Research compendium for AL treatment failure in Kenya

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/kenya_al_failure.git
cd kenya_al_failure
open kenya_al_failure.Rproj
devtools::install_deps()

Overview

The structure within analysis is as follows:

|
|──R/                      # R functions used throughout analysis
|
|──analysis/
   |
   ├── 00_<>.R             # analysis scripts
   |
   ├── data/
   │   ├── DO-NOT-EDIT-ANY-FILES-IN-HERE-BY-HAND
   │   ├── raw/            # data obtained from elsewhere
   │   └── derived/        # data generated during the analysis
   |
   ├── plots/              # plots generated by analysis
   |
   ├── tables/             # table generated by analysis

Compendium DOI:

http://doi.org/xx.xxxx/zenodo.xxxxxxx

The files at the URL above will generate the results as found in the publication. The files hosted at github.com/OJWatson/kenya_al_failure 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://github.com/OJWatson/kenya_al_failure. The compendium contains all data, code, and text associated with the publication. The R files in the analysis 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 and derived data generated.

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/kenya_al_failure.git

Once the download is complete, open the kenya_al_failure.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