rOpenSci News Digest, September 2024

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

Community call recording: Navigating the R ecosystem using R-universe

Video and resources.

Learn more about R-Universe and how you can use it to improve your R package development workflow.

In this community call, Jeroen Ooms provided details on what R-Universe is and an update on what you can do with it today. He also discussed the future of R-Universe and how it can be used to navigate the R ecosystem.

R-Universe list pages

R-Universe now features a list of all datasets in all packages and a list of all vignettes from CRAN, Bioconductor, and others.

Another important global table is the package scoreboard that lets you explore the scores used by R-Universe search engine for ranking, which is based on:

• Stars: Number of stars on GitHub;
• Downloads per month from CRAN or Bioconductor mirrors;
• Scripts: (NEW) number of files on GitHub that mention ’library(pkgname)’;
• Dependents: recursive reverse dependencies;
• Unique contributors;
• Yearly commits.

Resources from rOpenSci training sessions

We’ve added a searchable table of past training sessions to our resources hosted on the rOpenSci website. Explore the full list of our resources.

Noam Ross, rOpenSci, and communities empowering open science

DataLatam Podcast interviewed rOpenSci director Noam Ross. Learn about his work at the intersection of health and the environment and his journey with rOpenSci.

Materials: Screen Reader Accessible Tools and Resources for Learning and Working with R

We have now published the recording of the webinar that walks through learning and using R with screen readers — and it’s bilingual (English & Turkish)! with subtitles in English.

📹 Webinar video featuring Liz Hare, PhD and Alican Cagri Gokcek

Also, don’t miss the detailed technical note by Liz Hare with all the necessary resources to get started.

The rOpenSci community at upcoming events

rOpenSci Community Manager Yanina Bellini Saibene will deliver a keynote talk at BioNT Community Event & CarpentryConnect-Heidelberg 2024, on November 14th in Heidelberg, Germany.

Will Landau will deliver a keynote talk at LatinR (Latin American Conference About the Use of R in R&D). The conference is happening online from November 18-22.

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, October 1st, 14h00 Europe Central (12:00 UTC), “Using R to tell (data science) stories” with cohost Apoorv Anand and Steffi LaZerte.
  • Explore how others use R to tell data stories
  • Start work on a project using R to craft a narrative through data
  • Chat with our cohost to discuss and explore the use of R in data stories
• Tuesday, November 5th, 09:00 Americas Pacific (17:00 UTC), “Getting to know Openscapes” with cohost Stefanie Butland and Steffi LaZerte.
  • Look up Openscapes
  • Chat with our cohost to learn more about the Openscapes organization, and how they use R to automate creating open education infrastructure

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 two packages recently became a part of our software suite:

• eDNAjoint, developed by Abigail G. Keller: Models integrate environmental DNA (eDNA) detection data and traditional survey data to jointly estimate species catch rate (see package vignette: https://bookdown.org/abigailkeller/eDNAjoint_vignette/). Models can be used with count data via traditional survey methods (i.e., trapping, electrofishing, visual) and replicated eDNA detection/nondetection data via polymerase chain reaction (i.e., PCR or qPCR) from multiple survey locations. Estimated parameters include probability of a false positive eDNA detection, a site-level covariates that scale the sensitivity of eDNA surveys relative to traditional surveys, and catchability coefficients for traditional gear types. Models are implemented with a Bayesian framework (Markov chain Monte Carlo) using the Stan probabilistic programming language. It has been reviewed by Chitra M Saraswati and Saras Windecker.

• rix, developed by Bruno Rodrigues together with Philipp Baumann: Simplifies the creation of reproducible data science environments using the Nix package manager, as described in Dolstra (2006) <ISBN 90-393-4130-3>. The included rix() function generates a complete description of the environment as a default.nix file, which can then be built using Nix. This results in project specific software environments with pinned versions of R, packages, linked system dependencies, and other tools. Additional helpers make it easy to run R code in Nix software environments for testing and production. It is available on CRAN. It has been reviewed by David Watkins and Jacob Wujiciak-Jens.

