TE and MI under null hypotheses of no relationship; the demo is run under Octave or Matlab -- see description at https://code.google.com/p/information-dynamics-toolkit/wiki/NullDistributions
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h. demos/octave/NullDistributions -- investigating the correspondence between analytic and bootstrapped distributions for TE and MI under null hypotheses of no relationship; the demo is run under Octave or Matlab -- see description at https://github.com/jlizier/jidt/wiki/NullDistributions
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i. java/unittests -- the JUnit test cases for the Java toolkit are included in the distribution -- these case also be browsed to see simple use cases for the various calculators in the toolkit -- see description at http://code.google.com/p/information-dynamics-toolkit/wiki/JUnitTestCases
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i. java/unittests -- the JUnit test cases for the Java toolkit are included in the distribution -- these case also be browsed to see simple use cases for the various calculators in the toolkit -- see description at https://github.com/jlizier/jidt/wiki/JUnitTestCases
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=============
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Citation
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@ -112,7 +113,7 @@ Please cite your use of this toolkit as:
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Joseph T. Lizier, "JIDT: An information-theoretic toolkit for studying the dynamics of complex systems", Frontiers in Robotics and AI 1:11, 2014; doi:10.3389/frobt.2014.00011
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A pre-print of this paper is distributed with this toolkit (InfoDynamicsToolkit.pdf) and is available at arXiv:1408.3270
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A pre-print of this paper is distributed with this toolkit (InfoDynamicsToolkit.pdf) and is available at arXiv:1408.3270 (https://arxiv.org/abs/1408.3270)
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=============
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Notices
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@ -132,6 +133,24 @@ Notices for this software are found in the notices/JAMA directory.
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Release notes
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===============
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v1.3.1 21/10/2016
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-----------------
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(after 385 commits recorded by github, repository as at https://github.com/jlizier/jidt/tree/269e263a84998807c5c02f36397b585a19205938 save for this file update)
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Major update to TransferEntropyCalculatorDiscrete so as to implement arbirtray source and dest embeddings and source-dest delay;
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Conditional TE calculators (continuous) handle empty conditional variables;
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Added auto-embedding method for AIS and TE which maximises bias corrected AIS;
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Added getNumSeparateObservations() method to TE calculators to make reconstructing/separating local values easier after multiple addObservations() calls;
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Fixed kernel estimator classes to return proper densities, not probabilities;
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Bug fix in mixed discrete-continuous MI (Kraskov) implementation;
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Added simple interface for adding joint observations for MultiInfoCalculatorDiscrete
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Including compiled class files for the AutoAnalyser demo in distribution;
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Updated Python demo 1 to show use of numpy arrays with ints;
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Added Python demo 7 and 9 for TE Kraskov with ensemble method and auto-embedding respectively;
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Added Matlab/Octave example 10 for conditional TE via Kraskov (KSG) algorithm;
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Added utilities to prepare for enhancing surrogate calculations with fast nearest neighbour search;
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Minor bug patch to Python readFloatsFile utility;
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v1.3 10/7/2015 at r691
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----------------------
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Added AutoAnalyser (Code Generator) GUI demo for MI and TE;
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Java Information Dynamics Toolkit
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Copyright (C) 2012-2014 Joseph T. Lizier
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Copyright (C) 2014 Joseph T. Lizier and Ipek Özdemir
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Copyright (C) 2014-2016 Joseph T. Lizier and Ipek Özdemir
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Version @VERSION@
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