EEG Causality Tools

GUI tools for EEG pre-processing, analysis of dynamic regime, comparative analysis of brain networks obtained from different metrics, construction and comparative analysis of dynamic functional connectomes.

Version of 30 June 2022

GitHub source code download: https://github.com/artvalencio/EEG-causality-tools

If useful, please cite:

Valencio, A. EEG Causality Tools. 2022.

Dynamic Connect

Python package for building dynamic functional connectome from EEG

Version of 5 November 2021

GitHub source code download: https://github.com/artvalencio/dynamic-connect

If useful, please cite:

Valencio, A. Dynamic Connect: Python package for building dynamic functional connectome from EEG. 2021.

CaMI for Python

Causality toolbox for Python

Version of 11 October 2021

GitHub source code download: https://github.com/artvalencio/cami-python

If useful, please cite:

Valencio, A.; Valencio, N.; Baptista, M.S. CaMI-Python: Causality toolbox for Python. 2021.

Vicon package for Python

Functions for processing VICON Motion Capture data

Version of 30 July 2020

GitHub source code download: https://github.com/artvalencio/vicon

If useful, please cite:

Valencio, A. Vicon package for Python. 2020.

EpiCom

Simulates the epidemic spreading of a disease in a toy-model small community composed of three spaces: homes, work environment/school, and communal areas.

This model is an approximation and SHOULD NOT be used for real epidemic forecasting. Its purposes are EDUCATIONAL, aiming to support the visualization of how one could incrementally consider sociospatial variables and visualize their impacts in epidemic spreading.

Version of 28 April 2020

GitHub source code download: https://github.com/artvalencio/EpiCom
Windows .exe download: https://sourceforge.net/projects/epicom/files/latest/download

(If running from the Python 3 source code, it requires PySimpleGui, which can be installed from pip)

If useful, please cite:

Valencio, A.; Valencio, N. Subsidios à uma discussão comunitária acerca de modelagem de epidemias. In: Valencio, N.; Malan, C. COVID-19: Crises entremeadas no contexto de pandemia (antecedentes, cenários e recomendações). São Carlos: CPOI-UFSCar, 2020.

Functional Matrix

Calculates the dynamical functional connectivity (DFC) of brain areas given an EEG signal.

Each data point gives the peak sliding window correlation or information-theoretical measure between two EEG channels at a given time interval and the time lag where this peak is found. Such time lag could be interpreted as the time it takes for area j to receive signal from area i.

Version of 25 September 2019

GitHub Download: https://github.com/artvalencio/Functional-Matrix

If useful, please cite:

Arthur Valencio. Functional Matrix: functions to compute the dynamical functional connectivity (DFC) of the brain. Open source codes for Matlab. 2019. Available at: https://github.com/artvalencio/Functional-Matrix

Causality Toolbox

Functions for calculating information theory measures from time-series, with the purpose of distinguishing the cause and the effect variables on a physical process.

Calculates the Causal Mutual Information, Transfer Entropy, Mutual Information of a symbolic sequence, Directionality Index (net information flow), Causal Mutual Information Rate, Total Correlation of a multivariate system and Total (Joint) Entropy of a multivariate system.

Version of 17 May 2018

GitHub Download: https://github.com/artvalencio/causality-toolbox.git

If useful, please cite:

Arthur Valencio and Murilo S. Baptista. Causality Toolbox: functions for calculating information theory measures from time-series. Open source codes for Matlab. 2018. Available at: https://github.com/artvalencio/causality-toolbox/

Arthur Valencio. An Information-theoretical approach to identify seismic precursors and earthquake-causing variables. PhD Thesis, University of Aberdeen, 2018.

Multithread Causality

Functions for calculating information theory measures from multiple (possibly shorter) time-series, with the purpose of distinguishing the cause and the effect variables on a physical process.

Version of 07 July 2019

GitHub Download: https://github.com/artvalencio/multithread-causality

If useful, please cite:

Arthur Valencio, Norma Valencio and Murilo S. Baptista. Multithread causality: causality toolbox for systems observed through many short parallel experiments. Open source codes for Matlab. 2018. Available at: https://github.com/artvalencio/multithread-causality/

Coupled Logistic Maps

Functions for generating the time-series from networks of coupled logistic systems.

The time-series can be computed for any given network structure, and the coupling mechanism can be linear diffusive or Kaneko. It is also possible to include the effects of a dynamical noise.

Version of 25 Feb 2018

GitHub Download: https://github.com/artvalencio/coupled-logistic-maps.git

If useful, please cite:

Arthur Valencio and Murilo S. Baptista. Coupled Logistic Maps: functions for generating the time-series from networks of coupled logistic systems. Open source codes for Matlab. 2018. Available at: https://github.com/artvalencio/coupled-logistic-maps.