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pwollstadt committed May 20, 2021
2 parents d225f38 + bfb3bd1 commit d4245b7
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5 changes: 3 additions & 2 deletions README.md
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Expand Up @@ -56,8 +56,9 @@ http://www.mis.mpg.de/preprints/2012/preprint2012_25.pdf*
+ Kraskov estimator: [*Kraskov et al., 2004, Phys Rev E 69, 066138*](https://journals.aps.org/pre/abstract/10.1103/PhysRevE.69.066138)
+ Nonuniform embedding: [*Faes et al., 2011, Phys Rev E 83, 051112*](https://journals.aps.org/pre/abstract/10.1103/PhysRevE.83.051112)
+ Faes' compensated transfer entropy: [*Faes et al., 2013, Entropy 15, 198-219*](https://www.mdpi.com/1099-4300/15/1/198)
+ PID: [Williams & Beer, 2010, arXiv:1004.2515 [cs.IT]](http://arxiv.org/abs/1004.2515);
[Makkeh et al., 2020, arXiv:2002.03356 [cs.IT]](https://arxiv.org/abs/2002.03356)
+ PID: [*Williams & Beer, 2010, arXiv:1004.2515 [cs.IT]*](http://arxiv.org/abs/1004.2515);
[*Makkeh et al., 2021, Phys Rev E 103, 032149*](https://doi.org/10.1103/PhysRevE.103.032149);
[*Gutknecht et al., 2020, arXiv:2008.09535 [cs.AI]*](https://arxiv.org/abs/2008.09535)
+ PID estimators: *[Bertschinger et al., 2014, Entropy, 16(4)](https://www.mdpi.com/1099-4300/16/4/2161);
[Makkeh et al., 2017, Entropy, 19(10)](https://www.mdpi.com/1099-4300/19/10/530);
[Makkeh et al., 2018, Entropy, 20(271)](https://www.mdpi.com/1099-4300/20/4/271)*
4 changes: 3 additions & 1 deletion README.txt
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Expand Up @@ -51,6 +51,8 @@ http://www.mis.mpg.de/preprints/2012/preprint2012_25.pdf*
+ Kraskov estimator: *Kraskov et al., 2004, Phys Rev E 69, 066138*
+ Nonuniform embedding: *Faes et al., 2011, Phys Rev E 83, 051112*
+ Faes' compensated transfer entropy: *Faes et al., 2013, Entropy 15, 198-219*
+ PID: *Williams & Beer, 2010, arXiv preprint: http://arxiv.org/abs/1004.2515*
+ PID: Williams & Beer, 2010, arXiv:1004.2515 [cs.IT];
Makkeh et al., 2021, Phys Rev E 103, 032149;
Gutknecht et al., 2020, arXiv:2008.09535 [cs.AI]
+ PID estimators: *Bertschinger et al., 2014, Entropy, 16(4); Makkeh et al., 2017, Entropy, 19(10),
Makkeh et al., 2018, Entropy, 20(271)*
5 changes: 3 additions & 2 deletions idtxl/network_inference.py
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Expand Up @@ -78,7 +78,7 @@ def _check_source_set(self, sources, n_processes):
self.target, self.source_set))

def _include_candidates(self, candidate_set, data):
"""Inlcude informative candidates into the conditioning set.
"""Include informative candidates into the conditioning set.
Loop over each candidate in the candidate set and test if it has
significant mutual information with the current value, conditional
Expand Down Expand Up @@ -137,7 +137,8 @@ def _include_candidates(self, candidate_set, data):
self._idx_to_lag([max_candidate])[0]), end='')
try:
significant = stats.max_statistic(
self, data, candidate_set, te_max_candidate)[0]
self, data, candidate_set, te_max_candidate,
conditional=self._selected_vars_realisations)[0]
except ex.AlgorithmExhaustedError as aee:
# The algorithm cannot continue here, so we'll terminate the
# check of significance for this candidate, though those
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7 changes: 3 additions & 4 deletions idtxl/stats.py
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Expand Up @@ -395,7 +395,7 @@ def omnibus_test(analysis_setup, data):


def max_statistic(analysis_setup, data, candidate_set, te_max_candidate,
conditional=None):
conditional):
"""Perform maximum statistics for one candidate source.
Test if a transfer entropy value is significantly bigger than the maximum
Expand All @@ -420,10 +420,9 @@ def max_statistic(analysis_setup, data, candidate_set, te_max_candidate,
list of indices of remaning candidates
te_max_candidate : float
transfer entropy value to be tested
conditional : numpy array [optional]
conditional : numpy array
realisations of conditional, 2D numpy array where array dimensions
represent [realisations x variable dimension] (default=None, no
conditioning performed)
represent [realisations x variable dimension]
Returns:
bool
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2 changes: 1 addition & 1 deletion setup.py
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Expand Up @@ -10,7 +10,7 @@
name='idtxl',
packages=['idtxl'],
include_package_data=True,
version='1.0',
version='1.2.2',
description='Information Dynamics Toolkit xl',
author='Patricia Wollstadt, Joseph T. Lizier, Raul Vicente, Conor Finn, Mario Martinez-Zarzuela, Pedro Mediano, Leonardo Novelli, Michael Wibral',
author_email='p.wollstadt@gmail.com',
Expand Down

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