In mrc-ide/global-lmic-meffs: Analysis of LMIC COVID-19 Meffs

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-"
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Research compendium for COVID-19 reports in LMICs

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/global-lmic-meffs.git
cd global-lmic-meffs
open globalmicmeffs.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

The raw data is generated from the following orderly repository https://github.com/mrc-ide/global-lmic-reports-orderly. The results are pushed from the server where this orderly task is run to this repository for downstream analysis. This process removes the extra files (css, html templates etc) needed to make the website on which this analysis is based https://mrc-ide.github.io/global-lmic-reports/.

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/global-lmic-meffs 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 https://mrc-ide.github.io/global-lmic-reports/. The compendium contains all data, code, and text associated with the publication. The Rmd files in the analysis/paper/ directory contain details of how all the analyses reported in the paper were conducted, as well as instructions on how to rerun the analysis to reproduce the results. The data/ directory in the analysis/ directory contains all the raw data.

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 no/negligable 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/global-lmic-meffs.git

Once the download is complete, open the globallmicmeffs.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