Adding GPLv3 license statement to all code headers in the demos; also adding readme for use of octave-java code; correcting references to papers from CA code

demos/java/infodynamics/demos/Example1TeBinaryData.java

@@ -1,3 +1,21 @@
+/*
+ *  Java Information Dynamics Toolkit (JIDT)
+ *  Copyright (C) 2012, Joseph T. Lizier
+ *  
+ *  This program is free software: you can redistribute it and/or modify
+ *  it under the terms of the GNU General Public License as published by
+ *  the Free Software Foundation, either version 3 of the License, or
+ *  (at your option) any later version.
+ *  
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  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 <http://www.gnu.org/licenses/>.
+ */
+
 package infodynamics.demos;
 
 import infodynamics.utils.RandomGenerator;

demos/java/infodynamics/demos/Example2TeMultidimBinaryData.java

@@ -1,3 +1,21 @@
+/*
+ *  Java Information Dynamics Toolkit (JIDT)
+ *  Copyright (C) 2012, Joseph T. Lizier
+ *  
+ *  This program is free software: you can redistribute it and/or modify
+ *  it under the terms of the GNU General Public License as published by
+ *  the Free Software Foundation, either version 3 of the License, or
+ *  (at your option) any later version.
+ *  
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  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 <http://www.gnu.org/licenses/>.
+ */
+
 package infodynamics.demos;
 
 import infodynamics.utils.RandomGenerator;

demos/java/infodynamics/demos/Example3TeContinuousDataKernel.java

@@ -1,3 +1,21 @@
+/*
+ *  Java Information Dynamics Toolkit (JIDT)
+ *  Copyright (C) 2012, Joseph T. Lizier
+ *  
+ *  This program is free software: you can redistribute it and/or modify
+ *  it under the terms of the GNU General Public License as published by
+ *  the Free Software Foundation, either version 3 of the License, or
+ *  (at your option) any later version.
+ *  
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  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 <http://www.gnu.org/licenses/>.
+ */
+
 package infodynamics.demos;
 
 import infodynamics.utils.EmpiricalMeasurementDistribution;

demos/java/infodynamics/demos/Example4TeContinuousDataKraskov.java

@@ -1,3 +1,21 @@
+/*
+ *  Java Information Dynamics Toolkit (JIDT)
+ *  Copyright (C) 2012, Joseph T. Lizier
+ *  
+ *  This program is free software: you can redistribute it and/or modify
+ *  it under the terms of the GNU General Public License as published by
+ *  the Free Software Foundation, either version 3 of the License, or
+ *  (at your option) any later version.
+ *  
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  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 <http://www.gnu.org/licenses/>.
+ */
+
 package infodynamics.demos;
 
 import infodynamics.utils.RandomGenerator;

demos/java/infodynamics/demos/Example5TeBinaryMultivarTransfer.java

@@ -1,3 +1,21 @@
+/*
+ *  Java Information Dynamics Toolkit (JIDT)
+ *  Copyright (C) 2012, Joseph T. Lizier
+ *  
+ *  This program is free software: you can redistribute it and/or modify
+ *  it under the terms of the GNU General Public License as published by
+ *  the Free Software Foundation, either version 3 of the License, or
+ *  (at your option) any later version.
+ *  
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  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 <http://www.gnu.org/licenses/>.
+ */
+
 package infodynamics.demos;
 
 import infodynamics.utils.MatrixUtils;

demos/java/infodynamics/demos/Example6LateBindingMutualInfo.java

@@ -1,3 +1,21 @@
+/*
+ *  Java Information Dynamics Toolkit (JIDT)
+ *  Copyright (C) 2012, Joseph T. Lizier
+ *  
+ *  This program is free software: you can redistribute it and/or modify
+ *  it under the terms of the GNU General Public License as published by
+ *  the Free Software Foundation, either version 3 of the License, or
+ *  (at your option) any later version.
+ *  
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  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 <http://www.gnu.org/licenses/>.
+ */
+
 package infodynamics.demos;
 
 import infodynamics.measures.continuous.MutualInfoCalculatorMultiVariate;

demos/java/infodynamics/demos/Example7EnsembleMethodTeContinuousDataKraskov.java

@@ -1,3 +1,21 @@
+/*
+ *  Java Information Dynamics Toolkit (JIDT)
+ *  Copyright (C) 2012, Joseph T. Lizier
+ *  
+ *  This program is free software: you can redistribute it and/or modify
+ *  it under the terms of the GNU General Public License as published by
+ *  the Free Software Foundation, either version 3 of the License, or
+ *  (at your option) any later version.
+ *  
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  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 <http://www.gnu.org/licenses/>.
+ */
+
 package infodynamics.demos;
 
