joseph.lizier
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7d95954c55
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Patched bug in interface for old Kernel AIs calculator (now in unit tests)
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2014-04-08 11:27:10 +00:00 |
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joseph.lizier
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9cad2737af
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Added unit tests for TransferEntropyCalculatorMultiVariateViaCondMutualInfo and derived classes for Kraskov and Gaussian estimators.
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2014-04-08 11:21:40 +00:00 |
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joseph.lizier
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7a40b433b7
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Added TransferEntropyCalculatorMultiVariateViaCondMutualInfo to facilitate estimation of multivariate TE by an underlying conditional mutual information calculator. Added linear-Gaussian TE estimator using this. Switched Kraskov multivariate TE estimator from a two MI estimator to use an underlying conditional mutual information calculator; removed old Kraskov "ByMulti" classes now. Removed some initialisation routines for TransferEntropyCalculatorViaCondMutualInfo so they tie in ok.
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2014-04-08 10:41:49 +00:00 |
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joseph.lizier
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b81ccccee1
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Added unit tests for TransferEntropyCalculatorViaCondMutualInfo implementations: Gaussian simply tests the computeStartAndEndTimePairs; Kraskov tests against TRENTOOL.
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2014-04-07 05:33:30 +00:00 |
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joseph.lizier
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fd9bf116f9
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Added TransferEntropyCalculatorViaCondMutualInfo to allow calculation of TE via any implementation of a conditional MI calculator. Added concrete implementations using this for Gaussian estimators (Gaussian TE estimator is equivalent to Granger causality). Replaced existing Kraskov TE calculator (which used two MI calculators) with one which uses one conditional MI estimator via this new method. Also patched TransferEntropyCommon.computeStartAndEndTimePairs
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2014-04-07 05:31:52 +00:00 |
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joseph.lizier
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c5402e8c48
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Added ActiveInfoStorageCalculatorViaMutualInfo to allow calculation of AIS via any implementation of an MI calculator. (Forgot to add this before -- its child classes are already committed).
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2014-04-04 06:02:04 +00:00 |
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joseph.lizier
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1827ec23c2
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Fixed lack of initialisation of MI calculators in Kraskov MI unit tests
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2014-03-26 05:09:20 +00:00 |
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joseph.lizier
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12fc61d396
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Moved Kraskov mutual info calculator multivariate to inherit from the common MI multivariate class, so as to share code for adding observations, statistical tests, etc. Passed unit testing.
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2014-03-26 05:08:46 +00:00 |
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joseph.lizier
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06d0ddf07d
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Added functions to discrete Entropy calculators for single dimensional arrays, plus local values of MI for single supplied values and statistical signficance testing for Active info storage.
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2014-03-26 04:08:44 +00:00 |
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joseph.lizier
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3e017d1be4
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Added unit tests for Rearchitecting Active Info Storage calculators to use a common parent class for data collection. Mainly includes testing kernel AIS calculator against the older direct implementation of this (which is now moved into the unit test area only)
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2014-03-26 04:07:13 +00:00 |
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joseph.lizier
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2571c3ae9e
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Rearchitected Active Info Storage calculators to use a common parent class for data collection, and underlying mutual information classes for the implementation specifics. Includes adding Kraskov and Gaussian Active Info Storage calculators, and implementing embedding delay for the past history.
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2014-03-26 04:05:20 +00:00 |
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joseph.lizier
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c949339574
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Allowing comment lines starting with % character in ArrayFileReader
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2014-01-31 11:32:20 +00:00 |
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joseph.lizier
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6db8a070e1
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Updated heart-breath demo with Kraskov estimation, to make it runnable in Matlab, and restrict to the same subset of samples used by Schreiber.
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2014-01-29 11:03:40 +00:00 |
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joseph.lizier
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cee9b3dbd3
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Added Schreiber heart-breath rate example using Kraskov estimator.
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2014-01-29 05:33:08 +00:00 |
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joseph.lizier
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2b8ab0e939
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Adding error check to constructor of discrete MI calculator;
and making method of generating random permutations more efficient (using native library).
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2013-10-22 04:08:21 +00:00 |
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joseph.lizier
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5d0934bd85
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Updating unit tests to reflect changes to discrete MI calculator and method of generating random permutations.
