This is a working R compendium (think R package but for reproducible analysis). The analysis directory contains R scripts used to generate the results. 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/.
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-results are the development versions and may have changed since the report was published
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 analysis/
directory contains:
data/
directory) 01_xxxx
directories)figures/
directory)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
Code: MIT year: 2020, copyright holder: OJ Watson
Data: CC-0 attribution requested in reuse
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.