README.Rmd

---
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r, echo = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-"
)
# Please put your title here to include it in the file below.
Title <- "More Than Smell—COVID-19 Is Associated With Severe Impairment of Smell, Taste, and Chemesthesis"
```

# GCCR001

[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/vparmac/GCCR-001/master?urlpath=rstudio)

This repository contains the data and code for our paper:

> Parma et. al., (2020). _`r Title`_. Chemical Senses <https://doi.org/10.1093/chemse/bjaa041>


### How to cite

Please cite this compendium as:

> Valentina Parma, Kathrin Ohla, Maria G Veldhuizen, Masha Y Niv, Christine E Kelly, Alyssa J Bakke, Keiland W Cooper, Cédric Bouysset, Nicola Pirastu, Michele Dibattista, Rishemjit Kaur, Marco Tullio Liuzza, Marta Y Pepino, Veronika Schöpf, Veronica Pereda-Loth, Shannon B Olsson, Richard C Gerkin, Paloma Rohlfs Domínguez, Javier Albayay, Michael C Farruggia, Surabhi Bhutani, Alexander W Fjaeldstad, Ritesh Kumar, Anna Menini, Moustafa Bensafi, Mari Sandell, Iordanis Konstantinidis, Antonella Di Pizio, Federica Genovese, Lina Öztürk, Thierry Thomas-Danguin, Johannes Frasnelli, Sanne Boesveldt, Özlem Saatci, Luis R Saraiva, Cailu Lin, Jérôme Golebiowski, Liang-Dar Hwang, Mehmet Hakan Ozdener, Maria Dolors Guàrdia, Christophe Laudamiel, Marina Ritchie, Jan Havlícek, Denis Pierron, Eugeni Roura, Marta Navarro, Alissa A Nolden, Juyun Lim, Katherine L Whitcroft, Lauren R Colquitt, Camille Ferdenzi, Evelyn V Brindha, Aytug Altundag, Alberto Macchi, Alexia Nunez-Parra, Zara M Patel, Sébastien Fiorucci, Carl M Philpott, Barry C Smith, Johan N Lundström, Carla Mucignat, Jane K Parker, Mirjam van den Brink, Michael Schmuker, Florian Ph S Fischmeister, Thomas Heinbockel, Vonnie D C Shields, Farhoud Faraji, Enrique Santamaría, William E A Fredborg, Gabriella Morini, Jonas K Olofsson, Maryam Jalessi, Noam Karni, Anna D’Errico, Rafieh Alizadeh, Robert Pellegrino, Pablo Meyer, Caroline Huart, Ben Chen, Graciela M Soler, Mohammed K Alwashahi, Antje Welge-Lüssen, Jessica Freiherr, Jasper H B de Groot, Hadar Klein, Masako Okamoto, Preet Bano Singh, Julien W Hsieh, GCCR Group Author, Danielle R Reed, Thomas Hummel, Steven D Munger, John E Hayes, More Than Smell—COVID-19 Is Associated With Severe Impairment of Smell, Taste, and Chemesthesis, Chemical Senses, Volume 45, Issue 7, September 2020, Pages 609–622, <https://doi.org/10.1093/chemse/bjaa041>

## Contents

The **analysis** directory contains:

  - [:file\_folder: paper](/analysis/paper): R Markdown source document
    for manuscript. Includes code to reproduce the figures and tables
    generated by the analysis. It also has a rendered version,
    `paper.docx`, suitable for reading (the code is replaced by figures
    and tables in this file)
  - [:file\_folder: data](/analysis/data): Data used in the analysis.
  - [:file\_folder: figures](/analysis/figures): Plots and other
    illustrations
  - [:file\_folder:
    supplementary-materials](/analysis/supplementary-materials):
    Supplementary materials including notes and other documents
    prepared and collected during the analysis.

## How to run in your broswer or download and run locally

This research compendium has been developed using the statistical programming
language R. To work with the compendium, you will need
installed on your computer the [R software](https://cloud.r-project.org/)
itself and optionally [RStudio Desktop](https://rstudio.com/products/rstudio/download/).

The simplest way to explore the text, code and data is to click on
[binder](https://mybinder.org/v2/gh/vparmac/GCCR-001/master?urlpath=rstudio)
to open an instance of RStudio in your browser, which will have the
compendium files ready to work with. Binder uses rocker-project.org
Docker images to ensure a consistent and reproducible computational
environment. These Docker images can also be used locally.

You can download the compendium as a zip from from this URL:
[master.zip](/archive/master.zip). After unzipping:
- open the `.Rproj` file in RStudio
- run `devtools::install()` to ensure you have the packages this analysis depends on (also listed in the
[DESCRIPTION](/DESCRIPTION) file).
- finally, open `analysis/paper/paper.Rmd` and knit to produce the `paper.docx`, or run `rmarkdown::render("analysis/paper/paper.Rmd")` in the R console

### Licenses

**Text and figures :**  [CC-BY-4.0](http://creativecommons.org/licenses/by/4.0/)

**Code :** See the [DESCRIPTION](DESCRIPTION) file

**Data :** [CC-0](http://creativecommons.org/publicdomain/zero/1.0/) attribution requested in reuse

### Contributions

We welcome contributions from everyone. Before you get started, please see our [contributor guidelines](CONTRIBUTING.md). Please note that this project is released with a [Contributor Code of Conduct](CONDUCT.md). By participating in this project you agree to abide by its terms.