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+# Java Information Dynamics Toolkit (JIDT)
+
+Copyright (C) 2012-2014 [Joseph T. Lizier](http://lizier.me/joseph/); 2014-2015 [Joseph T. Lizier](http://lizier.me/joseph/) and Ipek Özdemir
+
+*JIDT* provides a stand-alone, open-source code Java implementation (also usable in [Matlab, Octave](UseInOctaveMatlab.md), [Python](UseInPython.md), [R](UseInR.md), [Julia](UseInJulia.md) and [Clojure](UseInClojure.md)) of information-theoretic measures of distributed computation in complex systems: i.e. information storage, transfer and modification.
+
+JIDT includes implementations:
+ * principally for the measures *transfer entropy*, *mutual information*, and their conditional variants, as well as *active information storage*, entropy, etc;
+ * for both _discrete_ and _continuous_-valued data;
+ * using various types of estimators (e.g. _Kraskov-Stögbauer-Grassberger estimators_, _box-kernel estimation_, _linear-Gaussian_),
+as described in full at ImplementedMeasures.
+
+JIDT is distributed under the [GNU GPL v3 license](http://www.gnu.org/licenses/gpl.html) (or later).
+
+# Getting started
+
+ 1. [Download](Downloads.md) and [Installation](Installation.md) is very easy!
+   1. _Quick start_: download the latest [v1.3 full distribution](http://lizier.me/joseph/software/jidt/download.php?file=infodynamics-dist-1.3.zip) (suitable for all platforms) and see the readme.txt file therein.
+ 1. [Documentation](Documentation.md) including: the paper describing JIDT at [arXiv:1408.3270](http://arxiv.org/abs/1408.3270) (distributed with the toolkit), a [Tutorial](Tutorial.md), and [Javadocs (v1.3 here)](http://lizier.me/joseph/software/jidt/javadocs/v1.3/);
+ 1. [Demos](Demos.md) are included with the full distribution, including a [GUI app](AutoAnalyser.md) for automatic analysis and code generation, [simple java demos](SimpleJavaExamples.md) and [cellular automata (CA) demos](CellularAutomataDemos.md).
+  1. These Java tools can easily be used in [Matlab/Octave](OctaveMatlabExamples.md), [Python](PythonExamples.md), [R](R_Examples.md), [Julia](JuliaExamples.md) and [Clojure](Clojure_Examples.md)! (click on each language here for examples)
+
+For further information or announcements:
+ * Join our discussion group: http://groups.google.com/d/forum/jidt-discuss
+ * See also the [FAQs](FAQs.md)
+ * Follow [@infodynamicstkt](http://twitter.com/infodynamicstkt) on twitter
+
+# Citation
+
+Please *cite* your use of this toolkit as:
+
+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](http://dx.doi.org/10.3389/frobt.2014.00011) (pre-print: [arXiv:1408.3270](http://arxiv.org/abs/1408.3270))
+
+And please [let me know](mailto:joseph.lizier_AT_gmail.com.md) about any publications resulting from its use!
+
+See other PublicationsUsingThisToolkit.
+
+# News
+
+_19/7/2015_ - New jar and full distribution files available for *release v1.3*; Changes for v1.3 include:
+Added AutoAnalyser (Code Generator) GUI demo for MI and TE;
+Added auto-embedding capability via Ragwitz criteria for AIS and TE calculators (KSG estimators);
+Added Java demo 9 for showcasing use of Ragwitz auto-embedding;
+Adding small amount of noise to data in all KSG estimators now by default (may be disabled via setProperty());
+Added getProperty() methods for all conditional MI and TE calculators;
+Upgraded Python demos for Python 3 compatibility;
+Fixed bias correction on mixed discrete-continuous KSG calculators;
+Updated the tutorial slides to those in use for ECAL 2015 JIDT tutorial.
+
+_12/2/2015_ - New jar and full distribution files available for *release v1.2.1*; Changes for v1.2.1 include:
+Added tutorial slides, description of exercises and sample exercise solutions;
+Made jar target Java 1.6;
+Added Schreiber TE heart-breath rate with KSG estimator demo code for Python.
