ojwatson / india-ascertainment

Research compendium for COVID-19 analysis in India

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/mrc-ide/india-ascertainment.git
cd india-rascertainment
open india-rascertainment.Rproj
devtools::install_deps()

Overview

The structure within analysis is as follows:

analysis/
    |
    ├── 01_xxxxx /           # analysis scripts used for generating figures
    |
    ├── figures/              # 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
    |
    ├── src/                # orderly files

Compendium DOI:

http://dx.doi.org/xxxxxxx

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/india-ascertainment.git

Once the download is complete, open the india-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. This has the advantage of allowing devtools::install_dev_deps() to install the required R packages needed to run the code in this repository

Licenses

Code: MIT year: 2021, copyright holder: OJ Watson

Data: CC-0 attribution requested in reuse