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2013-10-22 04:06:58 +00:00 |
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joseph.lizier
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6fe22e39cb
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Added unit tests for new method generateRandomPerturbations(int, int) in RandomGenerator, and for sortIndices(double[]) method to MatrixUtils
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2013-10-18 00:45:46 +00:00 |
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joseph.lizier
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b4645584fe
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Added new method generateRandomPerturbations(int, int) to RandomGenerator, and switched all computeSignificance methods to use this (since there's no need for checking for distinct perturbations really, and this is much faster). Required adding sortIndices(double[]) method to MatrixUtils
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2013-10-18 00:42:12 +00:00 |
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joseph.lizier
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1d5ae4a176
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Added unit test for bug fix to computeSignificance() of ConditionalMutualInformationCalculator, simply to make sure it doesn't throw an exception
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2013-10-17 13:20:42 +00:00 |
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joseph.lizier
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c7b42e38ae
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Bug fix to computeSignificance() of ConditionalMutualInformationCalculator
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2013-10-17 13:19:58 +00:00 |
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joseph.lizier
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8991b4176c
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Minor changes to method header comments
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2013-09-10 22:50:30 +00:00 |
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joseph.lizier
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6e06b9f6b5
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Altering ant script for version 0.1.4
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2013-09-10 22:48:31 +00:00 |
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joseph.lizier
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b20d103b56
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Continuing (2) to make CA demo scripts have full Matlab compatibility, including loading initial state of CAs from file (since octave and matlab generate different initial states)
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2013-09-10 15:27:02 +00:00 |
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joseph.lizier
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23bffaf688
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Continuing to make CA demo scripts have full Matlab compatibility, including loading initial state of CAs from file (since octave and matlab generate different initial states)
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2013-09-10 15:12:03 +00:00 |
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joseph.lizier
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6cd0e522fa
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Patching CA demo scripts for full Matlab compatibility, including loading initial state of CAs from file (since octave and matlab generate different initial states)
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2013-09-10 14:37:28 +00:00 |
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joseph.lizier
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28911ef2f4
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Made octave/examples 4 to 6 Matlab compatible
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2013-09-05 05:03:42 +00:00 |
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joseph.lizier
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46a5cb208f
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Made octave/example3 Matlab compatible
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2013-09-05 04:57:36 +00:00 |
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joseph.lizier
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c159cc51b8
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Fixed ordering of CA plots in demo script to generate CA plots in my book chapter in the "Directed information measures in neurosciences" book (2013)
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2013-08-25 15:12:42 +00:00 |
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joseph.lizier
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c20546bd55
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Adding demo script to generate CA plots in my book chapter in the "Directed information measures in neurosciences" book (2013)
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2013-08-25 15:10:19 +00:00 |
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joseph.lizier
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baf66c713a
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Added script to reproduce results from the GSO 2013 book chapter on CA results. Several updates to CA scripts associated with this are also uploaded, including ability to save PDF images, nonlinear colour scaling, and alignment of image plot with cell boundaries
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2013-08-15 06:59:13 +00:00 |
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joseph.lizier
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9c03691c09
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Predictive information calculator unit tests added
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2013-08-13 04:33:45 +00:00 |
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joseph.lizier
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7f48066b57
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Predictive information calculator implementation made from active information storage
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2013-08-13 04:33:18 +00:00 |
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joseph.lizier
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1c0e9098cc
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Extra unit test for Issue 16
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2013-07-06 18:36:03 +00:00 |
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joseph.lizier
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68b0233e28
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Extended fix to handle zero-covariance conditionals for handling linear redundancies amongst variables properly in ConditionalMICalculatorMultivariateGaussian - this contributes to resolution (closed) for Issue 16
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2013-07-06 18:24:13 +00:00 |
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joseph.lizier
|
ce1a3b4b31
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Extended fix to local cond MI values for handling linear redundancies amongst variables properly in ConditionalMICalculatorMultivariateGaussian - this resolves Issue 16
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2013-07-06 13:54:02 +00:00 |
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joseph.lizier
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0907ed495e
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Handle linear redundancies amongst variables properly in ConditionalMICalculatorMultivariateGaussian. Still need to extend this to the local conditional MI values
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2013-07-06 11:11:56 +00:00 |
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joseph.lizier
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34c9d31018
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Renaming lateBindingMutualInfo to example6LateBindingMutualInfo (4) - completing internal name changes and comments
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2013-06-18 12:08:06 +00:00 |
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joseph.lizier
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1656ba8730
|
Renaming lateBindingMutualInfo to example6LateBindingMutualInfo (3)
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2013-06-18 11:57:58 +00:00 |
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joseph.lizier
|
f6f41afdba
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Renaming lateBindingMutualInfo to example6LateBindingMutualInfo (2 - 1 more to come ...)
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2013-06-18 11:57:21 +00:00 |
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joseph.lizier
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b9aa85055d
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Renaming lateBindingMutualInfo to example6LateBindingMutualInfo
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2013-06-18 11:55:52 +00:00 |
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joseph.lizier
|
6554180b98
|
Adding Java simple demo 5
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2013-06-18 11:28:06 +00:00 |
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joseph.lizier
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63f9da620e
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Adding sample data file 10ColsRandomGaussian-1.txt
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2013-06-18 07:37:16 +00:00 |
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joseph.lizier
|
524b277b54
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Adding minor utility functions
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2013-06-18 07:31:18 +00:00 |
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joseph.lizier
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f0dee75f18
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Added Java example 4
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2013-06-18 06:32:46 +00:00 |
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joseph.lizier
|
bc677030da
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Adding Java simple demo 3 and shell script to run it
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2013-06-14 08:02:10 +00:00 |
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joseph.lizier
|
06fa1567ab
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Adding Java demo examples 1 and 2
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2013-06-12 00:33:09 +00:00 |
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joseph.lizier
|
f006c53e46
|
Adding python examples 5 and 6. Minor tweaks to octave examples 5 and 6 to clarify comments or minor conflicts. Error corrected in comment of python example 2
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2013-06-07 05:58:47 +00:00 |
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joseph.lizier
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88b33308c6
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Tweaked python example 2 to add minor comment
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2013-06-05 05:39:39 +00:00 |
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joseph.lizier
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15647840f8
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Tweaked python example 2 to keep print statement thin
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2013-06-05 05:38:12 +00:00 |
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joseph.lizier
|
7336780b2b
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Added python example 2. Patched octave example 2 comments and python example 1 comments
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2013-06-05 05:33:49 +00:00 |