Seychelles Cancer Quality of Care Scoping Review

This repository is a template for a docker-containerised, {targets}-based, {renv}-enabled R workflow for Seychelles cancer quality of care scoping review.

Repository Structure

The project repository is structured as follows:

sc-ca-qoc-review
    |-- .github/
    |-- data/
    |-- data-raw/
    |-- outputs/
    |-- R/
    |-- renv
    |-- reports
    |-- _targets.R
    |-- .Rprofile
    |-- packages.R
    |-- renv.lock

• .github contains project testing and automated deployment of outputs workflows via continuous integration and continuous deployment (CI/CD) using Github Actions.

• data/ contains intermediate and final data outputs produced by the workflow.

• data-raw/ contains raw datasets, usually either downloaded from source or added manually, that are used in the project.

• outputs/ contains compiled reports and figures produced by the workflow.

• R/ contains functions developed/created specifically for use in this workflow.

• renv/ contains renv package specific files and directories used by the package for maintaining R package dependencies within the project. The directory renv/library, is a library that contains all packages currently used by the project. This directory, and all files and sub-directories within it, are all generated and managed by the renv package. Users should not change/edit these manually.

• reports/ contains literate code for R Markdown and/or Quarto reports rendered in the workflow.

• _targets.R file defines the steps in the workflow’s data ingest, data processing, data analysis, and reporting pipeline.

• .Rprofile file is a project R profile generated when initiating renv for the first time. This file is run automatically every time R is run within this project, and renv uses it to configure the R session to use the renv project library.

• packages.R file lists out all R package dependencies required by the workflow.

• renv.lock file is the renv lockfile which records enough metadata about every package used in this project that it can be re-installed on a new machine. This file is generated by the renv package and should not be changed/edited manually.

Reproducibility

R version

This project was built using R 4.5.1. To manage R versions, it is recommended to use rig - an R installation manager - to be able to install multiple versions of R and switch between them as needed.

R package dependencies

This project uses the {renv} framework to record R package dependencies and versions. Packages and versions used are recorded in renv.lock and code used to manage dependencies is in the renv directory and other files in the root project directory.

On starting an R session in the working directory of this repository, first run

renv::restore()

to install R package dependencies.

The workflow

The current workflow has the following steps:

graph LR
  style Graph fill:#FFFFFF00,stroke:#000000;
  subgraph Graph
    direction LR
    x302aac5a349e94c8(["extraction_matrix_data"]):::skipped --> xf69487b7eb1bdf74(["data_review_report"]):::completed
    x81531a598a877851(["extraction_matrix_data_file"]):::skipped --> x302aac5a349e94c8(["extraction_matrix_data"]):::skipped
    xa1f98815230ee6ce(["sids_list"]):::skipped --> xe888894c32b82646(["sids_islands"]):::skipped
    
  end

Loading

To run the workflow, issue the following command in R from within the project directory

targets::tar_make()

or issue the following command in Terminal from within the project directory

Rscript -e  "targets::tar_make()"

Authors

• Dr Nyasha Manyeruke - University of Oxford
• Dr Johanna Rapanarilala - Oncology Unit, Ministry of Health, Seychelles
• Dr Sylvie Pool - Ministry of Health, Seychelles and University of Oxford
• Dr Ernest Guevarra - University of Oxford

License

All code in this workflow is released under a GPL-3.0 license. All text and reports in this workflow is released under a CC-BY-4.0 license. All data is released under a CC0 license.