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

Meeting the stars of the R-universe: PEcAn, an Open Source Project to Take Care of the Planet

Knowing our community’s stories helps us to learn about the people behind our software, brings us closer and offers us new opportunities. To share some of these community stories, we created the rOpenSci interview series “Meeting the stars of the R-Universe”.

Climate change and research in this area have diverse and complex data that demand increasingly complex analysis models. The PEcAn project works to develop this ability.

In this interview, we go into the science of climate change, and explore where data analysis and ecosystem modeling tools are developed. That is the main objective of the PEcAn project, where they collaboratively seek new ways to collect and synthesize data and develop accessible tools to perform these tasks in a reproducible way. Our discussion was attended by Rob Kooper, Chris Black, Eric Scott, Michael C. Dietze, and David LeBauer. All members of the PEcAn project with the same goal: to find more and better ways to integrate the enormous amount of existing data on climate change.

You can also read the post in Spanish.

Downloading snapshots and creating stable R packages repositories using R-universe!

The new snapshot API lets you download a full copy of any CRAN-like repository on R-universe. You can use such a snapshot to mirror the entire CRAN-like repository on your own servers, or for example to build a stable, validated release of your package suite.

Statistical software review now completely integrated with standard review process

Statistical software review has finally reached a stable and mature state, with all organizational processes now entirely integrated with the standard review process. Developers submitting software should notice little difference, except hopefully faster initial processing of submissions. Each submission is now smoothly handled by members of our team of statistical software editors:

• Adam Sparks
• Emi Tanaka
• Jouni Helske
• Paula Moraga
• Rebecca Killick
• Toby Hocking

We currently accept software in the eight categories described in our Statistical Software Development Guide, and are still working on integrating the two additional categories of Statistical Workflow and Network Software. We encourage anybody thinking about submitting to contact any one of the editors, or the two leaders of the software review team, Noam Ross and Mark Padgham, at any time, including anybody interested in submitting software in the upcoming categories of workflow or network software.

rOpenSci’s Communication Channels for Safe and Friendly Exchange

As we anticipated in November 2022 the changes implemented by Twitter have generated a less safe and friendly space for our community. That is why from June 2023, we will stop interacting on this platform. We will maintain the account in hopes that we can return when Twitter is once again a safe and supportive space, but in the meanwhile will focus our communication efforts elsewhere. Read more in our announcement.

Two upcoming community calls!

A Journey through Arrow in R

Wednesday, 28 June 2023 16:00 UTC. More info.

Apache Arrow is a software development platform for building high performance applications that process and transport large data sets. It is designed to improve the performance of data analysis methods, and to increase the efficiency of moving data from one system or programming language to another.

In this community call moderated by Stephanie Hazlitt, our speakers, Nic Crane and Jonathan Keane, will lead us through the Arrow R package.

Mentoring & training program for Scientific Open Source Champions

Tuesday, 25 July 2023 14:00 UTC. More info.

Champions programs are designed to identify, recognize, and reward emerging leaders within a community. The rOpenSci Champions Program is part of a series of activities and projects we are carrying out to ensure our research software serves everyone in our communities, which means that it needs to be sustainable and open, and built by and for all groups.

On this call Beatriz Milz, Victor Ordu and Carolina Pradier will share their experience of being rOpenSci mentors and champions. We will highlight the benefits of being part of the program for you and for your community, what kind of learning, activities and opportunities an open source community champions program provides. Yani will present the details of our Champion Program and answer all your question about it.

Coworking

Read all about coworking in our new post!

Join us for social coworking & office hours monthly on first Tuesdays! Hosted by Steffi LaZerte and various community hosts. Everyone welcome. No RSVP needed. Consult our Events page to find your local time and how to join.

• Tuesday, July 4th, 14:00 European Central / 12:00 UTC “Create/Update your ‘Happy File’/‘Brag Document’!” Hosted by Maëlle Salmon and Steffi LaZerte
  • Explore what goes into a ‘Happy File’/‘Brag Document’ and why you need one.
  • Start collecting items to add to your ‘Happy File’.

• Tuesday, August 1st, 09:00 Americas Pacific (16:00 UTC), “Spatial data in R” Hosted by Mike Mahoney and Steffi LaZerte
  • Work on a project related to spatial data.
  • Explore R packages for working with spatial data.

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 package recently became a part of our software suite:

• dwctaxon, developed by Joel H. Nitta: Edit and validate taxonomic data in compliance with Darwin Core standards (Darwin Core Taxon class https://dwc.tdwg.org/terms/#taxon). It is available on CRAN. It has been reviewed by Collin Schwantes, and Stephen Formel.

Discover more packages, read more about Software Peer Review.

New versions

The following fifteen packages have had an update since the last newsletter: biomartr (v1.0.4), dwctaxon (v2.0.2), FedData (v3.0.4), lingtypology (v1.1.14), MODIStsp (v2.0.10), nodbi (v0.9.5), osmdata (v0.2.3), predictNMB (v0.2.1), rnaturalearth (v0.3.3), rotl (v3.1.0), tarchetypes (0.7.7), targets (1.1.3), tic (v0.13.3), UCSCXenaTools (v1.4.8), and webchem (v1.3.0).

Software Peer Review

There are ten recently closed and active submissions and 3 submissions on hold. Issues are at different stages:

• One at ‘6/approved’:

  • dwctaxon, Tools for Working with Darwin Core Taxon Data. Submitted by Joel Nitta.

• Three at ‘4/review(s)-in-awaiting-changes’:

  • ohun, Optimizing Acoustic Signal Detection. Submitted by Marcelo Araya-Salas.

  • wmm, World Magnetic Model. Submitted by Will Frierson.

  • octolog, Better Github Action Logging. Submitted by Jacob Wujciak-Jens.

