README.Rmd

---
output:
  rmarkdown::github_document
---

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```{r, echo = FALSE}
knitr::opts_chunk$set(
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[![minimal R version](https://img.shields.io/badge/R%3E%3D-`r as.character(getRversion())`-brightgreen.svg)](https://cran.r-project.org/)
[![Licence](https://img.shields.io/github/license/mashape/apistatus.svg)](http://choosealicense.com/licenses/mit/) 

## Research compendium for alternative COVID-19 mortality analyses

This is a working R compendium (think R package but for reproducible analysis). A good overview on research compendiums, see the [R for Reproducible Research](https://annakrystalli.me/rrresearch/index.html) course.

### Installation

```
git clone https://github.com/bailey-lab/selmar.git
cd selmar
open selmar.Rproj
```

Next, if `renv` has been used in this repository (look out for `renv.lock`) then use `renv::restore` to set up package dependencies. Otherwise `devtools::install_dev_deps()` will install all required packages, as specified in the Imports in DESCRIPTION. 

### 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: 
 
https://doi.org/X/X

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 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. For any R packages that are used frequently in this repository, they are documented in `R/` and are used in the analysis folder using `devtools::load_all()`. 

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):

```{r eval=FALSE}
git clone https://github.com/bailey-lab/selmar.git
```

Once the download is complete, open the `selmar.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. 

<!-- To add this once all the analysis is done -->
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](http://opensource.org/licenses/MIT) year: `r format(Sys.Date(), "%Y")`, copyright holder: OJ Watson

Data: [CC-0](http://creativecommons.org/publicdomain/zero/1.0/) attribution requested in reuse