diff --git a/InfoDynamicsToolkit.pdf b/InfoDynamicsToolkit.pdf
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diff --git a/build.xml b/build.xml
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--- a/build.xml
+++ b/build.xml
@@ -5,7 +5,7 @@
-
+
diff --git a/readme-template.txt b/readme-template.txt
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--- 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