Discover more packages, read more about Software Peer Review.

New versions

The following thirteen packages have had an update since the last newsletter: comtradr (v1.0.2), DataPackageR (v0.16.1), datefixR (v1.7.0), epubr (v0.6.5), git2rdata (v0.4.1), GSODR (v4.1.2), jagstargets (1.2.1), mregions2 (v1.1.1), occCite (v0.5.8), osmapiR (v0.2.1), robotstxt (v0.7.15), tarchetypes (0.10.0), and tiler (v0.3.2).

Software Peer Review

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

• Three at ‘6/approved’:

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

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

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

• Two at ‘5/awaiting-reviewer(s)-response’:

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

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

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

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

• Five at ‘3/reviewer(s)-assigned’:

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

  • emodnet.wfs, Access EMODnet Web Feature Service data through R. Submitted by Maëlle Salmon.

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

  • 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).

• Two at ‘2/seeking-reviewer(s)’:

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

  • galamm, Generalized Additive Latent and Mixed Models. Submitted by Øystein Sørensen. (Stats).

• One at ‘1/editor-checks’:

  • mbquartR, Finding Manitoba Quarter Sections. Submitted by Alex Koiter.

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

On the blog

• Deposits In The Wild by Collin Schwantes. Using the deposits and frictionless packages to create FAIR data for a complex project.

• Resources For Using R With Screen Readers by Liz Hare. Tools and resources to use R with screen readers. Other languages: Recursos para utilizar R con lectores de pantalla (es), Ekran Okuyucularla R Kullanımı İçin Kaynaklar (tr).

• Capturing Screenshots Programmatically With R by Maëlle Salmon.

• Labels For Technical Writing Projects by Greg Wilson. Greg discusses the challenges of organizing non-software projects in GitHub and shares the label system he uses for technical writing projects like books and lessons.

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?.

• medrxivr, access and search MedRxiv and BioRxiv preprint data. Issue for volunteering.

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

• historydata, datasets for historians. 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. 👀

Reminder: R Consortium Infrastructure Steering Committee (ISC) Grant Program Accepting Proposals until October 1st!

The R Consortium Call for Proposals might be a relevant funding opportunity for your package! If you can’t prepare your proposal in time, the next call should start March 1st 2025.

How to demonstrate an error in an R Markdown vignette

An useful piece of information shared by Hugo Gruson in our Slack workspace. To demonstrate an error in a vignette, try setting purl = FALSE in chunks with error = TRUE. More info in a knitr issue.

Better titles for roxygen2 “family” cross-references

Do you use the “family” roxygen2 tag for grouping and cross-linking manual pages? Did you know you can override the default title from, for instance, “Other blabla” to “blabla functions and related data”? If not, refer to roxygen2 documentation.

Create and use a custom roxygen2 tag

Read more about creating a custom tag that adds a new section to a manual page in this blog post by Maëlle Salmon.

Materials from posit::conf(2024) workshops

Materials from posit::conf(2024) workshops have been posted. Especially relevant to package developers: From R User to R Programmer by Emma Rand and Ian Lyttle; and Package Development: The Rest of the Owl by Jenny Bryan whose introduction slidedeck features GitHub search tips.

Some tips when searching GitHub issues

Speaking of GitHub search…

Michael Chirico shared the following tip on Mastodon: "[you can use] the ‘in:title’ operator in GitHub search to restrict a search to issues/PRs matching a query in the title".

Jenny Bryan answered with another tip: “involves:USERNAME” for “I was once part of a conversation about this”.

A usethis function to create a test helper file

The new usethis function usethis::use_test_helper("mocks") will create a helper file under tests/testthat/helper-mocks.R.

A devtools function for building the README and vignettes

Not a new function, but in case you missed it… The devtools::build_rmd() and devtools::build_readme() functions render R Markdown files using a temporary install of your current development package.

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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