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Tutorial to accompany Fink et al. (2023)

This repository contains code and toy data associated with the paper:

Fink, L., Simola, J., Tavano, A., Lange, E. B., Wallot, S., & Laeng, B. (2023). From pre-processing to advanced dynamic modeling of pupil data. Behavior Research Methods. https://doi.org/10.3758/s13428-023-02098

Please note that for users who do not have MATLAB, all code can be viewed in the .html file of this repository.
Alternatively, users can run all MATLAB code on a virtual machine in a public Code Ocean capsule, available here: https://codeocean.com/capsule/1209338/tree/v1

Contents

Main interactive tutorial script

Fink_pupilCodeTutorial_interactive.mlx is the main tutorial script. It contains text, MATLAB code, and interactive user interfaces for understanding some fundamentals of time series and signal-to-signal analyses.

Fink_pupilCodeTutorial_interactive.html is an html print out of the code and figures in the above .mlx script, for those who want to browse online, or who do not have MATLAB. Note that the interactive controls are not available in the html version.

Fink_toydata.mat contains the toy data set for the tutorial.

Helper functions

The helperFunctions folder contains custom and third-party functions necessary for running the interactive tutorial.

The latter three functions were written by Sebastian Wallot. Please see the citation in the code for proper reference.

Dependencies

This code was written in MATLAB verion 9.11.0.1769968 (R2021b) and relies on the following toolboxes:

  • Signal Processing Toolbox: Version 8.7
  • Statistics and Machine Learning Toolbox: Version 12.2
  • Symbolic Math Toolbox: Version 9.0

Development machine details: Operating System: macOS Version: 11.6.6 Build: 20G624 Java Version: Java 1.8.0_202-b08 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode

Running this code

Download this Github repository. Open Fink_pupilCodeTutorial_interactive.mlx.

As long as all the file structure and names in this repository have not been altered, MATLAB should find the required data and functions and all should run without problem.

Should trouble occur, or bugs be found, please open an issue.

Citation

If using anything from this repository, cite:

Fink, L., Simola, J., Tavano, A., Lange, E. B., Wallot, S., & Laeng, B. (2023). From pre-processing to advanced dynamic modeling of pupil data. Behavior Research Methods. https://doi.org/10.3758/s13428-023-02098

UPDATES / Additional resources

Since this publication, we have given a 4 hour Pupillometry Methods Workshop at the University of Konstanz. All of the materials from that workshop are linked here:

https://beatlab.mcmaster.ca/KonstanzWorkshopSummary.html