 import infodynamics.utils.RandomGenerator;

demos/java/infodynamics/demos/Example8TeContinuousDataByBinning.java

@@ -1,3 +1,21 @@
+/*
+ *  Java Information Dynamics Toolkit (JIDT)
+ *  Copyright (C) 2012, Joseph T. Lizier
+ *  
+ *  This program is free software: you can redistribute it and/or modify
+ *  it under the terms of the GNU General Public License as published by
+ *  the Free Software Foundation, either version 3 of the License, or
+ *  (at your option) any later version.
+ *  
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  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 <http://www.gnu.org/licenses/>.
+ */
+
 package infodynamics.demos;
 
 import infodynamics.utils.MatrixUtils;

demos/octave/CellularAutomata/DirectedMeasuresChapterDemo2013.m

@@ -1,6 +1,25 @@
+%%
+%%  Java Information Dynamics Toolkit (JIDT)
+%%  Copyright (C) 2012, Joseph T. Lizier
+%%  
+%%  This program is free software: you can redistribute it and/or modify
+%%  it under the terms of the GNU General Public License as published by
+%%  the Free Software Foundation, either version 3 of the License, or
+%%  (at your option) any later version.
+%%  
+%%  This program is distributed in the hope that it will be useful,
+%%  but WITHOUT ANY WARRANTY; without even the implied warranty of
+%%  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+%%  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 <http://www.gnu.org/licenses/>.
+%%
+
 % To recreate the plots in:
 % J. T. Lizier, "Measuring the dynamics of information processing on a local scale in time and space",
-%  accepted for "Directed Information Measures in Neuroscience", edited by M. Wibral, R. Vicente, J. T. Lizier, to be published by Springer, 2013
+%  in "Directed Information Measures in Neuroscience", edited by M. Wibral, R. Vicente, J. T. Lizier,
+%  pp. 161-193, Springer, Berlin/Heidelberg, 2014; doi: 10.1007/978-3-642-54474-3_7
 
 clear all;
 

demos/octave/CellularAutomata/GsoChapterDemo2013.m

@@ -1,6 +1,23 @@
+%%
+%%  Java Information Dynamics Toolkit (JIDT)
+%%  Copyright (C) 2012, Joseph T. Lizier
+%%  
+%%  This program is free software: you can redistribute it and/or modify
+%%  it under the terms of the GNU General Public License as published by
+%%  the Free Software Foundation, either version 3 of the License, or
+%%  (at your option) any later version.
+%%  
+%%  This program is distributed in the hope that it will be useful,
+%%  but WITHOUT ANY WARRANTY; without even the implied warranty of
+%%  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+%%  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 <http://www.gnu.org/licenses/>.
+%%
+
 % To recreate the plots in:
-% Lizier, Prokopenko and Zomaya, "A framework for the local information dynamics of distributed computation in complex systems",
-%  accepted for "Guided Self-Organization: Inception", edited by M. Prokopenko, to be published by Springer, 2013
+% J.T. Lizier, M. Prokopenko and A.Y. Zomaya, "A framework for the local information dynamics of distributed computation in complex systems", in Guided self-organisation: Inception, ed. M. Prokopenko, pp. 115-158, Springer, Berlin/Heidelberg, 2014; doi: 10.1007/978-3-642-53734-9_5, arXiv:0811.2690.
 
 clear all;
 

demos/octave/CellularAutomata/TeBook2013.m

@@ -1,8 +1,25 @@
+%%
+%%  Java Information Dynamics Toolkit (JIDT)
+%%  Copyright (C) 2012, Joseph T. Lizier
+%%  
+%%  This program is free software: you can redistribute it and/or modify
+%%  it under the terms of the GNU General Public License as published by
+%%  the Free Software Foundation, either version 3 of the License, or
+%%  (at your option) any later version.
+%%  
+%%  This program is distributed in the hope that it will be useful,
+%%  but WITHOUT ANY WARRANTY; without even the implied warranty of
+%%  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+%%  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 <http://www.gnu.org/licenses/>.
+%%
+
 % To recreate the plots in:
-% chapter 5 of T. Bossomaier, L. Barnett, M. Harr&eacute; and J.T. Lizier, "An Introduction to Transfer Entropy: Information Flow in Complex Systems", Springer, to be published, 2013.
+% chapter 5 of T. Bossomaier, L. Barnett, M. Harr&eacute; and J.T. Lizier, "An Introduction to Transfer Entropy: Information Flow in Complex Systems", Springer, to be published, 2014.
 % These plots were first published in (see DirectedMeasuresChapterDemo2013.m):
-% J. T. Lizier, "Measuring the dynamics of information processing on a local scale in time and space",
-%  accepted for "Directed Information Measures in Neuroscience", edited by M. Wibral, R. Vicente, J. T. Lizier, to be published by Springer, 2013
+% J.T. Lizier, "Measuring the dynamics of information processing on a local scale in time and space", in Directed information measures in Neuroscience, ed. M. Wibral, R. Vicente and J.T. Lizier, pp. 161-193, Springer, Berlin/Heidelberg, 2014; doi: 10.1007/978-3-642-54474-3_7
 
