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AB-tDCS: Overview

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In this study we examined whether electrical brain stimulation of the prefrontal cortex can change the size of the attentional blink.

Project title: Effects of tDCS on the attentional blink revisited: A statistical evaluation of a replication attempt
Project code: AB-tDCS
Authors: Reteig, L.C., Newman, L.A., Ridderinkhof, K.R., & Slagter, H.A.
Affiliation: Department of Psychology, University of Amsterdam
Year: 2021

Don't hesitate to get in touch if you have any questions; find my contact details on my personal website.

Resources

Project website: https://lcreteig.github.io/AB-tDCS

Published paper: PLOS ONE

Preprint: bioRxiv

Behavioral data and other resources: Open Science Framework (OSF)

EEG data: OpenNeuro

Code: GitHub

Project setup

Directory structure

After downloading everything from Github and/or the OSF, your directory structure should look like this (N.B. this is just a sketch; does not include every single file):

AB-tDCS
│   AB-tDCS.Rproj
|   renv.lock
│
└───data
│   │   subject_info.csv
│   │   tDCS_AE.csv
│   │   AB-tDCS_study1.txt
│   │
│   └───S01
│   │   │   AB_S01_1B_pre.txt
│   │   │   AB_S01_1B_tDCS.txt
│   │   │   AB_S01_1B_post.txt
│   │   │   AB_S01_2D_pre.txt
│   │   │   AB_S01_2D_tDCS.txt
│   │   │   AB_S01_2D_post.txt
│   │   
│   └───S02
│       │  ...
│
└───docs
│
└───paper
│   │   AB-tDCS_paper.Rmd
│   │   AB-tDCS_paper_appendix.Rmd
│   │   AB-tDCS.bib
│   │
│   └───figures
│   
└───records
│   │   participant_log.csv
│   │   study_protocol.pdf
│   │   tDCS_blinding.md
│   │
│   └───questionnaires
│
└───renv
│   │   .gitignore
│   │   activate.R
│   │   settings.dcf
│
└───site
│   │   _site.yml_
│   │   build_site.R
│   │   footer.html
│   │   header.html
│   │   styles.css
│
└───src
│   │   AB-tDCS_anodal-vs-cathodal.Rmd
│   │   AB-tDCS_change-from-baseline.Rmd
│   │   AB-tDCS_group.Rmd
│   │   AB-tDCS_questionnaires.Rmd
│   │   AB-tDCS_replication-analyses.Rmd
│   │
│   └───func
│   │   │   behavioral_analysis.R
│   │   │   load_data.Rmd
│   │   │   
│   └───lib
│       │   appendixCodeFunctionsJeffreys.R
│       │   corr_change_baseline.R
│   
└───task
    │   AB_tDCS-EEG.exp
    │   mainTask.sce
    │   practice.sce

Descriptions

AB-tDCS.Rproj: Config file with options for the R project; also determines top-level folder.
renv.lock: Contains information on all the packages and their versions that were used for this project, and (along with the contents of the renv/ folder) can be used to recreate the computational environment

N.B. The following folders each have their own README.md (GitHub) and/or wiki page (OSF) with more detailed information on their contents.

EEG/: Metadata files and one example subject for an EEG dataset in [BIDS] format associated with this project (see [Resources]).
data/: All the behavioral and metadata collected during this project, as well as the task data from London & Slagter (2021).
docs/: Holds the project website's files
paper/: AB_tDCS_paper.Rmd is the R Markdown source file for the paper; running it produces the rendered version on this website (.html) and the preprint (.pdf)
records/: Documentation, logbooks and protocols
site/: Source code for the website; runs the source code in paper/ and src/ to produce the website as in docs/
src/: All other analysis code used in the project
task/: Code for the experimental task used during data collection

Reproducibility

Make sure you've downloaded all the data and code and that they're placed in the data, src and paper folders (as outlined in the [Directory structure] section). To do so:
- Download or clone the GitHub repository, using the big green "Code" button in the top right.
- From the Open Science Framework, download the contents of the Data and Records (optional) components.
- Download appendixCodeFunctionsJeffreys.R per the instructions in src/README, and place in src/lib.
Open the AB-tDCS.Rproj file in RStudio.
Run the command renv::restore() in the Console to install all the required packages in a separate library for this project.
If you're interested in recreating the paper, run the command tinytex::install_tinytex() to install a LaTeX distribution, which will enable you to build the pdf.

💡 Or, if you just want to quickly play around with the code, simply click this link to create a remote RStudio session in your browser with Binder:

This will already set everything up for you on the server, including all packages (and LaTeX) that the analysis code depends upon.

Then, run the .Rmd notebooks in the src folder to reproduce the contents under the Analyses tab on the project website. These contain all analyses (and their results) performed for this project.

Run the paper/AB-tDCS_paper.Rmd notebook to reproduce all the results, figures and statistics, and the paper as under the Paper tab on the project website, or in the preprint (see [Resources]).

Licensing

All components of this project are open and under non-restrictive licenses:

The data are released to the public domain under a CC0 1.0 Universal license
The preprint and other written materials are licensed under a CC-By Attribution 4.0 International license
The code is licensed under the MIT license

lcreteig / AB-tDCS