We’re rolling out two new newsletter sections:

  • Call for Contributors: Software occassionally needs new maintainers. Checkout this section if you’re looking to get involved in maintaining software.
  • Related News: If you’re interested to hear what’s going in related communities, this section is for you.

Keep reading to see the first installment of these new sections.


Software 📦

CRAN: GitHub:

New Packages

  • The firsts version (v0.1.1) of stats19 is on CRAN - Work with Open Road Traffic Casualty Data from Great Britain. See the release notes for changes. Checkout the docs to get started.

New Versions

  • A new version (v0.2.0) of pubchunks is on CRAN - Fetch Sections of XML Scholarly Articles. See the release notes for changes. Checkout the README to get started.

    default extraction attempts for most section types; better pub_chunks print fxn

  • A new version (v3.0.6) of rotl is on CRAN - an interface to the Open Tree of Life API. See the release notes for changes. Checkout the vignettes to get started.

    minor update for CRAN warnings

  • A new version (v0.3.0) of geojson is on CRAN - Classes for GeoJSON. See the release notes for changes. See also our forum post with details on the major updates. Checkout the vignettes to get started.

    new fxns ndgeo_read/ndgeo_write for newline-delimited GeoJSON; sf method for as.geojson

  • A new version (v1.3.2) of GSODR is on CRAN - Global Surface Summary of the Day (GSOD) Weather Data from R. See the release notes for changes. Checkout the docs to get started.

    get_gsod bug fix

  • A new version (v2.1) of pdftools is on CRAN - Text extraction, rendering and converting of PDF documents. See the release notes for changes. Checkout the README to get started.

    update poppler to v0.73 for Windows/macOS

  • A new version (v0.2.2) of rdflib is on CRAN - high level wrapper around the redland rdf package. See the release notes for changes. Checkout the docs to get started.

    fix license file; hex in docs

  • A new version (v0.9.0) of rcrossref is on CRAN - R client for the Crossref API. See the release notes for changes. Checkout the rcrossref vignette to get started.

    big update to the Crossref RStudio Addin; async HTTP requests for some fxns

  • A new version (v0.8.4) of rnoaa is on CRAN - NOAA Weather Data from R. See the release notes for changes. Checkout the vignettes to get started.

    fail better during US federal government shutdown

  • A new version (v1.0.4) of skimr is on CRAN - compact and flexible summaries of data. See the release notes for changes. Checkout the vignettes to get started.

    fix to handling dplyr verbs

  • A new version (v0.2.2) of vcr is on CRAN - record HTTP calls to disk for test caching. See the release notes for changes. Checkout the HTTP testing book to get started.

    change suggested usage of vcr::use_cassette()

  • A new version (v0.6.0) of epubr is on CRAN - read EPUB File Metadata and Text. See the release notes for changes. Checkout the docs to get started.

    improved word count accuracy; new fxns count_words(), epub_recombine(), epub_sift(), epub_reorder()

  • A new version (v2.5.6) of FedData is on CRAN - get geospatial data from several federated government data sources. See the release notes for changes. Checkout the README to get started.

    remove dependency on soilDB pkg

  • A new version (v0.1.6) of spatsoc is on CRAN - detecting spatial and temporal groups in GPS relocations. See the release notes for changes. Checkout the docs to get started.

    bug fix

  • A new version (v0.4.1) of nomisr is on CRAN - access UK official statistics from the Nomis database. See the release notes for changes. Checkout the docs to get started.

    add query_id parameter to nomis_get_data(); bug fix

  • A new version (v0.3.0) of webmockr is on CRAN - stubbing and setting expectations on HTTP requests. See the release notes for changes. Checkout the HTTP testing book to get started.

    mocked response header fixes; update to match new response_headers_all output for crul package responses

  • A new version (v3.2-1) of clifro is on CRAN - easily download and visualise climate data from CliFlo. See the release notes for changes. Checkout the vignettes to get started.
  • A new version (v1.0.4) of nasapower is on CRAN - NASA POWER API Client. See the release notes for changes. Checkout the docs to get started.

    better docs; vignette fix for CRAN

  • A new version (v0.0.9) of piggyback is on CRAN - Managing larger data on a GitHub repository. See the release notes for changes. Checkout the docs to get started.