 clear all;
 

demos/octave/CellularAutomata/movingFrame.m

@@ -1,6 +1,23 @@
+%%
+%%  Java Information Dynamics Toolkit (JIDT)
+%%  Copyright (C) 2012, Joseph T. Lizier
+%%  
+%%  This program is free software: you can redistribute it and/or modify
+%%  it under the terms of the GNU General Public License as published by
+%%  the Free Software Foundation, either version 3 of the License, or
+%%  (at your option) any later version.
+%%  
+%%  This program is distributed in the hope that it will be useful,
+%%  but WITHOUT ANY WARRANTY; without even the implied warranty of
+%%  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+%%  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 <http://www.gnu.org/licenses/>.
+%%
+
 % To recreate the plots in:
-% Lizier and Mahoney, "Moving Frames of Reference, Relativity and Invariance in Transfer Entropy and Information Dynamics",
-%  submitted to Entropy, 2012
+% J.T. Lizier and J.R. Mahoney, "Moving frames of reference, relativity and invariance in transfer entropy and information dynamics", Entropy, vol. 15, no. 1, p. 177-197, 2013; doi: 10.3390/e15010177
 
 clear all;
 

demos/octave/CellularAutomata/plotLocalInfoMeasureForCA.m

@@ -1,3 +1,21 @@
+%%
+%%  Java Information Dynamics Toolkit (JIDT)
+%%  Copyright (C) 2012, Joseph T. Lizier
+%%  
+%%  This program is free software: you can redistribute it and/or modify
+%%  it under the terms of the GNU General Public License as published by
+%%  the Free Software Foundation, either version 3 of the License, or
+%%  (at your option) any later version.
+%%  
+%%  This program is distributed in the hope that it will be useful,
+%%  but WITHOUT ANY WARRANTY; without even the implied warranty of
+%%  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+%%  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 <http://www.gnu.org/licenses/>.
+%%
+
 % function plotLocalInfoMeasureForCA(neighbourhood, base, rule, cells, timeSteps, measureId, measureParams, options)
 % 
 % Plot one run of the given CA and compute and plot a local information dynamics profile for it

demos/octave/CellularAutomata/plotLocalInfoValues.m

@@ -1,3 +1,21 @@
+%%
+%%  Java Information Dynamics Toolkit (JIDT)
+%%  Copyright (C) 2012, Joseph T. Lizier
+%%  
+%%  This program is free software: you can redistribute it and/or modify
+%%  it under the terms of the GNU General Public License as published by
+%%  the Free Software Foundation, either version 3 of the License, or
+%%  (at your option) any later version.
+%%  
+%%  This program is distributed in the hope that it will be useful,
+%%  but WITHOUT ANY WARRANTY; without even the implied warranty of
+%%  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+%%  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 <http://www.gnu.org/licenses/>.
+%%
+
 % function h = plotLocalInfoValues(localResults, plotOptions)
 %
 % J. Lizier, 2012.

demos/octave/CellularAutomata/plotRawCa.m

@@ -1,3 +1,21 @@
+%%
+%%  Java Information Dynamics Toolkit (JIDT)
+%%  Copyright (C) 2012, Joseph T. Lizier
+%%  
+%%  This program is free software: you can redistribute it and/or modify
+%%  it under the terms of the GNU General Public License as published by
+%%  the Free Software Foundation, either version 3 of the License, or
+%%  (at your option) any later version.
+%%  
+%%  This program is distributed in the hope that it will be useful,
+%%  but WITHOUT ANY WARRANTY; without even the implied warranty of
+%%  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+%%  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 <http://www.gnu.org/licenses/>.
+%%
+
 % function plotRawCa(states, saveIt)
 %
 % Plot the given raw values of a cellular automata run

