README.md

In mrc-ide/covid-mortality-ascertainment: Analysis of COVID-19 mortality ascertainment

Research compendium for analysis of COVID-19 mortality ascertainment

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/covid-mortality-ascertainment.git
cd covid-mortality-ascertainment
open covid-mortality-ascertainment.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

Compendium DOI:

http://dx.doi.org/xxxxxxx

The files at the URL above will generate the results as found in the publication. The files hosted at github.com/mrc-ide/covid-mortality-ascertainment are the development versions and may have changed since the report was published

Overview of contents

This repository is our research compendium for our analysis of the ascertainment of COVID-19 mortality. The compendium contains all data, code, and text associated with the publication (inquire for being added to google doc). For analysis that was conducted on cluster/remote resources due to size of analysis, the code used to conduct analysis is included and the outputs saved in the raw directory in the data/ directory in the analysis/ directory. Data generated through analysis of these model runs or of other raw data is in the derived data directory.

The supplementary files

The analysis/ directory contains:

• all the data files (in csv or rds format, in the data/ directory)
• all analysis R scripts (in the 01_xxxx directories)
• all the figures that are included in the paper (in the figures/ directory)

The R package

This repository is organized as an R package. There are a few R functions exported in this package - the majority of the R code is in the analysis 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/covid-mortality-ascertainment.git

Once the download is complete, open the covid-mortality-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

mrc-ide/covid-mortality-ascertainment documentation built on Dec. 21, 2021, 10:03 p.m.