rOpenSci News Digest, July 2024

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Dear rOpenSci friends, it’s time for our monthly news roundup!

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You can read this post on our blog. Now let’s dive into the activity at and around rOpenSci!

rOpenSci HQ

Announcing New Software Peer Review Editors: Beatriz Milz and Margaret Siple

We are excited to welcome Beatriz Milz and Margaret Siple to our team of Associate Editors for rOpenSci Software Peer Review. They join Laura DeCicco, Julia Gustavsen, Anna Krystalli, Mauro Lepore, Noam Ross, Maëlle Salmon, Emily Riederer, Adam Sparks, and Jeff Hollister.

Meet Beatriz and Margaret in their introduction blog post. Welcome on board to you both, thank you for your service!

A fresh new look for R-universe!

You might have noticed that R-universe got a big refresh. 🍦 Read all about this big overhaul of the interface.

Resources from the rOpenSci community at useR! 2024

While some video recordings have not yet been posted on the useR! YouTube channel, some slidedecks and materials are already available.

• Maëlle Salmon’s keynote talk “How your code might get rusty” (Slides | Recording)
• Jeroen Ooms’ talk “Navigating the R Ecosystem Using R-Universe” (Slides)
• Jon Harmon’s virtual talk “Learning Together at the Data Science Learning Community”
• Paola Corrales and Elio Campitelli’s tutorial “Efficient Data Analysis with data.table” (Website)
• Elio Campitelli’s talk “Building Bilingual Bridges with Multilingual Manuals” (Slides)
• Hugo Gruson’s
  • Talk “Building Interoperability in Existing Software Ecosystems with S3 Classes” (Slides).
  • Poster “A reproducible analysis of CRAN Task Views to understand the state of an R package ecosystem”
• Lluís Revilla and Henrik Bengtsson’s poster about CRAN packages archived and the cranhaven.org R-universe created to reduce the impact of that on users
• Will Landau and Charlie Gao’s talk “Moju-Kapu: How {Mirai} and {Crew} Are Powering the Next Generation of Parallel Computing in R” (Slides)
• Binod Jung Bogati’s talks
  • “Generate Raw Synthetic Dataset for Clinical Trial – Binod Jung Bogati, Numeric Mind” (Slides)
  • “Translate R for Global Reach”

Coworking

Read all about coworking!

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, August 6th, 9:00 America Pacific (16:00 UTC), Building your first R package with cohost Carolina Pradier and Steffi LaZerte.

  • Explore how to make R packages
  • Plan out that package you’ve always wanted to create
  • Chat with our cohost about tips and tricks for making your first R package

• Tuesday, September 3rd, 9:00 Australia Western (01:00 UTC), Theme TBA with cohost TBA and Steffi LaZerte.

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:

• osmapiR, developed by Joan Maspons: Interface to OpenStreetMap API for fetching and saving data from/to the OpenStreetMap database (https://wiki.openstreetmap.org/wiki/API_v0.6). It is available on CRAN. It has been reviewed by Jon Harmon and Carlos Cámara.

Discover more packages, read more about Software Peer Review.

New versions

The following nine packages have had an update since the last newsletter: rotemplate (pkgdown-2.0.9), gitignore (v0.1.7), nodbi (v0.10.5), nuts (v1.1.0), occCite (v0.5.7), osmapiR (v0.1.0), phonfieldwork (v0.0.16), taxlist (v0.3.0), and waywiser (v0.6.0).

Software Peer Review

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

• One at ‘6/approved’:

  • osmapiR, OpenStreetMap API. Submitted by Joan Maspons.

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

  • chopin, CHOPIN: Computation for Climate and Health research On Parallelized INfrastructure. Submitted by Insang Song.

  • cancerprof, API Client for State Cancer Profiles. Submitted by Brian Park.

  • rix, Rix: Reproducible Environments with Nix. Submitted by Bruno Rodrigues.

  • agromet, Índices y Estadísticos Climáticos e Hidrológicos. Submitted by Paola Corrales.

• Four at ‘3/reviewer(s)-assigned’:

  • eDNAjoint, Joint Modeling of Traditional and Environmental DNA Survey Data. Submitted by Abigail Keller.

  • rsi, Efficiently Retrieve and Process Satellite Imagery. Submitted by Michael Mahoney.

  • sits, Satellite Image Time Series Analysis for Earth Observation Data Cubes. Submitted by Gilberto Camara.

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

• One at ‘2/seeking-reviewer(s)’:

  • QuadratiK, A Collection of Methods Using Kernel-Based Quadratic Distances for. Submitted by Giovanni Saraceno. (Stats).

• One at ‘1/editor-checks’:

  • gigs, Assess Fetal, Newborn, and Child Growth with International Standards. Submitted by Simon Parker. (Stats).

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

On the blog

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Software Review

• Announcing New Software Peer Review Editors: Beatriz Milz and Margaret Siple by Mark Padgham, Beatriz Milz, and Margaret Siple. Introducing two new editors for rOpenSci software review.

Other topics

• Multilingual Documentation in R Packages by Elio Campitelli. Multilingual documentation coming to an R package near you. Other languages: Documentación multilingüe en paquetes de R (es).

• rOpenSci Community Collaboration Insight Using Social Networks Analysis by Yanina Bellini Saibene and Sandro Camargo. In this blog post we present how we have used Social Network Analysis with R, to better understand and manage the rOpenSci community.