demos/octave/CellularAutomata/prepareColourmap.m

@@ -1,4 +1,21 @@
-% J. Lizier, 2012.
+%%
+%%  Java Information Dynamics Toolkit (JIDT)
+%%  Copyright (C) 2012, Joseph T. Lizier
+%%  
+%%  This program is free software: you can redistribute it and/or modify
+%%  it under the terms of the GNU General Public License as published by
+%%  the Free Software Foundation, either version 3 of the License, or
+%%  (at your option) any later version.
+%%  
+%%  This program is distributed in the hope that it will be useful,
+%%  but WITHOUT ANY WARRANTY; without even the implied warranty of
+%%  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+%%  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 <http://www.gnu.org/licenses/>.
+%%
+
 %
 % Function to create a colourmap of a given length.
 % 

demos/octave/CellularAutomata/runCA.m

@@ -1,8 +1,23 @@
+%%
+%%  Java Information Dynamics Toolkit (JIDT)
+%%  Copyright (C) 2012, Joseph T. Lizier
+%%  
+%%  This program is free software: you can redistribute it and/or modify
+%%  it under the terms of the GNU General Public License as published by
+%%  the Free Software Foundation, either version 3 of the License, or
+%%  (at your option) any later version.
+%%  
+%%  This program is distributed in the hope that it will be useful,
+%%  but WITHOUT ANY WARRANTY; without even the implied warranty of
+%%  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+%%  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 <http://www.gnu.org/licenses/>.
+%%
+
 % function [caStates, ruleTable, executedRules] = runCA(neighbourhood, base, rule, cells, steps, debug, seedOrState)
 %
-% Joseph Lizier
-% 2012
-% Distributed under GPLv3 (see distribution of license with the code)
 %
 % Please cite:
 % Joseph T. Lizier, "JIDT: An information-theoretic toolkit for studying the dynamics of complex systems", 2012, https://code.google.com/p/information-dynamics-toolkit/

demos/octave/DetectingInteractionLags/coupledLogisticMap.m

@@ -1,3 +1,21 @@
+%%
+%%  Java Information Dynamics Toolkit (JIDT)
+%%  Copyright (C) 2012, Joseph T. Lizier
+%%  
+%%  This program is free software: you can redistribute it and/or modify
+%%  it under the terms of the GNU General Public License as published by
+%%  the Free Software Foundation, either version 3 of the License, or
+%%  (at your option) any later version.
+%%  
+%%  This program is distributed in the hope that it will be useful,
+%%  but WITHOUT ANY WARRANTY; without even the implied warranty of
+%%  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+%%  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 <http://www.gnu.org/licenses/>.
+%%
+
 % Examine transfer entropy from variable X to Y for coupled logistic maps X and Y
 %  where the process is as defined in Example V.A of:
 %  Pompe and Runge, Momentary information transfer as a coupling measure of time series,

demos/octave/DetectingInteractionLags/transferWithSourceMemory.m

@@ -1,3 +1,21 @@
+%%
+%%  Java Information Dynamics Toolkit (JIDT)
+%%  Copyright (C) 2012, Joseph T. Lizier
+%%  
+%%  This program is free software: you can redistribute it and/or modify
+%%  it under the terms of the GNU General Public License as published by
+%%  the Free Software Foundation, either version 3 of the License, or
+%%  (at your option) any later version.
+%%  
+%%  This program is distributed in the hope that it will be useful,
+%%  but WITHOUT ANY WARRANTY; without even the implied warranty of
+%%  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+%%  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 <http://www.gnu.org/licenses/>.
+%%
+
 % Compute the transfer entropy (te) and the Pompe-Runge Momentary information transfer (mit)
 %  in an example where we have short-term source memory (with decay).
 %

demos/octave/SchreiberTransferEntropyExamples/activeInfoStorageHeartBreathRatesKraskov.m

@@ -1,3 +1,21 @@
+%%
+%%  Java Information Dynamics Toolkit (JIDT)
+%%  Copyright (C) 2012, Joseph T. Lizier
+%%  
+%%  This program is free software: you can redistribute it and/or modify
+%%  it under the terms of the GNU General Public License as published by
+%%  the Free Software Foundation, either version 3 of the License, or
+%%  (at your option) any later version.
+%%  
+%%  This program is distributed in the hope that it will be useful,
+%%  but WITHOUT ANY WARRANTY; without even the implied warranty of
+%%  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+%%  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 <http://www.gnu.org/licenses/>.
+%%
+
 % function [aisHeart, aisBreath] = activeInfoStorageHeartBreathRatesKraskov(kHistories, knn, numSurrogates)
 %
 % activeInfoStorageHeartBreathRatesKraskov