    Enable re-upload and deletion of partially uploaded files

  • A new version (v0.24.0) of git2r is on CRAN - an interface to the libgit2 library, a pure C implementation of the Git core methods. See the release notes for changes. Checkout the README to get started.

    bug fixes



Software Review ✔

We accept community contributed packages via our onboarding system - an open software review system, sorta like scholarly paper review, but way better. We’ll highlight newly onboarded packages here. A huge thanks to our reviewers, who do a lot of work reviewing (see the blog post on our review system), and the authors of the packages!

If you want to be a reviewer fill out this short form, and we’ll ping you when there’s a submission that fits in your area of expertise.

The following packages recently went through our onboarding process and have been approved!

The following packages were recently submitted:



On the blog

rOpenSci HQ

rOpenSci has a new code of conduct! Make sure to read the blog post rOpenSci’s new Code of Conduct, the new text of the code of conduct, which also contains reporting guidelines.


Software Review

Stin Van Hoey and Peter Desmet wrote about their recently rOpenSci reviewed package wateRinfo, for downloading time series data from Waterinfo.be. wateRinfo - Downloading tidal data to understand the behaviour of a migrating eel

Australia Unconference

Nicholas Tierney wrote about the recent ozunconf held in Brisbane, Australia: Continuing to Grow Community Together at ozunconf, 2018. Nick does a nice job describing the unconference, some highlights of the projects, and some great pictures of the event. Also, check out Episode 6 of Credibly Curious, a podcast by Nick and Saskia Freytag, for a discussion of the unconference.


Mitchell O’Hara-Wild wrote about one ozunconf project called vitae - vitae: Dynamic CVs with R Markdown. He writes about the motivation for the package, the design of the package, and goes through an example. vitae source is on GitHub, and is on CRAN.

Tech Notes

Maëlle Salmon wrote about changes to the rOpenSci website: An even better rOpenSci website with Hugo. A few highlights: new authors pages with posts by each author; cool new error page; the new place to go to find out about rOpenSci community calls is https://ropensci.org/commcalls/.



Use Cases

The following 18 works use/cite rOpenSci software:



In The News

Maarten Hermans wrote a nice post, Exploring historical maps and spatial data with R and OpenStreetMap, using many packages, including our package osmdata maintained by Mark Padgham et al.



Call For Contributors

Part of the mission of rOpenSci is making sustainable software that users can rely on. Some software maintainers need to give up maintanence due to a variety of circumstances. When that happens we try to find new maintainers. We’ve had two recent examples of maintainer transitions within rOpenSci:

We’ve got one package in need of a new maintainer:



  • The Python programming language is going through a change of leadership. It used to have a BDFL model, a single leader. But the leader has left and now the Python community is deciding what leadership model they want. Brett Cannon has a nice post on the topic: An update on Python’s governance.
  • The US federal government shutdown is still going. Bob Rudis wrote a nice post on Roll Your Own Federal Government Shutdown-caused SSL Certificate Expiration Monitor in R in which he shows some very on topic data munging of federal government websites.
  • A shout out to a probably lesser know place to share and gain R knowledge: If you haven’t heard of dev.to, it’s a sort of developer forum for sharing articles and discussing. They have an R tag https://dev.to/t/r and an rstats tag https://dev.to/t/rstats - the former has more traffic.
  • Some rOpenSci community members are running independent local unconferences (inspired by but not affiliated with rOpenSci). The Uncoast Unconference aims to bring R users and developers together in flyover country and runs April 14-16 in Des Moines, Iowa. Application deadline is 5 February. The Chicago R Unconference runs March 9-10. Application deadline is 16 February.






Keep up with rOpenSci


Footnotes

  1. Duan, J., Wei Shi, Nathaniel K Jue, Zongliang Jiang, Lynn Kuo, Rachel O’Neill, Eckhard Wolf, Hong Dong, Xinbao Zheng, Jingbo Chen, Xiuchun (Cindy) Tian. 2018. Dosage Compensation of the X Chromosomes in Bovine Germline, Early Embryos and Somatic Tissues. Genome Biology and Evolution. https://academic.oup.com/gbe/advance-article/doi/10.1093/gbe/evy270/5253178 

