Research compendium for COVID-19 analysis in Iran

This is a working R compendium (think R package but for reproducible analysis). The analysis directory contains R scripts used to generate the results.

Installation

git clone https://github.com/OJWatson/iran-ascertainment.git
cd iran-rascertainment
open iran-rascertainment.Rproj
devtools::install_deps()

Overview

The structure within analysis is as follows:

analysis/
    |
    ├── xxxxx /             # analysis scripts used for generating figures
    |
    ├── plots/              # location of figures produced by the analysis scripts
    |
    ├── data/
    │   ├── DO-NOT-EDIT-ANY-FILES-IN-HERE-BY-HAND
    │   ├── raw_data/       # data obtained from elsewhere
    │   └── derived_data/   # data generated during the analysis
    |
    ├── tables/             # location of tables produced by the analysis scripts

Compendium DOI:

https://doi.org/10.5281/zenodo.6475585

The files at the URL above will generate the results as found in the publication.

The R package

This repository is organized as an R package. There are no/negligable R functions exported in this package - the majority of the R code is in the analysis and src directory. The R package structure is here to help manage dependencies, to take advantage of continuous integration, and so we can keep file and data management simple.

To download the package source as you see it on GitHub, for offline browsing, use this line at the shell prompt (assuming you have Git installed on your computer):

git clone https://github.com/OJWatson/iran-ascertainment.git

Once the download is complete, open the iran-ascertainment.Rproj in RStudio to begin working with the package and compendium files. We will endeavour to keep all package dependencies required listed in the DESCRIPTION.

In addition we use renv to track package dependencies for reproducibility. Please use renv::restore to restore the state of the project and see https://rstudio.github.io/renv/articles/renv.html for more information.

Licenses

Code: MIT year: 2022, copyright holder: OJ Watson

Data: CC-0 attribution requested in reuse