demos/octave/SchreiberTransferEntropyExamples/runHeartBreathRateKernel.m

@@ -1,3 +1,21 @@
+%%
+%%  Java Information Dynamics Toolkit (JIDT)
+%%  Copyright (C) 2012, Joseph T. Lizier
+%%  
+%%  This program is free software: you can redistribute it and/or modify
+%%  it under the terms of the GNU General Public License as published by
+%%  the Free Software Foundation, either version 3 of the License, or
+%%  (at your option) any later version.
+%%  
+%%  This program is distributed in the hope that it will be useful,
+%%  but WITHOUT ANY WARRANTY; without even the implied warranty of
+%%  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+%%  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 <http://www.gnu.org/licenses/>.
+%%
+
 % function [teHeartToBreath, teBreathToHeart] = runHeartBreathRateKernel(rs)
 %
 % runHeartBreathRateKernel

demos/octave/SchreiberTransferEntropyExamples/runHeartBreathRateKraskov.m

@@ -1,3 +1,21 @@
+%%
+%%  Java Information Dynamics Toolkit (JIDT)
+%%  Copyright (C) 2012, Joseph T. Lizier
+%%  
+%%  This program is free software: you can redistribute it and/or modify
+%%  it under the terms of the GNU General Public License as published by
+%%  the Free Software Foundation, either version 3 of the License, or
+%%  (at your option) any later version.
+%%  
+%%  This program is distributed in the hope that it will be useful,
+%%  but WITHOUT ANY WARRANTY; without even the implied warranty of
+%%  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+%%  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 <http://www.gnu.org/licenses/>.
+%%
+
 % function [teHeartToBreath, teBreathToHeart] = runHeartBreathRateKraskov(kHistory, lHistory, knns, numSurrogates)
 %
 % runHeartBreathRateKraskov

demos/octave/SchreiberTransferEntropyExamples/runTentMap.m

@@ -1,3 +1,21 @@
+%%
+%%  Java Information Dynamics Toolkit (JIDT)
+%%  Copyright (C) 2012, Joseph T. Lizier
+%%  
+%%  This program is free software: you can redistribute it and/or modify
+%%  it under the terms of the GNU General Public License as published by
+%%  the Free Software Foundation, either version 3 of the License, or
+%%  (at your option) any later version.
+%%  
+%%  This program is distributed in the hope that it will be useful,
+%%  but WITHOUT ANY WARRANTY; without even the implied warranty of
+%%  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+%%  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 <http://www.gnu.org/licenses/>.
+%%
+
 % function Values = runTentMap()
 %
 % Version 1.0

demos/octave/SchreiberTransferEntropyExamples/runUlamMap.m

@@ -1,3 +1,21 @@
+%%
+%%  Java Information Dynamics Toolkit (JIDT)
+%%  Copyright (C) 2012, Joseph T. Lizier
+%%  
+%%  This program is free software: you can redistribute it and/or modify
+%%  it under the terms of the GNU General Public License as published by
+%%  the Free Software Foundation, either version 3 of the License, or
+%%  (at your option) any later version.
+%%  
+%%  This program is distributed in the hope that it will be useful,
+%%  but WITHOUT ANY WARRANTY; without even the implied warranty of
+%%  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+%%  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 <http://www.gnu.org/licenses/>.
+%%
+
 % function [teValues1to2, teValues2to1] = runUlamMap()
 %
 % Version 1.0

demos/octave/example1TeBinaryData.m

@@ -1,3 +1,21 @@
+%%
+%%  Java Information Dynamics Toolkit (JIDT)
+%%  Copyright (C) 2012, Joseph T. Lizier
+%%  
+%%  This program is free software: you can redistribute it and/or modify
+%%  it under the terms of the GNU General Public License as published by
+%%  the Free Software Foundation, either version 3 of the License, or
+%%  (at your option) any later version.
+%%  
+%%  This program is distributed in the hope that it will be useful,
+%%  but WITHOUT ANY WARRANTY; without even the implied warranty of
+%%  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+%%  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 <http://www.gnu.org/licenses/>.
+%%
+
 % = Example 1 - Transfer entropy on binary data =
 
 % Simple transfer entropy (TE) calculation on binary data using the discrete TE calculator:

demos/octave/example2TeMultidimBinaryData.m

@@ -1,3 +1,21 @@
+%%
+%%  Java Information Dynamics Toolkit (JIDT)
+%%  Copyright (C) 2012, Joseph T. Lizier
+%%  
+%%  This program is free software: you can redistribute it and/or modify
+%%  it under the terms of the GNU General Public License as published by
+%%  the Free Software Foundation, either version 3 of the License, or
+%%  (at your option) any later version.
+%%  
+%%  This program is distributed in the hope that it will be useful,
+%%  but WITHOUT ANY WARRANTY; without even the implied warranty of
+%%  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+%%  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 <http://www.gnu.org/licenses/>.
+%%
+
 % = Example 2 - Transfer entropy on multidimensional binary data =
 
