Friday, May 20, 2022 From rOpenSci (https://ropensci.org/blog/2022/05/20/ropensci-news-digest-may-2022/). Except where otherwise noted, content on this site is licensed under the CC-BY license.
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
🔗 R-universe prominently displays more information on packages!
We have extended the r-universe.dev platform to provide even more real-time information and metadata about R packages to help users quickly find and compare relevant software for a given topic, maintainer or organization:
Package homepages on https://t.co/vudEyol2tw now include the README content, showing you absolutely everything there is to know about an R package in one single place! pic.twitter.com/KmH4GgaDOa
— Jeroen Ooms (@opencpu) May 13, 2022
In addition to descriptive information about the package and its authors, the dashboard now shows some basic usage metrics, such as the number of GitHub stars, (transitive) dependencies, and dependents, and an overall score that we use to rank search results (similar to pagerank).
You will see these numbers both in the search results and in package individual pages (we’ll be posting a more detailed technote about the search ranking soon).
These metrics are not the only improvement to package individual pages: You might have also noticed readme content and installation instructions:
And towards the bottom of the page you can find information about the commit and release activity, contributors, and reverse dependencies of the package:
Happy space travels! 🚀 Please report bugs or feature requests to our central station.
🔗 pkgcheck updates
Our automated package checking system was extended last month to include a report on package dependency use. Another check has been added this month which indicates if a package has any functions with names duplicated in other packages. Having unique function names is the best way to avoid namespace conflicts. One of the easiest ways to ensure unique function names is to name all functions with a package-specific prefix, like in the gh or gert packages.
Packages with duplicate function names will produce an initial check summary like this:
The “Details” section which follows will then include additional information like this:
This check relies on a database of the names of every function from every current CRAN package, which is also available for download with the latest release of the pkgstats package in the file, “pkgstats-fn-names.Rds”. Package authors can confirm the uniqueness of their function names by running pkgcheck locally.
🔗 Next coworking sessions
Join us for social coworking & office hours monthly on 1st 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, 07 June 2022 9 AM Australian Western / 1:00 UTC “Tackle something you’ve always wanted to learn” Hosted by community host Nick Tierney and Steffi LaZerte
- Cowork on a project of your choice;
- Take this time to tackle something you’ve always wanted to learn;
- Or talk to Nick Tierney and discuss what it is you want to learn, and get some tips and resources to get yourself started!
We’re taking a break on Coworking events for July and August, so we’ll see you in September!
Find out about more events.
🔗 Software 📦
🔗 New packages
The following four packages recently became a part of our software suite:
gitcellar, developed by Maëlle Salmon together with Jeroen Ooms: Provide functionality to download archives (backups) for all repositories in a GitHub organization (useful for backups!).
EDIutils, developed by Colin Smith: A client for the Environmental Data Initiative repository REST API. The EDI data repository https://portal.edirepository.org/nis/home.jsp is for publication and reuse of ecological data with emphasis on metadata accuracy and completeness. It is built upon the PASTA+ software stack https://pastaplus-core.readthedocs.io/en/latest/index.html# and was developed in collaboration with the US LTER Network https://lternet.edu/. EDIutils includes functions to search and access existing data, evaluate and upload new data, and assist other data management tasks common to repository users. It has been reviewed by Jasmine Lai, and Rodrigo Pires.
ReLTER, developed by Alessandro Oggioni together with Micha Silver, Paolo Tagliolato, and Luigi Ranghetti: ReLTER provides access to DEIMS-SDR (https://deims.org/), and allows interaction with data and software implemented by eLTER Research Infrastructure (RI) thus improving data sharing among European LTER projects. ReLTER uses the R language to access and interact with the DEIMS-SDR archive of information shared by the Long Term Ecological Research (LTER) network. This package grew within eLTER H2020 as a major project that will help advance the development of European Long-Term Ecosystem Research Infrastructures (eLTER RI - https://elter-ri.eu). The ReLTER package functions in particular allow to:
- retrieve the information about entities (e.g. sites, datasets, and activities) shared by DEIMS-SDR (see e.g. get_site_info function);
- interact with the ODSEurope starting with the dataset shared by DEIMS-SDR (see e.g. get_site_ODS function);
- use the eLTER site informations to download and crop geospatial data from other platforms (see e.g. get_site_ODS function);
- improve the quality of the dataset (see e.g. get_id_worms).
Functions currently implemented are derived from discussions of the needs among the eLTER users community. The ReLTER package will continue to follow the progress of eLTER-RI and evolve, adding new tools and improvements as required.
unifir, developed by Michael Mahoney: Functions for the creation and manipulation of scenes and objects within the Unity 3D video game engine (https://unity.com/). Specific focuses include the creation and import of terrain data and GameObjects as well as scene management. It is available on CRAN. It has been reviewed by Will Jones, and Tan Tran.
