diff --git a/InfoDynamicsToolkit.pdf b/InfoDynamicsToolkit.pdf new file mode 100755 index 0000000..349b4ec Binary files /dev/null and b/InfoDynamicsToolkit.pdf differ diff --git a/build.xml b/build.xml index 4bfde1f..4da9e99 100755 --- a/build.xml +++ b/build.xml @@ -5,7 +5,7 @@ - + diff --git a/readme-template.txt b/readme-template.txt index c37f249..437d93f 100755 --- a/readme-template.txt +++ b/readme-template.txt @@ -1,8 +1,14 @@ -Java Information Dynamics Toolkit +Java Information Dynamics Toolkit (JIDT) Copyright (C) 2012 Joseph T. Lizier Version @VERSION@ +JIDT provides a standalone, open source code Java implementation (usable in Matlab, Octave and Python) of information-theoretic measures of distributed computation in complex systems: i.e. information storage, transfer and modification. + +This includes implementations for: +- both discrete and continuous-valued variables, principally for the measures transfer entropy, mutual information and active information storage; +- using various types of estimators (e.g. Kraskov-Stögbauer-Grassberger estimators, kernel estimation, linear-Gaussian). + ============= License ============= @@ -20,14 +26,6 @@ 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 . -============= - 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 ============= @@ -65,6 +63,8 @@ Further, they will soon be posted on the web. Further documentation is provided by the Usage examples below. +You can also join our email discussion group jidt-discuss at http://groups.google.com/d/forum/jidt-discuss + ============= Usage ============= @@ -81,9 +81,21 @@ Several sets of demonstration code are distributed with the toolkit: 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. + 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 - 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 + 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 + + 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 + + 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 + +============= + 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, arXiv: ============= Notices