diff --git a/InfoDynamicsToolkit.pdf b/InfoDynamicsToolkit.pdf index 349b4ec..29daf4e 100755 Binary files a/InfoDynamicsToolkit.pdf and b/InfoDynamicsToolkit.pdf differ diff --git a/build.xml b/build.xml index 77bcab0..074b604 100755 --- a/build.xml +++ b/build.xml @@ -5,7 +5,7 @@ - + diff --git a/demos/clojure/README-ClojureExamples.pdf b/demos/clojure/README-ClojureExamples.pdf new file mode 100755 index 0000000..2938bc5 Binary files /dev/null and b/demos/clojure/README-ClojureExamples.pdf differ diff --git a/demos/java/README-SimpleJavaDemos.pdf b/demos/java/README-SimpleJavaDemos.pdf index 9ddfdfe..cdbe5ac 100755 Binary files a/demos/java/README-SimpleJavaDemos.pdf and b/demos/java/README-SimpleJavaDemos.pdf differ diff --git a/demos/julia/README-JuliaExamples.pdf b/demos/julia/README-JuliaExamples.pdf new file mode 100755 index 0000000..1219975 Binary files /dev/null and b/demos/julia/README-JuliaExamples.pdf differ diff --git a/demos/octave/README-OctaveMatlabDemos.pdf b/demos/octave/README-OctaveMatlabDemos.pdf index a4ec012..eade184 100755 Binary files a/demos/octave/README-OctaveMatlabDemos.pdf and b/demos/octave/README-OctaveMatlabDemos.pdf differ diff --git a/demos/octave/SchreiberTransferEntropyExamples/README-SchreiberTeDemos.pdf b/demos/octave/SchreiberTransferEntropyExamples/README-SchreiberTeDemos.pdf index a9460cf..09758cd 100755 Binary files a/demos/octave/SchreiberTransferEntropyExamples/README-SchreiberTeDemos.pdf and b/demos/octave/SchreiberTransferEntropyExamples/README-SchreiberTeDemos.pdf differ diff --git a/demos/python/README-PythonDemos.pdf b/demos/python/README-PythonDemos.pdf index 4973cf7..f067615 100755 Binary files a/demos/python/README-PythonDemos.pdf and b/demos/python/README-PythonDemos.pdf differ diff --git a/demos/r/README-R_Demos.pdf b/demos/r/README-R_Demos.pdf new file mode 100755 index 0000000..edb3221 Binary files /dev/null and b/demos/r/README-R_Demos.pdf differ diff --git a/readme-template.txt b/readme-template.txt index 1e89fa4..8bd33f0 100755 --- a/readme-template.txt +++ b/readme-template.txt @@ -1,5 +1,6 @@ Java Information Dynamics Toolkit (JIDT) -Copyright (C) 2012 Joseph T. Lizier +Copyright (C) 2012-2014 Joseph T. Lizier +Copyright (C) 2014 Joseph T. Lizier and Ipek Özdemir Version @VERSION@ (see release notes below) @@ -83,6 +84,10 @@ Several sets of demonstration code are distributed with the toolkit: 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 + 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 + + 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 + c. 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 d. 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 @@ -101,7 +106,9 @@ Several sets of demonstration code are distributed with the toolkit: Please cite your use of this toolkit as: -Joseph T. Lizier, "JIDT: An information-theoretic toolkit for studying the dynamics of complex systems", 2014, arXiv:1408.3270 +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 + +A pre-print of this paper is distributed with this toolkit (InfoDynamicsToolkit.pdf) and is available at arXiv:1408.3270 ============= Notices @@ -121,6 +128,16 @@ Notices for this software are found in the notices/JAMA directory. Release notes =============== +v1.1 14/11/2014 at r566 +----------------------- +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; + + v1.0 14/8/2014 at r434 ---------------------- Added the draft of the paper on the toolkit to the release;