CRAN task view: epidemiology

[sbfnk]

Identify tools, resources and potential blockers to facilitate activities on day 2 & 3.

[sbfnk]

The objective of this task is to adapt the CRAN task view for epidemiology to provide a more accessible resource for finding out which R packages are available for which epidemiological task.

Tools:

• (R)markdown, github pages, ...

Resources:

• The existing task view provides a good potential starting point

Potential blockers:

• no license in the CRAN repo
• limitations in what can be visualised as long as this lives in the CRAN task view
• need to avoid overlap with the Epi R Handbook
• not coding so potentially not good use of our time on the two days

Expected outcomes:

• to be decided: either an amended version of the existing task view or something that can meaningfully live besides it

[JamesABaker]

Link to cran repo: https://github.com/cran-task-views/Epidemiology

and the cran repo: https://cran.r-project.org/web/views/Epidemiology.html

[Bisaloo]

We are working towards an automated health check of the universe of Epidemiology R packages as defined in the CRAN Task View.

Development is ongoing at: https://github.com/Bisaloo/cran-task-view-analysis

[Bisaloo]

First working draft is live at https://hugogruson.fr/cran-task-view-analysis/ (to be moved to an organization GitHub repository later)

[JamesABaker]

We are also doing a check of as many repos as possible and adding GitHub Urls to the cran description. In the long term, this will help automate the "health check" once individual projects merge the PR.

PR example

The github URL is added to the description. This will give cran users awareness of the GitHub location.

From a technical point of view, this is useful for allowing autolinking in pkgdown websites. Here is the explanation: https://pkgdown.r-lib.org/articles/linking.html?q=cross#across-packages

For an example see https://github.com/tidyverse/dplyr/blob/main/DESCRIPTION

[JamesABaker]

📅 Day 1 recap

Contributors @Bisaloo @chathuracse

• Roadmap for repo health check
• Not all Cran entries were trivially associated with a GH repo. We tried to bolster this list for test purposes.
  • 🤝 Opened 10 PRs across the Cran ecosystem to include Git repos in Cran descriptions. 3 merged, 3 wontfix due to read only.
    • Added github url tobadia/R0#17
    • Added url for github reconhub/epicontacts#134
    • Added GitHub URL into the description cran/epiDisplay#1
    • Added github url reconhub/epiflows#47
    • Added GitHub URL EU-ECDC/EpiReport#17
    • Added github URL reconhub/incidence#133
    • Update DESCRIPTION cran/powerSurvEpi#1
    • Added github repo reconverse/i2extras#18
    • Update DESCRIPTION reconhub/epitrix#32
    • Update DESCRIPTION cran/epitools#1
• 🚀 New features for repo health analytics.
  • GH API calls Feature git api epiverse-connect/ctv-analysis#3
  • Cran scrape (PR WIP)
  • Linting issue ⚠️ working with larger package Remove non-existing stats::recode function from NAMESPACE bernadette-eu/Bernadette#10
  • md5 comparison for workflow files Feature GitHub workflow check epiverse-connect/ctv-analysis#4
  • File presence checks Feature git api epiverse-connect/ctv-analysis#3
    • pkgdown yamls
    • readme
    • workflow folder
    • license

[JamesABaker]

Day 2 morning

🚀 Features developed.

• Analytics of pass-fails Add summary plots epiverse-connect/ctv-analysis#11 📊
• Resolved and merged API Feature git api epiverse-connect/ctv-analysis#3 and Add table with info pulled from GitHub epiverse-connect/ctv-analysis#5 🤝
• Added fingerprint function Feature GitHub workflow check epiverse-connect/ctv-analysis#4
• MIT license added Add license epiverse-connect/ctv-analysis#1 📃

🛑 Issues encountered.

• Pre-commit hooks are not working BUG | pre-commit does not complete initial setup epiverse-connect/ctv-analysis#12
• Vectors should be implemented rather than functions, loops and OOP Vectorize gh_file_list_exists() epiverse-connect/ctv-analysis#8
• GH action can be checked directly Check presence of GitHub Actions CI via the dedicated endpoint epiverse-connect/ctv-analysis#7
• Many more features on roadmap Roadmap of elements to check epiverse-connect/ctv-analysis#2

[Bisaloo]

Results and summary plots are displayed via a quarto dashboard available at http://hugogruson.fr/cran-task-view-analysis/.

The dashboard is automatically re-rendered and deployed after each push on main via a GitHub Actions workflow.

[JamesABaker]

This directly shows how this resource will answer our two questions:

• Which packages are the most complete?
• What is the overall health & completeness of the epi package ecosystem?

[PatriciaRose963]

Comments from reviewers

General comments

1. The team has done a lot of great work flagging issues and making pull requests for existing packages to improve the overall health of the epi pipeline ecosystem.

2. The finalised report is likely most useful for the package developer community. It is not clear how unaware developers would be of the fact that their packages fail the presented checks.

3. For package users, this likely would not influence decision making on which packages to use - this is primarily determined by functionality.

4. We were confused about the deprecated deps check - would this cause the package to become archived in CRAN?

Future directions

1. Integration of checks into the existing task view or into a platform that lists functionality and categorises packages by into subtopics would be helpful

2. It would be helpful to understand what proportion of epi packages are not captured through the epidemiology CRAN tag (github or improperly tagged CRAN packages)

[JamesABaker]

Great suggestions! Thanks very much.

Hopefully our changes in epiverse-connect/ctv-analysis#16 and epiverse-connect/ctv-analysis#15 go some way to explaining our vision for the long term support of users as well as maintainers. They also should help define what each check is useful for as a proxy for quality.

The future directions suggestions are closely aligned to some of the issues on our roadmap, so it is good to hear that we are on the right track!