rOpenSci News Digest, March 2025

Posted on March 26, 2025 by rOpenSci - open tools for open science in R bloggers | 0 Comments

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Dear rOpenSci friends, it’s time for our monthly news roundup! You can read this post on our blog. Now let’s dive into the activity at and around rOpenSci!

rOpenSci HQ

rOpenSci Champions Program 2025 In Spanish: Apply before April 30th!

We have great news: The call for applications to be part of the new cohort of our 2025 Program is now open! And for the first time it will be in Spanish!

Our program seeks to identify, recognize and reward people who are leaders in an open science community, research software engineering and the R programming community.

This year’s program is focused on people from Latin America and for the first time will be conducted entirely in Spanish. The main goal is to foster sustainable research software as a pillar of Open Science in Latin America through capacity and community building.

Find out more in our call for applications open until Wednesday, April 30, 2025.

Better documentation for R-universe!

Thanks to funding by Google Season of Docs, we were able to start a new comprehensive documentation project for all users and developers of R-universe. We established a central place where we collect the various sources of information and describe examples and use cases, using popular authoring tools to support collective maintenance.

Read more in our blog post, read the documentation website.

rOpenSci Participation at NumFOCUS’ DISC Unconf 2025

The NumFOCUS Diversity & Inclusion in Scientific Computing (“DISC”) Unconf took place as a hybrid event in São Paulo, Brazil, from March 14 to 16, 2025. Our community manager, Yanina Bellini Saibene, and rOpenSci Champions, Andrea Gomez Vargas and Liz Hare, participated.

Read more in our report from the event.

This event also presented the opportunity to meet in person with other members of the rOpenSci community in Sao Paulo, in the picture we can see Francesca Palmeira (rOpenSci Champions), Andrea Gomez Vargas (rOpenSci Champions), Beatriz Milz (rOpenSci Editor and Mentor), Haydee Svab (rOpenSci Champions) and Yanina Bellini Saibene (rOpenSci Community Manager).

Francesca, Andrea, Beatriz, Heydee and Yani stand up and smiling for the picture

Community Call “Fomentando la Ciencia Abierta en América Latina – Programa de rOpenSci” Resources

All the resources for the community call in Spanish Fomentando la Ciencia Abierta en América Latina – Programa de rOpenSci are now available on our website. Check the video and links to other resources related to speakers’ experience as mentors and mentees in the rOpenSci Champions Program.

Coworking

Read all about coworking!

And remember, you can always cowork independently on work related to R, work on packages that tend to be neglected, or work on what ever you need to get done!

Software 📦

New packages

The following five packages recently became a part of our software suite:

  • pangoling, developed by Bruno Nicenboim: Provides access to word predictability estimates using large language models (LLMs) based on transformer architectures via integration with the Hugging Face ecosystem. The package interfaces with pre-trained neural networks and supports both causal/auto-regressive LLMs (e.g., GPT-2; Radford et al., 2019) and masked/bidirectional LLMs (e.g., BERT; Devlin et al., 2019, doi:10.48550/arXiv.1810.04805) to compute the probability of words, phrases, or tokens given their linguistic context. By enabling a straightforward estimation of word predictability, the package facilitates research in psycholinguistics, computational linguistics, and natural language processing (NLP). It has been reviewed by Lisa Levinson and Utku Turk.

  • mbquartR, developed by Alex Koiter: This package has four main functions: 1) download the Manitoba Original Survey Legal Descriptions data set; 2) find the coordinates of a quarter sections given the legal land description (e.g., “NE-11-33-29W”); 3) find the legal land description using coordinates (lat and long); and 4) plot these points on a map. It has been reviewed by Emily H Markowitz and Sheila Saia.

  • mapmetadata, developed by Rachael Stickland: Prior to gaining full access to health datasets, explore publicly available metadata and map metadata onto predefined research domains. This package uses structural metadata files downloaded from the Health Data Research Gateway (https://healthdatagateway.org/en). In theory, any metadata file with the same structure as the files downloaded from this gateway can be used with this package, but the package has been developed and tested on metadata files from this gateway only. It has been reviewed by Zoë Turner and Yohann Mansiaux.

  • geotargets, developed by Nicholas Tierney together with Eric Scott and Andrew Brown: Provides extensions for various geographic spatial file formats, such as shape files and rasters. Currently provides support for the terra geographic spatial formats. See the vignettes for worked examples, demonstrations, and explanations of how to use the various package extensions. It has been reviewed by Anthony Martinez and Denisse Fierro Arcos.

  • saperlipopette, developed by Maëlle Salmon: Holds functions creating Git messes, that users would then solve, to follow https://ohshitgit.com/.

Discover more packages, read more about Software Peer Review.

New versions

The following five packages have had an update since the last newsletter: ijtiff (v3.1.0), mapmetadata (v4.0.2), tidyhydat (0.7.1), vcr (v1.7.0), and waywiser (v0.6.2).

Software Peer Review

There are twelve recently closed and active submissions and 6 submissions on hold. Issues are at different stages:

Find out more about Software Peer Review and how to get involved.

On the blog

Software Review

Use cases

Three use cases of our packages and resources have been reported since we sent the last newsletter.

Explore other use cases and report your own!

Calls for contributions

Calls for maintainers

If you’re interested in maintaining any of the R packages below, you might enjoy reading our blog post What Does It Mean to Maintain a Package?.

Calls for contributions

Refer to our help wanted page – before opening a PR, we recommend asking in the issue whether help is still needed.

The bib2df package, for parsing BibTeX files into tibbles, would need some help! Issue for volunteering.

Package development corner

Some useful tips for R package developers. 👀

lintr::use_lintr()

If you use the lintr package for static code analysis, you might need to add a configuration file that will activate some linters, deactive others, exclude files from the linting. To create it, you can run lintr::use_lintr(). Remember this is a function of lintr, not usethis!

flint renamed flir

Speaking of linting, you might remember about a package we mentioned in last August’s newsletter, that would not only find problems in your package like lintr, but also fix them. This package by Etienne Bacher is now called flir.

Air, a new formatter for R

Have you ever used the styler R package to style your codebase? You might be interested in the new formatter Air. Read more in the post by Davis Vaughan and Lionel Henry on the tidyverse blog.

Compared to styler, Air offers much less customization, but is much faster. A section of the announcement is dedicated to the comparison with styler.

IDEs for R package developers

Have you heard of the beta IDE Positron developed by Posit (formerly RStudio)? It might be worth a try, for instance for being able to install Git extensions like GitLens, or for the nice UI for unit tests. Note that it’s still in beta.

Other IDEs popular in the R community are

  • The precursor of Positron developed by Posit: RStudio that Posit said will still be maintained;
  • The cousins of Positron VSCodium or VSCode with the R Extension. Positron is a fork of VSCode like VSCodium, therefore its interface will be familiar to VSCode or VSCodium users.
  • Neovim
  • ESS

Penguins data in base R!

Looking for a dataset for tests or docs, available in base R? The penguins dataset, originally from the palmerpenguins package, is coming to the base R datasets package! Thanks to to Ella Kaye, Heather Turner, and Kristen Gorman for their work on this.

Git Stash for Newbies

Read all about Git Stash, and why and how you might use it, in a post by Meghan Harris.

Last words

Thanks for reading! If you want to get involved with rOpenSci, check out our Contributing Guide that can help direct you to the right place, whether you want to make code contributions, non-code contributions, or contribute in other ways like sharing use cases. You can also support our work through donations.

If you haven’t subscribed to our newsletter yet, you can do so via a form. Until it’s time for our next newsletter, you can keep in touch with us via our website and Mastodon account.

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