README.md

In mrc-ide/india-ascertainment: Analysis of COVID-19 mortality in India

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/
    |
    ├── downstream.R                    # Generating figures from model runs
    ├── cluster_submitting.R            # Script for submitting model fits to cluster
    ├── sourcing_data.R                 # Script to fetch data from external sources for model fits
    ├── pars_best.R                     # Script for updating initial parameters used in model fitting
    ├── safir.R                         # IBM example model run
    |
    ├── plots/                          # location of figures produced by the analysis scripts
    |
    ├── tables/                         # location of tables 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

The R package

This repository is organized as an R package. There are some 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/mrc-ide/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: 2022, copyright holder: OJ Watson

Data: CC-0 attribution requested in reuse

mrc-ide/india-ascertainment documentation built on Jan. 20, 2022, 11:51 p.m.