 % Simple transfer entropy (TE) calculation on multidimensional binary data using the discrete TE calculator.

demos/octave/example3TeContinuousDataKernel.m

@@ -1,3 +1,21 @@
+%%
+%%  Java Information Dynamics Toolkit (JIDT)
+%%  Copyright (C) 2012, Joseph T. Lizier
+%%  
+%%  This program is free software: you can redistribute it and/or modify
+%%  it under the terms of the GNU General Public License as published by
+%%  the Free Software Foundation, either version 3 of the License, or
+%%  (at your option) any later version.
+%%  
+%%  This program is distributed in the hope that it will be useful,
+%%  but WITHOUT ANY WARRANTY; without even the implied warranty of
+%%  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+%%  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 <http://www.gnu.org/licenses/>.
+%%
+
 % = Example 3 - Transfer entropy on continuous data using kernel estimators =
 
 % Simple transfer entropy (TE) calculation on continuous-valued data using the (box) kernel-estimator TE calculator.

demos/octave/example4TeContinuousDataKraskov.m

@@ -1,3 +1,21 @@
+%%
+%%  Java Information Dynamics Toolkit (JIDT)
+%%  Copyright (C) 2012, Joseph T. Lizier
+%%  
+%%  This program is free software: you can redistribute it and/or modify
+%%  it under the terms of the GNU General Public License as published by
+%%  the Free Software Foundation, either version 3 of the License, or
+%%  (at your option) any later version.
+%%  
+%%  This program is distributed in the hope that it will be useful,
+%%  but WITHOUT ANY WARRANTY; without even the implied warranty of
+%%  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+%%  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 <http://www.gnu.org/licenses/>.
+%%
+
 % = Example 4 - Transfer entropy on continuous data using Kraskov estimators =
 
 % Simple transfer entropy (TE) calculation on continuous-valued data using the Kraskov-estimator TE calculator.

demos/octave/example5TeBinaryMultivarTransfer.m

@@ -1,3 +1,21 @@
+%%
+%%  Java Information Dynamics Toolkit (JIDT)
+%%  Copyright (C) 2012, Joseph T. Lizier
+%%  
+%%  This program is free software: you can redistribute it and/or modify
+%%  it under the terms of the GNU General Public License as published by
+%%  the Free Software Foundation, either version 3 of the License, or
+%%  (at your option) any later version.
+%%  
+%%  This program is distributed in the hope that it will be useful,
+%%  but WITHOUT ANY WARRANTY; without even the implied warranty of
+%%  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+%%  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 <http://www.gnu.org/licenses/>.
+%%
+
 % = Example 5 - Multivariate transfer entropy on binary data =
 
 % Multivariate transfer entropy (TE) calculation on binary data using the discrete TE calculator:

demos/octave/example6DynamicCallingMutualInfo.m

@@ -1,3 +1,21 @@
+%%
+%%  Java Information Dynamics Toolkit (JIDT)
+%%  Copyright (C) 2012, Joseph T. Lizier
+%%  
+%%  This program is free software: you can redistribute it and/or modify
+%%  it under the terms of the GNU General Public License as published by
+%%  the Free Software Foundation, either version 3 of the License, or
+%%  (at your option) any later version.
+%%  
+%%  This program is distributed in the hope that it will be useful,
+%%  but WITHOUT ANY WARRANTY; without even the implied warranty of
+%%  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+%%  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 <http://www.gnu.org/licenses/>.
+%%
+
 % Example 6 - Mutual information calculation with dynamic specification of calculator
 
 % This example shows how to write Matlab/Octave code to take advantage of the

demos/octave/javaMatrixToOctave.m

@@ -1,3 +1,21 @@
+%%
+%%  Java Information Dynamics Toolkit (JIDT)
+%%  Copyright (C) 2012, Joseph T. Lizier
+%%  
+%%  This program is free software: you can redistribute it and/or modify
+%%  it under the terms of the GNU General Public License as published by
+%%  the Free Software Foundation, either version 3 of the License, or
+%%  (at your option) any later version.
+%%  
+%%  This program is distributed in the hope that it will be useful,
+%%  but WITHOUT ANY WARRANTY; without even the implied warranty of
+%%  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+%%  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 <http://www.gnu.org/licenses/>.
+%%
+
 % function octaveMatrix = javaMatrixToOctave(javaMatrix)
 %
 % Convert a java matrix (1 or 2D, double or int - but not Integer!!) to an octave or matlab matrix