Discover more packages, read more about Software Peer Review.
🔗 New versions
The following eleven packages have had an update since the last newsletter: EML (v2.0.6), GSODR (3.1.5), jagstargets (1.0.2), lightr (v1.7.0), mctq (v0.2.0), nodbi (v0.7.1), opencv (v0.2.2), skimr (v2.1.4), stplanr (v0.9.0), terrainr (v0.7.0), and unifir (v0.2.1).
🔗 Software Peer Review
There are seventeen recently closed and active submissions and 4 submissions on hold. Issues are at different stages:
Two at ‘6/approved’:
unifir, A Unifying API for Calling Unity from R. Submitted by Michael Mahoney.
ReLTER, An interface to the eLTER for the R statistical programming environment. Submitted by Alessandro Oggioni.
Five at ‘4/review(s)-in-awaiting-changes’:
npi, Access the U.S. National Provider Identifier Registry API. Submitted by Frank Farach.
tidyqpcr, Quantitative PCR Analysis with the Tidyverse. Submitted by Edward Wallace.
phruta, Phylogenetic Reconstruction and Time-dating. Submitted by Cristian Román-Palacios.
epair, Grabs data from EPA API, simplifies getting pollutant data. Submitted by Leo Orozco-Mulfinger.
healthdatacsv, Access data in the healthdata.gov catalog. Submitted by iecastro.
Seven at ‘3/reviewer(s)-assigned’:
datefixR, Fix Really Messy Dates. Submitted by Nathan Constantine-Cooke.
hudr, A R interface for accessing HUD (US Department of Housing and Urban Development) APIs. Submitted by Emmet Tam.
yfR, Downloads and Organizes Financial Data from Yahoo Finance. Submitted by Marcelo S. Perlin.
octolog, Better Github Action Logging. Submitted by Jacob Wujciak-Jens.
canaper, Categorical Analysis of Neo- And Paleo-Endemism. Submitted by Joel Nitta. (Stats).
tsbox, Class-Agnostic Time Series. Submitted by Christoph Sax. (Stats).
ROriginStamp, Interface to OriginStamp API to Obtain Trusted Time Stamps. Submitted by Rainer M Krug.
Two at ‘2/seeking-reviewer(s)’:
aorsf, Accelerated Oblique Random Survival Forests. Submitted by Byron.
bssm, Bayesian Inference of Non-Linear and Non-Gaussian State Space. Submitted by Jouni Helske. (Stats).
One at ‘1/editor-checks’:
- rdbhapi, Interface to DBH-API. Submitted by Marija Ninic.
Find out more about Software Peer Review and how to get involved.
🔗 On the blog
🔗 Tech Notes
Don’t Lose your HEAD over Default Branches by Maëlle Salmon. Use “HEAD” instead of the default branch name in links to files on GitHub, as it will work for any default branch name.
Requiring 2FA for Our Main GitHub Organization by Maëlle Salmon. How we went about requiring two-factor authentication for our main GitHub organization.
🔗 Use cases
Two use cases of our packages and resources have been reported since we sent the last newsletter.
Estimating leaf temperatures worldwide. Reported by Paul Melloy.
Analyze your Twitter timeline with {rtweet} and {lubridate}. Reported by Albert Rapp.
Explore other use cases and report your own!
🔗 Call for maintainers
We’re looking for a new maintainer, or a new maintainer team, for each of the following packages:
phylotaR, Automated Retrieval of Orthologous DNA Sequences from GenBank. Issue for volunteering.
outsider, Install and run programs, outside of R, inside of R. Issue for volunteering.
hddtools, Hydrological Data Discovery Tools. Issue for volunteering.
gistr, Work with GitHub Gists. Issue for volunteering.
geojsonio, Convert many data formats to & from GeoJSON & TopoJSON. Issue for volunteering.
If you’re interested, please comment in the issues or email [email protected].
For more info, see
🔗 Package development corner
Some useful tips for R package developers. 👀
🔗 Documentation: HTML > PDF
This paragraph is not about LaTeX, but about screen-reader users! Please take time to read this email by Jonathan Godfrey on R-pkg-devel.
Please consider the HTML alternative to any pdf, in any context, but especially in anything relating to R.
Community member Lluís Revilla Sancho also highlighted that search.r-project.org provides HTML documentation for all CRAN documentation.
🔗 Twelve quick tips for software design
You might enjoy the article “Twelve quick tips for software design” by Greg Wilson. It is not R specific but is relevant to package development. “Design with everyone in mind” can for instance remind of the previous point about HTML documentation.
🔗 Renaming the default branch
If you’ve been considering renaming the default branch from master (oppressive language) to main, do not miss the Tidyverse blog post Jenny Bryan wrote in October 2021 “Renaming the default branch”, especially as it features useful usethis functions!
🔗 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 Twitter account.
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