In this study we investigated whether spontaneous eye blink rate (a putative index of dopamine levels) can predict the size of the [attentional blink](http://www.scholarpedia.org/article/Attentional_blink), and/or the effect of electrical brain stimulation on the attentional blink.
* __Project title__: Spontaneous eye blink rate does not predict attentional blink size, nor the effects of tDCS on attentional blink size
* __Project code__: AB_tDCS-sEBR (Attentional Blink, transcranial Direct Current Stimulation, spontaneous Eye Blink Rate)
* __Authors__: Reteig LC, Newman LA, Ridderinkhof KR, Slagter HA
* __Affiliation__: Department of Psychology, University of Amsterdam
* __Year__: 2019
# Resources
__Project website__: <https://lcreteig.github.io/AB_tDCS-sEBR>
__Preprint__: [bioRxiv](bioRxiv link FIXME) (not yet available)
__Data, materials and code__: [Open Science Framework (OSF)](https://osf.io/pzbgy/)
Also see the [project website](<https://lcreteig.github.io/AB-tDCS>) and [OSF page](https://osf.io/y6hsf/) for the __AB-tDCS project__, which is based on the same dataset.
# Project setup
## Directory structure
After downloading everything from the OSF, your directory structure should look like this (N.B. this is just a sketch; does not include every single file):
```
AB_tDCS-sEBR
│ AB_tDCS-sEBR.Rproj
│
└───data
│ │ subject_info.csv
│ │ tdcs_AE.csv
│ │
│ └───AB
│ │ │
│ │ └───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
│ │ ...
│ │
│ └───sEBR
│ │ │ sEBR.csv
│ │ │
│ │ └───raw
│ │ │ │
│ │ │ └───S01
│ │ │ │ S01_1B_sEBR.bdf
│ │ │ │ S01_2D_sEBR.bdf
│ │ │ │
│ │ │ └───S02
│ │ │ ...
│ │ │
│ │ └───processed
│ │ │ │
│ │ │ └───S01
│ │ │ │ S01_1B_sEBR_blinkIC1.txt
│ │ │ │ S01_1B_sEBR_blinkIC1.txt_ibis.txt
│ │ │ │ S01_1B_sEBR_processed.mat
│ │ │ │ S01_1B_sEBR.bdf_ICA.mat
│ │ │ │ S01_2D_sEBR_blinkIC1.txt
│ │ │ │ S01_2D_sEBR_blinkIC1.txt_ibis.txt
│ │ │ │ S01_2D_sEBR_processed.mat
│ │ │ │ S01_2D_sEBR.bdf_ICA.mat
│ │ │ │
│ │ │ └───S02
│ │ │ ...
│
└───docs
│
└───paper
│ │ AB-tDCS_sEBR_paper.Rmd
│ │ AB-tDCS_sEBR.bib
│ │
│ └───figures
│
└───records
│ │ participant_log.csv
│ │ sEBR_log.csv
│ │ study_protocol.pdf
│ │ tDCS_blinding.md
│ │
│ └───questionnaires
│
└───site
│ │ _site.yml_
│ │ badges.png
│ │ build_site.R
│ │ footer.html
│ │ header.html
│ │ index.Rmd
│ │ style.css
│
└───src
│ │ AB-tDCS_sEBR.Rmd
│ │ read_sEBR.m
│ │ sEBR_part1.m
│ │ sEBR_part2.m
│ │
│ └───lib
│ │ appendixCodeFunctionsJeffreys.R
│ │ blocked_chans.m
│ │ ebr_scripts.zip
│ │ twolines.R
│ └───EBR
│ └───eeglab13_5_4b
│
└───task
│ AB_tDCS-EEG.exp
│ mainTask.sce
│ practice.sce
```
## Descriptions
* AB_tDCS-sEBR.Rproj: Config file with options for the R project; also determines top-level folder.
N.B. The following folders each have their own `README.md` and/or wiki page (OSF) with more detailed information on their contents.
* `data/`: All the behavioral-, sEBR- and metadata collected during this project.
* `docs/`: Holds the project website's files
* `paper/`: `AB_tDCS-sEBR_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 (meta)data and code and that they're placed in the `data`, `records`, `src` and `paper` folders (as outlined in the [Directory structure] section).
* __To reproduce all the behavioral and statistical results__: Open the `AB-tDCS_sEBR.Rproj` file in [RStudio](https://www.rstudio.com/). Run the `AB-tDCS_sEBR.Rmd` notebook in the `src` folder to reproduce the contents in `docs/AB-tDCS_sEBR.html`. This contains all analyses (and their results) performed for this project. Run the `paper/AB-tDCS_sEBR_paper.Rmd` notebook to reproduce all the results, figures and statistics contained in the paper. To reproduce the paper (pdf as in `paper/AB-tDCS_sEBR_paper.pdf`, or html as in `docs/AB-tDCS_sEBR_paper.html`), click "Knit" (to `apa6_pdf` or `html_document2`).
* __To reproduce the sEBR results in `data/sEBR.csv`__ : Run the `src/sEBR_part1.m` and the `src/sEBR_part2.m` scripts. This needs to be done for each sEBR data file separately (but can be batched easily with some knowledge of MATLAB). While going through the manual steps, you'll need to follow the decisions as noted in the `records/sEBR_log.csv` file if you want to get the exact same sEBR values. Finally, run the `read_sEBR.m` script to recreate the `data/sEBR.csv` file.
