mirror of https://github.com/jlizier/jidt
107 lines
4.9 KiB
Plaintext
Executable File
107 lines
4.9 KiB
Plaintext
Executable File
Java Information Dynamics Toolkit
|
|
Copyright (C) 2012 Joseph T. Lizier
|
|
|
|
Version @VERSION@
|
|
|
|
=============
|
|
License
|
|
=============
|
|
|
|
This program is free software: you can redistribute it and/or modify
|
|
it under the terms of the GNU General Public License as published by
|
|
the Free Software Foundation, either version 3 of the License, or
|
|
(at your option) any later version.
|
|
|
|
This program is distributed in the hope that it will be useful,
|
|
but WITHOUT ANY WARRANTY; without even the implied warranty of
|
|
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
|
GNU General Public License for more details.
|
|
|
|
You should have received a copy of the GNU General Public License
|
|
along with this program. If not, see <http://www.gnu.org/licenses/>.
|
|
|
|
=============
|
|
Citation
|
|
=============
|
|
|
|
Please cite your use of this toolkit as:
|
|
|
|
Joseph T. Lizier, "JIDT: An information-theoretic toolkit for studying the dynamics of complex systems", 2012, https://code.google.com/p/information-dynamics-toolkit/
|
|
|
|
=============
|
|
Website
|
|
=============
|
|
|
|
Full information on the JIDT (usage, etc) is provided at the project page on google code:
|
|
|
|
http://code.google.com/p/information-dynamics-toolkit/
|
|
|
|
=============
|
|
Installation
|
|
=============
|
|
|
|
"Full" description of any required installation is at: http://code.google.com/p/information-dynamics-toolkit/wiki/Installation
|
|
|
|
However, if you are reading this file, you've downloaded a distribution and you're halfway there!
|
|
|
|
There are no dependencies to download; unless:
|
|
a. You don't have java installed - download it from http://www.java.com/
|
|
b. You wish to build the project using the build.xml script - this requires ant: http://ant.apache.org/
|
|
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
|
|
|
|
Then just put the jar in a relevant location in your file structure.
|
|
|
|
That's it.
|
|
|
|
=============
|
|
Documentation
|
|
=============
|
|
|
|
A research paper describing the toolkit is included in the top level directory -- "InfoDynamicsToolkit.pdf".
|
|
|
|
Javadocs for the toolkit are included in the full distribution at javadocs.
|
|
They can also be generated using "ant javadocs" (useful if you are on an SVN view).
|
|
Further, they will soon be posted on the web.
|
|
|
|
Further documentation is provided by the Usage examples below.
|
|
|
|
=============
|
|
Usage
|
|
=============
|
|
|
|
Several sets of demonstration code are distributed with the toolkit:
|
|
|
|
a. 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
|
|
|
|
b. 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
|
|
|
|
c. 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
|
|
|
|
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
|
|
|
|
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
|
|
|
|
f. demos/octave/DetectingInteractionLags -- brief examples using the transfer entropy to examine source-delay interaction lags. Documentation to come soon; in the interim, see header comments in the .m files.
|
|
|
|
g. 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
|
|
|
|
=============
|
|
Notices
|
|
=============
|
|
|
|
This project includes modified files from the Apache Commons Math library -- http://commons.apache.org/proper/commons-math/
|
|
This Apache 2 software is now included as a derivative work in this GPLv3 licensed JIDT project, as per: http://www.apache.org/licenses/GPL-compatibility.html
|
|
Notices and license for this software are found in the notices/commons-math directory.
|
|
|
|
The project includes adapted code from the JAMA project -- http://math.nist.gov/javanumerics/jama/
|
|
Notices and license for this software are found in the notices/JAMA directory.
|
|
|
|
The project includes adapted code from the octave-java package of the Octave-Forge project -- http://octave.sourceforge.net/java/
|
|
Notices for this software are found in the notices/JAMA directory.
|
|
|
|
|
|
=============
|
|
|
|
Joseph T. Lizier, @DATE@
|
|
|