May 13, 2019

rOpenSci HQ

• Video of our Community Call on Security for R is up, along with a long list of resources. Hear from Bob Rudis on Zen and the art of ensuring confidentiality and integrity in analytics workflows and Ildi Czeller on authorization vs authentication explained through signing commits: why you should do it and how the ropsec package helps you do it the right way.
• Our Community Manager Stefanie Butland is speaking at an R-Ladies Seattle meetup Wed May 22nd on the theme of Learning R and Building Community. Other speakers are Malisa Smith, Bioinformatician at University of Washington, and Pamela Moriarty, Data Scientist at Zulily. See https://ropensci.org/events/ for details.
• The Scientific Committee on Antarctic Research is partnering with rOpenSci and the Antarctic Biodiversity Portal in organizing a short course on tools for Southern Ocean spatial analysis and modeling using R. Apply by Friday, June 15th. See https://github.com/SCAR/EGABIcourse19 for details.

Software 📦

CRAN: GitHub:

New Versions

• A new version (v0.2.9) of stplanr is on CRAN - sustainable transport planning. See the release notes for changes. Checkout the docs to get started.

  new fxns od_aggregate_from()/od_aggregate_to(); updates to many fxns; better website

• A new version (v0.2.3) of bikedata is on CRAN - download and aggregate data from public hire bicycle systems. See the release notes for changes. Checkout the docs to get started.

  fix dl_bikedata for Philadelphia

• A new version (v0.9.7) of taxize is on CRAN - taxonomic toolbelt for R. See the release notes for changes. Checkout the taxize book to get started.

  class2tree() gains node labels when present

• A new version (v0.6.0) of rerddap is on CRAN - General Purpose Client for ERDDAP Servers. See the release notes for changes. Checkout the vignettes to get started.

  info() gains base url in its output; improved griddap() docs and bug fixes

• A new version (v1.3.0) of rgbif is on CRAN - interface to the Global Biodiversity Information Facility API. See the release notes for changes. Checkout the occurrence manual to get started.

  occ_download()/occ_download_prep() gain new param. format (you can now get species lists)

• A new version (v0.4.2) of rdatacite is on CRAN - client for DataCite. See the release notes for changes. Checkout the README to get started.

  fixes for encoding in test fixtures

• A new version (v0.9.2) of rcrossref is on CRAN - R client for the Crossref API. See the release notes for changes. Checkout the rcrossref vignette to get started.

  main rcrossref fxns gain option to do progress bar when doing deep pagination

• A new version (v0.8.0) of rbison is on CRAN - interface to the USGS BISON API. See the release notes for changes. Checkout the vignette to get started.

  update readme/vignette wrt relationship between GBIF and BISON

• A new version (v0.8.6) of rplos is on CRAN - Interface to the Search API for Public Library of Science journals. See the release notes for changes. Checkout the vignettes to get started.

  fixes for encoding in test fixtures

• A new version (v1.2.2) of rentrez is on CRAN - ENTREZ in R. See the release notes for changes. Checkout the vignette to get started.

  force curl to use http/1.1; fix in parse_pubmed_xml; docs clarification for extract_from_esummary

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 package was recently submitted:

• rnassqs > Access the NASS Quick Stats API
  • Author: Nicholas Potter
  • Issue: ropensci/onboarding#298
  • Reviewers: not yet assigned

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

• rromeo > An R Client for SHERPA/RoMEO API
  • Author: Matthias Grenié
  • Issue: ropensci/onboarding#285
  • Reviewers:
    • Philipp Ottolinger
    • Bruna Wundervald
• tidync > A Tidy Approach to ‘NetCDF’ Data Exploration and Extraction
  • Author: Michael Sumner
  • Issue: ropensci/onboarding#174
  • Reviewers:
    • Tim Lucas
    • Jakub Nowosad

On the blog

Main blog

Julia Silge wrote a post on Relaunching the qualtRics package for the qualtRics package she maintains.

Pachá wrote a post on Open Trade Statistics for the tradestatistics package he maintains.

Use Cases

The following 10 works use/cite rOpenSci software:

• Hoban et al. used rgbif in their paper Inference of biogeographic history by formally integrating distinct lines of evidence: genetic, environmental niche, and fossil ¹
• Peignier et al. used spatsoc in their paper Space use and social association in a gregarious ungulate: Testing the conspecific attraction and resource dispersion hypotheses ²
• Campbell used plotly in their book Learn RStudio IDE ³
• Iqbal used pdftools in their paper Managerial Self-Attribution Bias and Banks’ Future Performance: Evidence from Emerging Economies ⁴
• Pinsky et al. used rfishbase and rnoaa in their paper Greater vulnerability to warming of marine versus terrestrial ectotherms ⁵
• Bacci et al. used rgbif in their paper Revisiting the classification of Melastomataceae: implications for habit and fruit evolution ⁶
• Domingos used rgbif in their thesis Oportunidades e desafios em macroecologia marinha ⁷
• Robbins et al. used nasapower in their paper The Scope and Impact of Open Source Software as Intangible Capital: A Framework for Measurement with an Application Based on the Use of R Packages ⁸
• Seyednasrollah et al. used plotly in their paper Data extraction from digital repeat photography using xROI: An interactive framework to facilitate the process ⁹
• Nicolas et al. used hunspell in their paper Automated Dictionary Creation for Analyzing Text: An Illustration from Stereotype Content ¹⁰

There’s three recent use cases in the Use Cases section of the rOpenSci discussion forum:

• qualtRics: the Stack Overflow Developer Survey by Julia Silge
• Using drake to power a new soil respiration database by Ben Bond Lamberty
• Can rainfall be a useful predictor of epidemic risk across temporal and spatial scales by Emerson Del Ponte

In The News

Arvia Sreenivasan highlighted example rnaturalearth usage

Hey #rstats #ggplot2 mappers, are you still using the map_data() function? Be alerted to @rOpenSci 's fabulous rnaturalearth package. Optionally returns sf & includes a bunch of other useful data https://t.co/oCTZLdbUWu pic.twitter.com/7brxWbaw33

— ★ Arvi Sreenivasan (@arvi1000) April 12, 2019

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 maintenance due to a variety of circumstances. When that happens we try to find new maintainers.

We’ve had six recent examples of maintainer transitions within rOpenSci:

• RSelenium: now maintained by Ju Kim
• chromer: now maintained by Paula Andrea
• qualtRics: now maintained by Julia Silge
• rsnps: now maintained by Julia Gustavsen and Sina Rüeger
• rdpla: now maintained by Alyssa Columbus
• webchem: now maintained by Erik Sapper

We don’t have any packages looking for new maintainers - if you are a maintainer and want to hand over that role to someone else get in touch with us.

Related News

• A recent paper - The Scope and Impact of Open Source Software as Intangible Capital: A Framework for Measurement with an Application Based on the use of R Packages - happens to mention our packages hunspell and nasapower, and is an interesting read about open source software.

Keep up with rOpenSci

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Footnotes