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

Open Call for rOpenSci Champions Program Applications!

We are pleased to open the call for the second cohort of Champions and Mentors for the rOpenSci Champions Program 🎉 !

This 12-month-long program will continue to support our goal of identifying, recognizing, and rewarding passionate community members who help the community grow and improve. The activities include cohort-based training, project development, and personal mentorship.

This program focuses on people who belong to groups that are historically and systematically excluded from the open software and research software communities and who are interested in contributing to rOpenSci and the broader open source and research software communities.

You can apply to be a champion or a mentor until September 4th.

More information on eligibility, timeline, curriculum, application process, etc. is on the program webpage.

Community call: 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. rOpenSci Community Manager Yani will present the details of our Champion Program and answer all your questions about it.

CRAN packages on R-universe

All CRAN packages indexed on R-universe!

We have now indexed all CRAN packages on r-universe.dev. You can use the R-universe powersearch to find any CRAN package with a particular topic, author, datasets etc.

R-universe cran.dev shortlinks

You can now use cran.dev shortlinks: https://cran.dev/{package}, https://docs.cran.dev/{package} to fly directly to the R-universe dev page or html manual for any CRAN package!

Example: https://cran.dev/xml2 and https://docs.cran.dev/xml2.

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, 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.
• Tuesday, September 5th, 09:00 Australia Western (01:00 UTC), TBA
• Note October coworking is cancelled (see you in November!)

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 versions

The following eight packages have had an update since the last newsletter: daiquiri (v1.1.1), datefixR (v1.5.0), ijtiff (v2.3.2), phylotaR (v1.3.0), rerddap (v1.0.3), rsnps (v0.6.0), targets (1.2.0), and waywiser (v0.4.1).

Software Peer Review

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

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

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

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

  • 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).

• Two at ‘2/seeking-reviewer(s)’:

  • rangr, Mechanistic Simulation of Species Range Dynamics. Submitted by Katarzyna Markowska.

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

• Two at ‘1/editor-checks’:

  • eph, Argentina’s Permanent Household Survey Data and Manipulation Utilities. Submitted by Carolina Pradier.

  • 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

• 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.

• rOpenSci Champions Program Teams: Meet Ghozayel Elotteebi and Zebulun Arendsee by Ghozayel Elotteebi, and Zebulun Arendsee. Introducing Champions and Mentors – Ghozayel Elotteebi and Zebulun Arendsee.

• Open Call for rOpenSci Champions Program Applications! by Yanina Bellini Saibene. We open the call for the second cohort of Champions and Mentors. Other languages: ¡Convocatoria abierta para la presentación de candidaturas al Programa de Campeonas y Campeones de rOpenSci! (es).

• Teaching targets with Penguins by Athanasia Mo Mowinckel, and Joel Nitta. An inspiring collaboration for reproducibility! rOpenSci members Joel and Mo’s fortuitous encounter led to an exciting targets workshop in Oslo.

Use cases

One use case of our packages and resources has been reported since we sent the last newsletter.

• Using targets for an omics analysis and report / manuscript. Reported by Robert M Flight.

Explore other use cases and report your own!

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.

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. 👀

Check for partial matching as part of your testing & CI process

You can change your options to generate warnings on partial matching:

options(
 warnPartialMatchAttr = TRUE,
 warnPartialMatchDollar = TRUE,
 warnPartialMatchArgs = TRUE
)

But your options and Rprofile are ignored by R CMD check.

A way to still get warnings in your continuous integration is to integrate it to testthat by creating a special setup-options.R file, as in https://github.com/epiverse-trace/packagetemplate/pull/61. This file could also be used to change any other options (but use with caution to not create situations where it’s too difficult to debug).

Thanks to Hugo Gruson for this tip!

Change in R-devel for comparing versions

Does your package compare version with code snippets like some_version >= 1.5? If so, you might encounter the warning below with R-devel.

Condition
Warning in `.make_numeric_version()`:
invalid non-character version specification 'x' (type: double)

Reference, toot.

To avoid it, you need to make your comparison a character vector: some_version >= '1.5'

Example commit fixing this, in usethis.

Thanks to Zhian Kamvar for this tip!

How to take vacation as an open-source maintainer

Some inspiration by Will Landau: https://mastodon.social/@[email protected]/110636695153363955 Take care, y’all.

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.

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