• Metrics, Impact and Community Management by Yanina Bellini Saibene. Our community manager Yani, shares experiences using multi-level metrics and participation models through a community management lens to measure rOpenSci impact.

Use cases

Three use cases of our packages and resources have been reported recently.

• Using {weatherOz} to Plot Perth’s May High Temperatures. Reported by Adam Sparks.

• OAI interface request, response, and data download with R. Reported by Jörg Lehmann.

• Translating Carpentries workbench lessons with babeldown. Reported by Hugo Gruson.

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?.

• historydata, datasets for historians. Issue for volunteering.

• USAboundaries (and USAboundariesdata), historical and contemporary boundaries of the United States of America . Issue for volunteering.

Calls for contributions

• Help make qualtRics better! Code contributions wanted

• Help make assertr better! Come close issues

• Help users and developers of targets by answering questions!

• Help make waywiser better! User requests wanted

Also refer to 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. 👀

Last call: your opinion on the CRAN submission process!

Shared by Lluís Revilla and Heather Turner in our Slack workspace, a crucial survey ending today!

“If you have R package development experience and would like to share your thoughts on the CRAN submission process, please fill this short survey from the CRAN Cookbook project!”

Please find the Google form and read more about the exciting cookbook project in this post by Jasmine Daly.

Robust type-checking with r-lib

Don’t miss this insightful short post by Josiah Parry, “Type safe(r) R code”. A related older blog post is “Checking the inputs of your R functions” by Hugo Gruson, Sam Abbott, Carl Pearson.

The one with all the useR! links

The useR! 2024 conference featured quite a few talks relevant to package development, beside the talks we mentioned in the HQ section. Not all recordings are available yet, but make sure to check out the useR! YouTube channel.

If we missed any relevant content, please get in touch so we might add missing pieces to our next newsletter!

Retrospectives

Kurt Hornik and Torsten Hothorn gave keynote talks “More than 25 years of CRAN” (Slides) and “Some things you can’t read from a NEWS file” (Slides | Recording) about maintaining a package for decades.

Edzer Pebesma and Roger Bivand reported on “The Retirement of R Packages with Many Reverse Dependencies” (Slides).

On validation of R packages

Coline Zeballos and Yann Féhat from the R Validation Hub discussed how to support (pharma) companies with validation of R Packages (Slides). They use a toolset based on r-hub/repos and the riskmetric package.

Szymon Maksymiuk and Lorenzo Braschi presented a Deep Dive Into Industry R Package Quality Assessment. Beside introducing the concepts, they mentioned three open-source R packages that they created: checked for running reverse dependencies checks; covtracer for contextualizing tests using covr test traces; rd2markdown for converting .Rd files into Markdown.

Also on reverse dependencies checks, Pawel Rucki and André Veríssimo presented {verdepcheck} – A Tool for Dependencies Check (Slides | Package Docs).

Franciszek Walkowiak discussed Systems Integration Tests for R Package Cohorts, including the introductions to two open-source utilities, scribe that creates complete build, check and install reports for a collection of R projects and locksmith that helps with renv.lock creation (Slides).

On good practice

Daniel Sabanés Bové introduced openstatsware’s work on minimal viable good practice standards for R packages.

Pedro Silva listed Seven Deadly Sins Holding You Back as a Software Developer (Slides).

Hugo Gruson had a poster on A reproducible analysis of CRAN Task Views to understand the state of an R package ecosystem. See the live analysis.

On learning with silly projects

Fonti Kar shared her experience in creating {ohwhaley} – a ‘toy’ R package which serves as a tool for learning package development and upskilling new learners (Slides).

On package design

Hugo Gruson highlighted the benefits of using S3 classes for interoperability in Existing Software Ecosystems (Slides). See also his recent blog posts on the topic.

Ligia Adamska used an onion analogy to explain Layered Design for R Package Development: Meeting the Needs of Pharmaceutical R&D Stakeholders (Slides).

On tools

Daphne Grasselly, Franciszek Walkowiak and Pawel Rucki lead a tutorial on Streamlining R package development with GitHub Actions Workflows (Slides).

Emil Hvitfeldt explained how to make better error messages with rlang and cli.

Ella Kaye shared her insights on C for R users (Slides).

Davis Vaughan introduced tree-sitter, an efficient incremental parsing library and the R package treesitter, which provides bindings to tree-sitter whose README states “tree-sitter is useful for a number of things, including syntax highlighting, go-to definition, code reshaping, and more.”

On multilingualism

Elio Campitelli spoke about Building Bilingual Bridges with Multilingual Manuals (Slides). See also their post on our blog!

On debugging

Shannon Pileggi delivered a tutorial on debugging in R (Materials).

Antoine Fabri gave an overview of the motivations behind, and features of, his constructive package, which, among other things, can be useful for troubleshooting (Package docs).

On wrapping APIs

Hadley Wickham introduced and demo-ed his httr2 package (Package docs).

Simon Haller explained the Automated Generation of R Client Packages for RESTful APIs (Slides). See also Jon Harmon’s work on the same topic.

On a last resort for archived CRAN packages

Henrik Bengtsson and Lluís Revilla had a poster about their CRANhaven project, a backup solution for end-users when a package falls of CRAN (and which is built using R-universe!).

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.

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