  2. Martinková, P., & Drabinová, A. ShinyItemAnalysis for Teaching Psychometrics and to Enforce Routine Analysis of Educational Tests. The R Journal. https://journal.r-project.org/archive/2018/RJ-2018-074/RJ-2018-074.pdf 

  3. Alexander, M., and Alexander, R. 2018. The Effect of Elections and Prime Ministers on Discussion in the Australian Federal Parliament (1901–2018). https://rohanalexander.com/pdf/2018-12-16-events.pdf 

  4. Da Silva, R., & Conde, D. A. (2018). Data on the conservation potential of fish and coral populations in aquariums. Data in Brief. https://doi.org/10.1016/j.dib.2018.12.083 

  5. Sclavi, B., & Herrick, J. (2018). Genome size variation and species diversity in salamanders. Journal of Evolutionary Biology. https://doi.org/10.1111/jeb.13412 

  6. López-Jurado, J., Mateos-Naranjo, E., & Balao, F. (2018). Niche divergence and limits to expansion in the high polyploid Dianthus broteri complex. New Phytologist. https://nph.onlinelibrary.wiley.com/doi/abs/10.1111/nph.15663 

  7. Green, D. M. (2019). Rarity of Size-Assortative Mating in Animals: Assessing the Evidence with Anuran Amphibians. The American Naturalist, 193(2) https://www.journals.uchicago.edu/doi/abs/10.1086/701124 

  8. Mathot, K. J., Dingemanse, N. J., & Nakagawa, S. (2018). The covariance between metabolic rate and behaviour varies across behaviours and thermal types: meta-analytic insights. Biological Reviews. https://doi.org/10.1111/brv.12491 

  9. Bennett, D., Hettling, H., Silvestro, D., Vos, R., & Antonelli, A. (2018). restez: Create and Query a Local Copy of GenBank in R. Journal of Open Source Software, 3(31), 1102. https://doi.org/10.21105/joss.01102 

  10. Vantas, K. (2018). hydroscoper: R interface to the Greek National Data Bank for Hydrological and Meteorological Information. Journal of Open Source Software, 3(23), 625. https://doi.org/10.21105/joss.00625 

  11. Rivero, R., Sessa, E. B., & Zenil-Ferguson, R. (2019). EyeChrom and CCDBcurator: Visualizing chromosome count data from plants. Applications in Plant Sciences, e01207. https://bsapubs.onlinelibrary.wiley.com/doi/full/10.1002/aps3.1207 

  12. Chelick, C. C. (2019). Predicting taxonomic, functional and phylogenetic diversity of plant assemblages in the Okanagan ecoregion (Doctoral dissertation, University of British Columbia). https://open.library.ubc.ca/collections/ubctheses/24/items/1.0375860 

  13. Langhammer, M., Thober, J., Lange, M., Frank, K., & Grimm, V. (2019). Agricultural landscape generators for simulation models: A review of existing solutions and an outline of future directions. Ecological Modelling, 393, 135–151. https://doi.org/10.1016/j.ecolmodel.2018.12.010 

  14. Yeomans, M., Kantor, A., & Tingley, D. (2018). The politeness Package: Detecting Politeness in Natural Language. The R Journal. https://journal.r-project.org/archive/2018/RJ-2018-067/RJ-2018-067.pdf 

  15. Spalink, D., MacKay, R., & Sytsma, K. J. (2019). Phylogeography, population genetics, and distribution modeling reveal vulnerability of Scirpus longii (Cyperaceae) and the Atlantic Coastal Plain Flora to climate change. Molecular Ecology. https://doi.org/10.1111/mec.15006 

  16. Brooks, L., Kaze, M., & Sistrom, M. (2019). A Curated, Comprehensive Database of Plasmid Sequences. Microbiology Resource Announcements, 8(1). https://doi.org/10.1128/mra.01325-18 

  17. Ficcadenti, V., Cerqueti, R., & Ausloos, M. (2019). A joint text mining-rank size investigation of the rhetoric structures of the US Presidents’ speeches. Expert Systems with Applications. https://doi.org/10.1016/j.eswa.2018.12.049 

  18. Muñoz, G., Trøjelsgaard, K., & Kissling, W. D. (2019). A synthesis of animal-mediated seed dispersal of palms reveals distinct biogeographical differences in species interactions. Journal of Biogeography. https://doi.org/10.1111/jbi.13493