+
+_28/1/2015_ - New jar and full distribution files available for *release v1.2*; Changes for v1.2 include:
+Dynamic correlation exclusion, or Theiler window, added to all Kraskov estimators;
+Added univariate MI calculation to simple demo 6;
+Added Java code for Schreiber TE heart-breath rate with KSG estimator, ready for use as a template in Tutorial;
+Patch for crashes in KSG conditional MI algorithm 2.
+
+_20/11/2014_ - New jar and full distribution files available for *release v1.1*; Changes for v1.1 include:
+Implemented Fast Nearest Neighbour Search for Kraskov-Stögbauer-Grassberger (KSG) estimators for MI, conditional MI, TE, conditional TE, AIS, Predictive info, and multi-information. This includes a general (multivariate) k-d tree implementation;
+Added multi-threading (using all available processors by default) for the KSG estimators -- code contributed by Ipek Özdemir;
+Added Predictive information / Excess entropy implementations for KSG, kernel and Gaussian estimators;
+Added R, Julia, and Clojure demos;
+Added Windows batch files for the Simple Java Demos;
+Added property for adding a small amount of noise to data in all KSG estimators;
+
+_15/8/2014_ JIDT paper finalised and uploaded to the website and [arXiv:1408.3270](http://arxiv.org/abs/1408.3270)
+
+_14/8/2014_ - New jar and full distribution files available for our *first official release, v1.0*; Changes for v1.0 include: Added the draft of the paper on the toolkit to the release;
+Javadocs made ready for release;
+Switched source->destination arguments for discrete TE calculators to be with source first in line with continuous calculators;
+Renamed all discrete calculators to have Discrete suffix -- TE and conditional TE calculators also renamed to remove "Apparent" prefix and change "Complete" to "Conditional";
+Kraskov estimators now using 4 nearest neighbours by default;
+Unit test for Gaussian TE against ChaLearn Granger causality measurement;
+Added Schreiber TE demos; Interregional transfer demos; documentation for Interaction lag demos; added examples 7 and 8 to Simple Java demos;
+Added property to add noise to data for Kraskov MI;
+Added derivation of Apache Commons Math code for chi square distribution, and included relevant notices in our release;
+Inserted translation class for arrays between Octave and Java;
+Added analytic statistical significance calculation to Gaussian calculators and discrete TE;
+Corrected Kraskov algorithm 2 for conditional MI to follow equation in Wibral et al. 2014.
+
+_20/4/2014_ - New jar and full distribution files available for v0.2.0; Moved downloads to http://lizier.me/joseph/ since google code has stopped the download facility here :(. Changes for v0.2.0 include: Rearchitected (most) Transfer Entropy and Multivariate TE calculators to use an underlying conditional mutual information calculator, and have arbitrary embedding delay, source-dest delay; this includes moving Kraskov-Grassberger Transfer Entropy calculator to use a single conditional mutual information estimator instead of two mutual information estimators; Rearchitected (most) Active Information Storage calculators to use an underlying mutual information calculator; Added Conditional Transfer Entropy calculators using underlying conditional mutual information calculators; Moved mixed discrete-continuous calculators to a new "mixed" package; bug fixes.
+
+_11/9/2013_ - New jar and full distribution files available for v0.1.4; added scripts to generate CA figures for 2013 book chapters; added general Java demo code; added Python demo code; made Octave/Matlab demos and CA demos properly compatible for Matlab; added extra Octave/Matlab general demos; added more unit tests for MI and conditional MI calculators, including against results from Wibral's TRENTOOL; bug fixes.
+
+_11/9/2013_ - New CA demo scripts for several review book chapters we're preparing in 2013 have been uploaded - see CellularAutomataDemos.
+
+_4/6/2013_ - Added instructions on how to [use in python](UseInPython.md) and several PythonExamples.
+
+_13/01/2013_ - New jar and full distribution files available for v0.1.3; existing Octave/Matlab demo code made compatible with Matlab; several bug fixes, including using max norm by default in Kraskov calculator (instead of requiring this to be set explicitly); more unit tests (including against results from Kraskov's own MI implementation)
+
+_19/11/2012_ - New jar and full distribution files available for v0.1.2, including demo code for two newly submitted papers
+
+_31/10/2012_ - Jar and full distribution files available for v0.1.1 (first distribution)
+
+_7/5/2012_ - JIDT project created and code uploaded