Demos

List of demonstration code sets distributed with the toolkit

Demos

Several sets of demonstration code are distributed with the toolkit (as well as sample data sets in the demos/data folder). Links to their wiki pages and their location in the distribution are given below:

• AutoAnalyser -- demos/AutoAnalyser -- a GUI tool to compute transfer entropy on a chosen data set with the toolkit (defaulting to those in the demos/data folder), and also automatically generate code in Java, Python and Matlab to show how to do this calculation with the toolkit.
• SimpleJavaExamples -- demos/java -- a set of basic examples using the Java toolkit;
• Several demo sets mirror the SimpleJavaExamples to demonstrate the use of the toolkit in non-Java environments:
  • OctaveMatlabExamples -- demos/octave -- basic examples on using the Java toolkit from Octave or Matlab environments;
  • PythonExamples -- demos/python -- basic examples on using the Java toolkit from Python using the JPype interface;
  • R_Examples -- demos/r -- basic examples on using the Java toolkit from R using the rJava interface;
  • JuliaExamples -- demos/julia -- basic examples on using the Java toolkit from Julia;
  • Clojure_Examples -- demos/clojure/examples -- basic examples on using the Java toolkit from Clojure;
• GPU -- describes how to use the GPU implementation of the KSG estimators (readme stored in cuda folder).
• SchreiberTeDemos -- demos/octave/SchreiberTransferEntropyExamples -- using the toolkit to reproduce the transfer entropy examples originally included in Schreiber's 2000 paper introducing transfer entropy;
• CellularAutomataDemos -- demos/octave/CellularAutomata -- using the Java toolkit to plot local information dynamics profiles in cellular automata; the demo is run under Octave or Matlab;
• Flocking/Swarming -- demos/octave/FlockingAnalysis -- a set of scripts to compute transfer entropy (and active information storage) for pairwise interactions within a flock or swarm, assuming the individuals are homogeneous
• DetectingInteractionLags -- demos/octave/DetectingInteractionLags -- demonstration of using the transfer entropy with source-destination lags; the demo is run under Octave or Matlab;
• InterregionalTransfer -- demos/java/interregionalTransfer -- higher level example using collective transfer entropy to infer effective connections between "regions" of data;
• NullDistributions -- demos/octave/NullDistributions -- investigating the correspondence between analytic and resampled distributions for TE and MI under null hypotheses of no relationship; the demo is run under Octave or Matlab;

You can also review the JUnitTestCases -- the test cases for the Java toolkit included in the distribution -- these case also be browsed to see simple use cases for the toolkit.

Extras

You may also be interested in several extra features that the toolkit has (in addition to the information dynamics calculators); e.g. Octave text file format reading and writing, matrix manipulation, mathematical functions, etc.