demos/octave/octaveToJavaDoubleArray.m

@@ -1,3 +1,21 @@
+%%
+%%  Java Information Dynamics Toolkit (JIDT)
+%%  Copyright (C) 2012, Joseph T. Lizier
+%%  
+%%  This program is free software: you can redistribute it and/or modify
+%%  it under the terms of the GNU General Public License as published by
+%%  the Free Software Foundation, either version 3 of the License, or
+%%  (at your option) any later version.
+%%  
+%%  This program is distributed in the hope that it will be useful,
+%%  but WITHOUT ANY WARRANTY; without even the implied warranty of
+%%  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+%%  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 <http://www.gnu.org/licenses/>.
+%%
+
 % function jDoubleArray = octaveToJavaDoubleArray(octaveArray)
 %
 % Convert a native octave array to a java double 1D array

demos/octave/octaveToJavaDoubleMatrix.m

@@ -1,3 +1,21 @@
+%%
+%%  Java Information Dynamics Toolkit (JIDT)
+%%  Copyright (C) 2012, Joseph T. Lizier
+%%  
+%%  This program is free software: you can redistribute it and/or modify
+%%  it under the terms of the GNU General Public License as published by
+%%  the Free Software Foundation, either version 3 of the License, or
+%%  (at your option) any later version.
+%%  
+%%  This program is distributed in the hope that it will be useful,
+%%  but WITHOUT ANY WARRANTY; without even the implied warranty of
+%%  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+%%  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 <http://www.gnu.org/licenses/>.
+%%
+
 % function jDoubleMatrix = octaveToJavaDoubleMatrix(octaveMatrix)
 %
 % Convert a native octave/matlab matrix to a java double 2D array

demos/octave/octaveToJavaIntArray.m

@@ -1,3 +1,21 @@
+%%
+%%  Java Information Dynamics Toolkit (JIDT)
+%%  Copyright (C) 2012, Joseph T. Lizier
+%%  
+%%  This program is free software: you can redistribute it and/or modify
+%%  it under the terms of the GNU General Public License as published by
+%%  the Free Software Foundation, either version 3 of the License, or
+%%  (at your option) any later version.
+%%  
+%%  This program is distributed in the hope that it will be useful,
+%%  but WITHOUT ANY WARRANTY; without even the implied warranty of
+%%  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+%%  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 <http://www.gnu.org/licenses/>.
+%%
+
 % function jIntArray = octaveToJavaIntArray(octaveArray)
 %
 % Convert a native octave array to a java int 1D array.

demos/octave/octaveToJavaIntMatrix.m

@@ -1,3 +1,21 @@
+%%
+%%  Java Information Dynamics Toolkit (JIDT)
+%%  Copyright (C) 2012, Joseph T. Lizier
+%%  
+%%  This program is free software: you can redistribute it and/or modify
+%%  it under the terms of the GNU General Public License as published by
+%%  the Free Software Foundation, either version 3 of the License, or
+%%  (at your option) any later version.
+%%  
+%%  This program is distributed in the hope that it will be useful,
+%%  but WITHOUT ANY WARRANTY; without even the implied warranty of
+%%  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+%%  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 <http://www.gnu.org/licenses/>.
+%%
+
 % function jIntMatrix = octaveToJavaIntMatrix(octaveMatrix)
 %
 % Convert a native octave matrix to a java int 2D array.

demos/python/example1TeBinaryData.py

@@ -1,3 +1,21 @@
+##
+##  Java Information Dynamics Toolkit (JIDT)
+##  Copyright (C) 2012, Joseph T. Lizier
+##  
+##  This program is free software: you can redistribute it and/or modify
+##  it under the terms of the GNU General Public License as published by
+##  the Free Software Foundation, either version 3 of the License, or
+##  (at your option) any later version.
+##  
+##  This program is distributed in the hope that it will be useful,
+##  but WITHOUT ANY WARRANTY; without even the implied warranty of
+##  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+##  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 <http://www.gnu.org/licenses/>.
+##
+
 # = Example 1 - Transfer entropy on binary data =
 
 # Simple transfer entropy (TE) calculation on binary data using the discrete TE calculator:

demos/python/example2TeMultidimBinaryData.py

@@ -1,3 +1,21 @@
+##
+##  Java Information Dynamics Toolkit (JIDT)
+##  Copyright (C) 2012, Joseph T. Lizier
+##  
+##  This program is free software: you can redistribute it and/or modify
+##  it under the terms of the GNU General Public License as published by
+##  the Free Software Foundation, either version 3 of the License, or
+##  (at your option) any later version.
+##  
+##  This program is distributed in the hope that it will be useful,
+##  but WITHOUT ANY WARRANTY; without even the implied warranty of
+##  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+##  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 <http://www.gnu.org/licenses/>.
+##
+
 # = Example 2 - Transfer entropy on multidimensional binary data =
 
