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39 Commits

Author SHA1 Message Date
jlizier 2b0a5cb943 Updated mixed-continiuous CMI KSG estimator, for the bias correction based on number of continuous variables. This was identified from testing, and aligns with testing so far. 2022-09-05 17:51:49 +10:00
jlizier 7fafabe451 Extending MI discrete calculator to allow different bases for each variable. This necessitates immediate removal of the (int,int) constructor (where the 2nd argument was the time difference), this will now be confusing between (base, timeDiff) and (base1, base2). In time we may bring it back, after we can be reasonably comfortable people have switched away from using (base, timeDiff). 2018-06-20 10:55:21 +10:00
jlizier 4170339426 Moving check of dimensionality for continuous variables in mixed CMI calculator common to the main setObservations() method 2018-06-19 23:57:41 +10:00
jlizier 5bde6f295b Fixes issue #70 by providing setObservations(double[], int[], double[]) methods for the mixed CMI calculators (i.e. allowing univariate arrays to be passed in if dimension 1 was defined for both the continuous data and conditional). Unit test validating is included. 2018-06-19 23:08:13 +10:00
Pedro Martinez Mediano b0fc309d6a Add overloadings for 1d continuous variables in KSG mixed calc. 2018-01-12 22:22:46 +00:00
Pedro Martinez Mediano ecda70f8e9 Hard-setting dynCorrExclTime to 0 in KSG mixed calc. 
Previous implementation was incomplete due to a mismatch between the
sample indices in the full and marginal KdTrees. Some code has been left
to guide future development.
 2017-11-20 14:47:00 +00:00
Pedro Martinez Mediano 25df49fa5a KSG mixed calc now allocates memory for locals only if requested. 2017-11-20 14:26:25 +00:00
Pedro Martinez Mediano 8f169171e1 Fixed small bug in KSG mixed calc surrogates. 
Surrogate calculator was applying timeDiff twice, so surrogate
dataset had abs(timeDiff) less observations than it should.
 2017-11-20 14:14:49 +00:00
Pedro Martinez Mediano d40024e1cd Allow negative timeDiff in KSG mixed calc. 2017-11-20 14:02:00 +00:00
Pedro Martinez Mediano f56ac6e69e Fix bug with Theiler window in KSG mixed calc. 2017-08-30 13:30:30 +01:00
Pedro Martinez Mediano 5961fb6246 Add Theiler window and jitter to KSG mixed calc. 2017-08-30 12:17:02 +01:00
Pedro Martinez Mediano 626293b84d More docs for KSG mixed calc. 2017-08-30 01:19:54 +01:00
Pedro Martinez Mediano e11218631e Added myself as author of KSG mixed calculator. 2017-08-29 23:56:28 +01:00
Pedro Martinez Mediano 49afa343fc Removed old variables and functions from KSG mixed, added docs. 2017-08-29 23:55:10 +01:00
Pedro Martinez Mediano bfe8156584 Add KDTrees to computeLocalUsingObservations in KSG mixed calc. 2017-08-16 19:28:24 +01:00
Pedro Martinez Mediano 641d17ec24 Fix bug with normalisation in KSG mixed and change unittest accordingly. 2017-08-16 19:18:51 +01:00
Pedro Martinez Mediano 7635cf8689 Added computeLocalOfPreviousObservations to KSG mixed. 
It follows the same pattern as the continuous MI: there is a
computeFromObservations method that returns either locals or average
based on a flag.
 2017-08-16 14:52:54 +01:00
Pedro Martinez Mediano 2d42e6ebad Removed unused function from KSG mixed. 2017-08-16 14:39:53 +01:00
Pedro Martinez Mediano 23bb573bb1 Replace computeSignificance method in KSG mixed with new one based on clone(). 2017-08-16 14:33:47 +01:00
Pedro Martinez Mediano 8251bdc1cb Removed unused variables from KSG mixed. 2017-08-16 13:35:03 +01:00
Pedro Martinez Mediano f55a7bd961 Add KdTrees to main compute() method in KSG mixed. 2017-08-16 13:31:18 +01:00
Pedro Martinez Mediano bad50ce663 KSG mixed now ignores batches of data shorter than timeDiff. 2017-08-16 13:27:05 +01:00
Pedro Martinez Mediano b5d2b7e367 KSG mixed now throws error if discrete data is out of range. 2017-08-16 13:25:44 +01:00
Pedro Martinez Mediano 437e606233 getNumObservations in KSG mixed now returns totalObservations. 
Before it returned continuousData.length, which more more prone
to null pointer errors, and therefore riskier.
 2017-08-16 00:07:51 +01:00
Pedro Martinez Mediano 39ad14d855 Added function to set timeDiff property. 2017-08-15 21:41:52 +01:00
Pedro Martinez Mediano abeb15cd6e Added standard start/finaliseAddObservations to mixed KSG calc. 2017-08-15 21:25:03 +01:00
Pedro Martinez Mediano 26137d12b1 Added precomputed digammas in KSG mixed calculator, fixed bug in locals. 2017-08-15 20:46:07 +01:00
jlizier 7d28e93913 Bug fix in mixed Kraskov implementation for computeUsingPreviousObservations (picked up by Rose Wang). Also acknowledged that this implementation is (mostly) as per Ross 2014. 2016-10-18 00:18:37 +11:00
joseph.lizier dbd1dcdd54 Fixing the bias correction on our experimental discrete-continuous KSG calculators 2015-07-19 17:19:59 +00:00
joseph.lizier 0767e2e57e Tweaks to javadocs 2014-08-14 06:26:06 +00:00
joseph.lizier f2c5ba4771 Appending suffix "Discrete" to all discrete calculators. Step 2 -- refactoring java files, which has flow on effects to other java files. All fixed here. 2014-08-14 03:00:15 +00:00
joseph.lizier e7b8958fda Adding package-info.java files for Javadocs for the various packages 2014-08-13 15:36:10 +00:00
joseph.lizier b916ac08e8 Javadocs noted as incomplete, and indeed the code itself experimental, for mixed package. 2014-08-13 14:53:57 +00:00
joseph.lizier 0e598bf81e In mixed.kraskov estimators switched to use 4 nearest neighbours by default (as recommended by Kraskov et al.), and Kraskov2 algorithm for conditional MI fixed to match Wibral et al. equation (as per the continuous calculator) 2014-08-13 02:57:54 +00:00
joseph.lizier 4a3532b25b Adding GPLv3 license statement to all code headers in the infodymamics.measures.mixed, utils and networkinference packages. 2014-08-06 06:31:24 +00:00
joseph.lizier 5a6fdb0ea7 Code edits to mixed calculators to fix compilation after moving them into the "mixed" package. Also needed to make some alternations to some of the continuous calculators to fix usage of protected members which are no longer accessible to the moved classes. 2014-04-17 11:10:58 +00:00
joseph.lizier 73ec340f44 Finalised moving mixed calculators into the new mixed directory. 2014-04-17 06:53:27 +00:00
joseph.lizier 91dbd9f772 Continuing to move mixed calculators into the new directory. Moving rest of interfaces from infodynamics.measures.continuous, as well as creating packages inside infodynamics.measures.mixed for the concrete implementations to come across. 2014-04-17 06:49:03 +00:00
joseph.lizier c253313724 Starting to move mixed calculators into the new directory. Testing first with Conditional MI one 2014-04-17 06:43:43 +00:00