From 82bb3baf332268c314ebc6d931a4c20bce46e66a Mon Sep 17 00:00:00 2001 From: jlizier Date: Fri, 21 Oct 2016 00:16:56 +1100 Subject: [PATCH] Updating readme information and release notes ready for release --- readme-template.txt | 63 ++++++++++++++++++++++++++++---------------- version-template.txt | 2 +- 2 files changed, 42 insertions(+), 23 deletions(-) diff --git a/readme-template.txt b/readme-template.txt index bf5a137..0f4c9f3 100755 --- a/readme-template.txt +++ b/readme-template.txt @@ -1,6 +1,6 @@ Java Information Dynamics Toolkit (JIDT) Copyright (C) 2012-2014 Joseph T. Lizier -Copyright (C) 2014-2015 Joseph T. Lizier and Ipek Özdemir +Copyright (C) 2014-2016 Joseph T. Lizier and Ipek Özdemir Version @VERSION@ (see release notes below) @@ -31,22 +31,23 @@ along with this program. If not, see . Website ============= -Full information on the JIDT (usage, etc) is provided at the project page and wiki on google code: +Full information on the JIDT (usage, etc) is provided at the project page and wiki on github: -http://code.google.com/p/information-dynamics-toolkit/ +https://github.com/jlizier/jidt/ +https://github.com/jlizier/jidt/wiki ============= Installation ============= -"Full" description of any required installation is at: http://code.google.com/p/information-dynamics-toolkit/wiki/Installation +"Full" description of any required installation is at: https://github.com/jlizier/jidt/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 + 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 https://github.com/jlizier/jidt/wiki/JUnitTestCases Then just put the jar in a relevant location in your file structure. @@ -61,10 +62,10 @@ A research paper describing the toolkit is included in the top level directory - A tutorial, providing background to the information-theoretic measures, various estimators, and then to the JIDT toolkit itself is included in the tutorial folder (see "JIDT-TutorialSlides.pdf" for the tutorial slides, and "README-TutorialAndExercise.pdf" for further description of the tutorial exercises). 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. +They can also be generated using "ant javadocs" (useful if you are on a git clone). +Further, they will are posted on the web via links at https://github.com/jlizier/jidt/wiki/Documentation -The project wiki also contains further information on various aspects; see http://code.google.com/p/information-dynamics-toolkit/ to start. +The project wiki also contains further information on various aspects; see https://github.com/jlizier/jidt/wiki to start. Further documentation is provided by the Usage demo examples below. @@ -76,33 +77,33 @@ You can also join our email discussion group jidt-discuss at http://groups.googl Several sets of demonstration code are distributed with the toolkit: - a. demos/AutoAnalyser -- a GUI tool to compute transfer entropy on a chosen data set with the toolkit, and also automatically generate code in Java, Python and Matlab to show how to do this calculation with the toolkit. See description at https://code.google.com/p/information-dynamics-toolkit/wiki/AutoAnalyser + a. demos/AutoAnalyser -- a GUI tool to compute transfer entropy on a chosen data set with the toolkit, and also automatically generate code in Java, Python and Matlab to show how to do this calculation with the toolkit. See description at https://github.com/jlizier/jidt/wiki/AutoAnalyser - b. 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/java -- basic examples on easily using the Java toolkit -- run these from the shell scripts in this directory -- see description at https://github.com/jlizier/jidt/wiki/SimpleJavaExamples c. Several demo sets mirror the SimpleJavaExamples to demonstrate the use of the toolkit in non-Java environments: - i. 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 + i. demos/octave -- basic examples on easily using the Java toolkit from Octave or Matlab environments -- see description at https://github.com/jlizier/jidt/wiki/OctaveMatlabExamples - ii. 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 + ii. demos/python -- basic examples on easily using the Java toolkit from Python -- see description at https://github.com/jlizier/jidt/wiki/PythonExamples - 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 + iii. demos/r -- basic examples on easily using the Java toolkit from R -- see description at https://github.com/jlizier/jidt/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 + iv. demos/julia -- basic examples on easily using the Java toolkit from Julia -- see description at https://github.com/jlizier/jidt/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 + v. demos/clojure -- basic examples on easily using the Java toolkit from Clojure -- see description at https://github.com/jlizier/jidt/wiki/Clojure_Examples - 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 + 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 https://github.com/jlizier/jidt/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 + 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 https://github.com/jlizier/jidt/wiki/SchreiberTeDemos - 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 + 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 https://github.com/jlizier/jidt/wiki/DetectingInteractionLags - 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 + g. demos/java/InterregionalTransfer -- higher level example using collective transfer entropy to infer effective connections between "regions" of data -- see description at https://github.com/jlizier/jidt/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 + 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://github.com/jlizier/jidt/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 + 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 https://github.com/jlizier/jidt/wiki/JUnitTestCases ============= Citation @@ -112,7 +113,7 @@ Please cite your use of this toolkit as: 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 +A pre-print of this paper is distributed with this toolkit (InfoDynamicsToolkit.pdf) and is available at arXiv:1408.3270 (https://arxiv.org/abs/1408.3270) ============= Notices @@ -132,6 +133,24 @@ Notices for this software are found in the notices/JAMA directory. Release notes =============== +v1.3.1 21/10/2016 +----------------- +(after 385 commits recorded by github, repository as at https://github.com/jlizier/jidt/tree/269e263a84998807c5c02f36397b585a19205938 save for this file update) +Major update to TransferEntropyCalculatorDiscrete so as to implement arbirtray source and dest embeddings and source-dest delay; +Conditional TE calculators (continuous) handle empty conditional variables; +Added auto-embedding method for AIS and TE which maximises bias corrected AIS; +Added getNumSeparateObservations() method to TE calculators to make reconstructing/separating local values easier after multiple addObservations() calls; +Fixed kernel estimator classes to return proper densities, not probabilities; +Bug fix in mixed discrete-continuous MI (Kraskov) implementation; +Added simple interface for adding joint observations for MultiInfoCalculatorDiscrete +Including compiled class files for the AutoAnalyser demo in distribution; +Updated Python demo 1 to show use of numpy arrays with ints; +Added Python demo 7 and 9 for TE Kraskov with ensemble method and auto-embedding respectively; +Added Matlab/Octave example 10 for conditional TE via Kraskov (KSG) algorithm; +Added utilities to prepare for enhancing surrogate calculations with fast nearest neighbour search; +Minor bug patch to Python readFloatsFile utility; + + v1.3 10/7/2015 at r691 ---------------------- Added AutoAnalyser (Code Generator) GUI demo for MI and TE; diff --git a/version-template.txt b/version-template.txt index 94ff24f..819041f 100755 --- a/version-template.txt +++ b/version-template.txt @@ -1,6 +1,6 @@ Java Information Dynamics Toolkit Copyright (C) 2012-2014 Joseph T. Lizier -Copyright (C) 2014 Joseph T. Lizier and Ipek Özdemir +Copyright (C) 2014-2016 Joseph T. Lizier and Ipek Özdemir Version @VERSION@