 # Simple transfer entropy (TE) calculation on multidimensional binary data using the discrete TE calculator.

demos/python/example3TeContinuousDataKernel.py

@@ -1,3 +1,21 @@
+##
+##  Java Information Dynamics Toolkit (JIDT)
+##  Copyright (C) 2012, Joseph T. Lizier
+##  
+##  This program is free software: you can redistribute it and/or modify
+##  it under the terms of the GNU General Public License as published by
+##  the Free Software Foundation, either version 3 of the License, or
+##  (at your option) any later version.
+##  
+##  This program is distributed in the hope that it will be useful,
+##  but WITHOUT ANY WARRANTY; without even the implied warranty of
+##  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+##  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 <http://www.gnu.org/licenses/>.
+##
+
 # = Example 3 - Transfer entropy on continuous data using kernel estimators =
 
 # Simple transfer entropy (TE) calculation on continuous-valued data using the (box) kernel-estimator TE calculator.

demos/python/example4TeContinuousDataKraskov.py

@@ -1,3 +1,21 @@
+##
+##  Java Information Dynamics Toolkit (JIDT)
+##  Copyright (C) 2012, Joseph T. Lizier
+##  
+##  This program is free software: you can redistribute it and/or modify
+##  it under the terms of the GNU General Public License as published by
+##  the Free Software Foundation, either version 3 of the License, or
+##  (at your option) any later version.
+##  
+##  This program is distributed in the hope that it will be useful,
+##  but WITHOUT ANY WARRANTY; without even the implied warranty of
+##  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+##  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 <http://www.gnu.org/licenses/>.
+##
+
 # = Example 4 - Transfer entropy on continuous data using Kraskov estimators =
 
 # Simple transfer entropy (TE) calculation on continuous-valued data using the Kraskov-estimator TE calculator.

demos/python/example5TeBinaryMultivarTransfer.py

@@ -1,3 +1,21 @@
+##
+##  Java Information Dynamics Toolkit (JIDT)
+##  Copyright (C) 2012, Joseph T. Lizier
+##  
+##  This program is free software: you can redistribute it and/or modify
+##  it under the terms of the GNU General Public License as published by
+##  the Free Software Foundation, either version 3 of the License, or
+##  (at your option) any later version.
+##  
+##  This program is distributed in the hope that it will be useful,
+##  but WITHOUT ANY WARRANTY; without even the implied warranty of
+##  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+##  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 <http://www.gnu.org/licenses/>.
+##
+
 # = Example 5 - Multivariate transfer entropy on binary data =
 
 # Multivariate transfer entropy (TE) calculation on binary data using the discrete TE calculator:

demos/python/example6DynamicCallingMutualInfo.py

@@ -1,3 +1,21 @@
+##
+##  Java Information Dynamics Toolkit (JIDT)
+##  Copyright (C) 2012, Joseph T. Lizier
+##  
+##  This program is free software: you can redistribute it and/or modify
+##  it under the terms of the GNU General Public License as published by
+##  the Free Software Foundation, either version 3 of the License, or
+##  (at your option) any later version.
+##  
+##  This program is distributed in the hope that it will be useful,
+##  but WITHOUT ANY WARRANTY; without even the implied warranty of
+##  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+##  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 <http://www.gnu.org/licenses/>.
+##
+
 # = Example 6 - Mutual information calculation with dynamic specification of calculator =
 
 # This example shows how to write Python code to take advantage of the

notices/octave-java/readme.txt

@@ -0,0 +1,7 @@
+octave-java package of the Octave-Forge project -- http://octave.sourceforge.net/java/
+
+This project is distributed under GPLv3 also; see the license file in the top level of this distribution.
+
+The code in infodynamics.utils.OctaveMatrix was adapted from this source.
+
+

readme-template.txt

@@ -93,9 +93,13 @@ This project includes modified files from the Apache Commons Math library -- htt
 This Apache 2 software is now included as a derivative work in this GPLv3 licensed JIDT project, as per: http://www.apache.org/licenses/GPL-compatibility.html
 Notices and license for this software are found in the notices/commons-math directory.
 
-The project also contains adapted code from the JAMA project -- http://math.nist.gov/javanumerics/jama/
+The project includes adapted code from the JAMA project -- http://math.nist.gov/javanumerics/jama/
 Notices and license for this software are found in the notices/JAMA directory.
 
+The project includes adapted code from the octave-java package of the Octave-Forge project -- http://octave.sourceforge.net/java/
+Notices for this software are found in the notices/JAMA directory.
+
+
 =============
 
 Joseph T. Lizier, @DATE@