• Four at ‘3/reviewer(s)-assigned’:

  • mregions2, Access Data from Marineregions.org: The Marine Regions Gazetteer and the Marine Regions Data Products. Submitted by salvafern.

  • pangoling, Access to Large Language Model Predictions. Submitted by Bruno Nicenboim.

  • dfms, Dynamic Factor Models. Submitted by Sebastian Krantz.

  • fwildclusterboot, Fast Wild Cluster Bootstrap Inference for Linear Models. Submitted by Alexander Fischer. (Stats).

• One at ‘2/seeking-reviewer(s)’:

  • bssm, Bayesian Inference of Non-Linear and Non-Gaussian State Space. Submitted by Jouni Helske. (Stats).

• One at ‘1/editor-checks’:

  • qualtdict, Generating Variable Dictionaries and Labelled Data Exports of Qualtrics. Submitted by lyh970817.

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

On the blog

• rOpenSci Champions Program Teams: Meet César and Marc by Cesar Luis Aybar Camacho, and Marc Choisy.

• Meeting the Stars of the R-Universe: PEcAn, an Open Source Project to Take Care of the Planet by Yanina Bellini Saibene, Alejandra Bellini, Lucio Casalla, and Steffi LaZerte. Climate change and research in this area have diverse and complex data that demand increasingly complex analysis models. The PEcAn project works to develop this ability. Other languages: Conociendo a las estrellas del Universo R: PEcAn, un proyecto de código abierto para cuidar el planeta (es).

• rOpenSci’s Communication Channels for Safe and Friendly Exchange by Yanina Bellini Saibene. Communication channels announcement. rOpenSci stop interacting on Twitter, but we can meet in many other spaces. Other languages: Los canales de comunicación de rOpenSci para un intercambio seguro y amigable (es).

• rOpenSci Champions Program Teams: Meet Cheryl Isabella Lim and Mauro Lepore by Cheryl Isabella Lim, and Mauro Lepore.

• How do you measure the impact of a champions program? by Yanina Bellini Saibene, and CSCCE Staff. A summary of the discussion session on measuring the impact of champion programs at CZI’s Accelerating Open Science in Latin America workshop.

• rOpenSci Champions Program Teams: Meet Alican Cagri Gokcek and Elio Campitelli by Alican Cagri Gokcek, and Elio Campitelli.

• All About Coworking Sessions with rOpenSci by Steffi LaZerte. Discover how rOpenSci coworking sessions have evolved to include themes and community hosts, while still providing a place of community to work and chat.

Tech Notes

• Downloading snapshots and creating stable R packages repositories using r-universe by Jeroen Ooms. We added a a new API on R-universe to download a full snapshot of any CRAN-like repo plus documentation, which you can use to mirror somewhere or just for backup.

• Troubleshooting Pandoc Problems as an R User by Maëlle Salmon, and Christophe Dervieux. How to solve your Pandoc problems thanks to documentation reading, experimentation… and a bit of experience 😅 . Other languages: Résoudre ses problèmes de Pandoc en tant qu’utilisateur·rice de R (fr).

Call for maintainers

Call 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? (or listening to its discussion on the R Weekly highlights podcast hosted by Eric Nantz and Mike Thomas)!

• rvertnet, Retrieve, map and summarize data from the VertNet.org archives (https://vertnet.org/). Functions allow searching by many parameters, including taxonomic names, places, and dates. In addition, there is an interface for conducting spatially delimited searches, and another for requesting large datasets via email. Issue for volunteering.

• natserv. Interface to NatureServe (https://www.natureserve.org/). Includes methods to get data, image metadata, search taxonomic names, and make maps. Issue for volunteering.

• geojsonlint, Tools for linting GeoJSON. Includes tools for interacting with the online tool https://geojsonlint.com, the Javascript library geojsonhint (https://www.npmjs.com/package/geojsonhint), and validating against a GeoJSON schema via the Javascript library (https://www.npmjs.com/package/is-my-json-valid). Some tools work locally while others require an internet connection. Issue for volunteering.

Call for comaintainers

Refer to our somewhat recent blog post to identify other packages where help is especially wished for! See also our help wanted page – before opening a PR, we recommend asking in the issue whether help is still needed.

Package development corner

Some useful tips for R package developers. 👀

How to produce code hints for users?

Sometimes your code can infer what the next user step should be, or what the next possible user steps could be. How to make it easy for the user to run these hints?

Here’s some inspiration:

• You could use cli::ui_todo(), as done in usethis. By the way if your package is using ui_ functions from usethis, don’t miss the cli article on how to migrate your code to using cli instead, as that’s what’s currently recommended.

• Also in the cli package, a you can provide a special kind of link that runs the code if clicked in the RStudio IDE: “Click to run code”. You might recognize this from running snapshot tests with testthat, and receiving the message to review/accept them with these special links.

cli::cli_text("Run {.run praise::praise()} now!")

• If your code is run in RStudio IDE (checkable with rstudioapi::isAvailable()), you could use rstudioapi::sendToConsole() to send example code to the console for the user to consider (example).

devtag: Restrict Some Help Files to Development

The new devtag package by Antoine Fabri “allows you to use @dev tags in your roxygen2 headers so you’ll generate help files for unexported objects, that you will enjoy during development but won’t be accessible for users that install your package”. This might be nicer to read than the classical @NoRd docs for internal functions!

Useful post on the retirement of popular spatial packages

Don’t miss Jakub Nowosad’ blog post “Upcoming changes to popular R packages for spatial data: what you need to do”! And again, tell your spatial R friends about this big change.

More on CRAN C++ requirements

Do you remember the tidyverse article “New CRAN requirements for packages with C and C++”? You might also enjoy this repo by rOpenSci Mark Padgham, “Test R package compilation with >= C++17”.

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.

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.