Packages

172

Package authors

609

GitHub stars

1,126

CRAN downloads

13M

Adherence to good practices

Good practices as defined by rOpenSci dev guide, and Epiverse-TRACE blueprints.
Metadata
Has Authors@R field
 83%
Uses a software forge
Links to a software forge (Codeberg, Gitea, GitHub, GitLab) in `URL` or `BugReports`		 58%
Has ORCID in Author field
 45%
Has LICENSE.md
 19%
Sustainability
Does not depend on deprecated packages
XML, RCurl, RUnit, plyr, or reshape2 packages		 82%
Documentation
Uses Roxygen
As indicated by the presence of the `RoxygenNote` field in `DESCRIPTION`		 80%
Has a knitr vignette
 47%
Has NEWS.md
 40%
Uses pkgdown
 23%
Has README.Rmd
 20%
Testing & CI
Uses a testing framework
As indicated by the presence of testthat, testit, unitizer, RUnit, tinytest in `Suggests`		 42%
Uses GitHub Actions
 30%
Community
Has a code of conduct
 9%
Has a contributing guide
 8%
References

The analysis was done using the R Statistical language (v4.4.2; R Core Team, 2024) on Ubuntu 22.04.5 LTS, using the packages pkgsearch (v3.1.3), stringi (v1.8.4), yaml (v2.3.10), lubridate (v1.9.3), glue (v1.7.0), gt (v0.11.0), report (v0.5.9), jsonlite (v1.8.8), askpass (v1.2.0), ggplot2 (v3.5.1), stringr (v1.5.1), dplyr (v1.1.4), purrr (v1.0.2), scales (v1.3.0), tidyr (v1.3.1) and ctv (v0.9.5).

Citations
  • Csárdi G, Salmon M (2023). pkgsearch: Search and Query CRAN R Packages. R package version 3.1.3, https://r-hub.github.io/pkgsearch/, https://github.com/r-hub/pkgsearch.
  • Gagolewski M (2022). “stringi: Fast and portable character string processing in R.” Journal of Statistical Software, 103(2), 1-59. doi:10.18637/jss.v103.i02 https://doi.org/10.18637/jss.v103.i02.
  • Garbett SP, Stephens J, Simonov K, Xie Y, Dong Z, Wickham H, Horner J, reikoch, Beasley W, O’Connor B, Warnes GR, Quinn M, Kamvar ZN, Gao C (2024). yaml: Methods to Convert R Data to YAML and Back. R package version 2.3.10, https://github.com/vubiostat/r-yaml/.
  • Grolemund G, Wickham H (2011). “Dates and Times Made Easy with lubridate.” Journal of Statistical Software, 40(3), 1-25. https://www.jstatsoft.org/v40/i03/.
  • Hester J, Bryan J (2024). glue: Interpreted String Literals. R package version 1.7.0, https://github.com/tidyverse/glue, https://glue.tidyverse.org/.
  • Iannone R, Cheng J, Schloerke B, Hughes E, Lauer A, Seo J, Brevoort K, Roy O (2024). gt: Easily Create Presentation-Ready Display Tables. R package version 0.11.0, https://github.com/rstudio/gt, https://gt.rstudio.com.
  • Makowski D, Lüdecke D, Patil I, Thériault R, Ben-Shachar M, Wiernik B (2023). “Automated Results Reporting as a Practical Tool to Improve Reproducibility and Methodological Best Practices Adoption.” CRAN. https://easystats.github.io/report/.
  • Ooms J (2014). “The jsonlite Package: A Practical and Consistent Mapping Between JSON Data and R Objects.” arXiv:1403.2805 [stat.CO]. https://arxiv.org/abs/1403.2805.
  • Ooms J (2023). askpass: Password Entry Utilities for R, Git, and SSH. R package version 1.2.0, https://github.com/r-lib/askpass.
  • R Core Team (2024). R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/.
  • Wickham H (2016). ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York. ISBN 978-3-319-24277-4, https://ggplot2.tidyverse.org.
  • Wickham H (2023). stringr: Simple, Consistent Wrappers for Common String Operations. R package version 1.5.1, https://github.com/tidyverse/stringr, https://stringr.tidyverse.org.
  • Wickham H, François R, Henry L, Müller K, Vaughan D (2023). dplyr: A Grammar of Data Manipulation. R package version 1.1.4, https://github.com/tidyverse/dplyr, https://dplyr.tidyverse.org.
  • Wickham H, Henry L (2023). purrr: Functional Programming Tools. R package version 1.0.2, https://github.com/tidyverse/purrr, https://purrr.tidyverse.org/.
  • Wickham H, Pedersen T, Seidel D (2023). scales: Scale Functions for Visualization. R package version 1.3.0, https://github.com/r-lib/scales, https://scales.r-lib.org.
  • Wickham H, Vaughan D, Girlich M (2024). tidyr: Tidy Messy Data. R package version 1.3.1, https://github.com/tidyverse/tidyr, https://tidyr.tidyverse.org.
  • Zeileis A, Bivand R, Eddelbuettel D, Hornik K, Vialaneix N (2023). “CRAN Task Views: The Next Generation.” arXiv 2305.17573, arXiv.org E-Print Archive. doi:10.48550/arXiv.2305.17573 https://doi.org/10.48550/arXiv.2305.17573. Zeileis A (2005). “CRAN Task Views.” R News, 5(1), 39-40. https://CRAN.R-project.org/doc/Rnews/.
Related work
Authors and acknowledgements

This analysis was initially started by Hugo Gruson, before being picked up in an Epiverse hackathon at the WHO Collaboratory in Berlin in September 2023 by James Baker, Chathura Edirisuriya and Hugo Gruson. The final dashboard creation and automation was done by Hugo Gruson.

Additional contributions and reviews were provided by Chris Hartgerink.

Funding

Hugo Gruson was funded for this work by the Wellcome Trust 224140/Z/21/Z.