Feb 4, 2019

Software 📦

CRAN: GitHub:

New Versions

• A new version (v0.3.2) of auk is on CRAN - eBird data extraction and processing. See the release notes for changes. Checkout the docs to get started.
• A new version (v1.0.7) of helminthR is on CRAN - Access London Natural History Museum Host-Helminth Record Database. See the release notes for changes. Checkout the vignette to get started.

  changes to listLocations() due to ggmap API key requirement; cleanData() changes

• A new version (v1.0.5) of nasapower is on CRAN - NASA POWER API Client. See the release notes for changes. Checkout the docs to get started.

  fixes problem with WS2M not being available through nasapower

• A new version (v0.5.0) of lawn is on CRAN - Client for Turf.js for geospatial analysis. See the release notes for changes. Checkout the vignette to get started.

  fix unit tests for upcoming V8 pkg changes

• A new version (v0.5.0) of rerddap is on CRAN - General Purpose Client for ERDDAP Servers. See the release notes for changes. Checkout the vignettes to get started.

  replace httr with crul; many griddap() fixes; set default server URL

• A new version (v0.3.2) of geojson is on CRAN - Classes for GeoJSON. See the release notes for changes. Checkout the vignettes to get started.

  ndgeo_read() bug fix

• A new version (v0.2.7) of ropenaq is on CRAN - Air quality data from the open data platform OpenAQ. See the release notes for changes. Checkout the vignettes to get started.

  better error messages; remove not used ggmap dep

• A new version (v0.9.5) of taxize is on CRAN - taxonomic toolbelt for R. See the release notes for changes. Checkout the taxize book to get started.

  iucn_summary_id defunct; downstream gains WORMS data source; col_downstream() gains extant_only param; new fxn id2name(); lots and lots of small changes and bug fixes

• A new version (v0.4.1) of NLMR is on CRAN - Simulating neutral landscape models. See the release notes for changes. Checkout the docs to get started.

  nlm_neigh, nlm_mpd, nlm_randomrectangularcluster now implemented in Rcpp; doc improvements; bug fixes

• A new version (v0.2.2) of patentsview is on CRAN - An R client to the PatentsView API. See the release notes for changes. Checkout the docs to get started.

  vignettes removed from package

• A new version (v0.6.1) of rdhs is on CRAN - Client for Demographic and Health Survey (DHS) Data. See the release notes for changes. Checkout the docs to get started.

  extraction(add_geo=TRUE) correction for Kenya 2014 surveys; Geospatial covariate data sets now supported correctly

• A new version (v2.3.0) of RNeXML is on CRAN - Semantically Rich I/O for the NeXML Format. See the release notes for changes. Checkout the vignettes to get started.

  add_meta() now works w/ trees and characters; pkg handles nested meta elements properly now

• A new version (v0.3.0) of natserv is on CRAN - NatureServe R Interface. See the release notes for changes. Checkout the vignette to get started.

  new vignette; improve failure behavior; bug fixes

• A new version (v2.6) of assertr is on CRAN - Assertive Programming for R Analysis Pipelines. See the release notes for changes. Checkout the vignette to get started.

  bug fix for rlang pkg changes

• A new version (v2.0-7) of CoordinateCleaner is on CRAN - automated cleaning of occurrence records from biological collections. See the release notes for changes. Checkout the docs to get started.

  add pkg citation; improved docs for cc_outl()

• A new version (v1.2.0) of fulltext is on CRAN - full text of scholarly articles across many data sources. See the release notes for changes. Checkout the fulltext book to get started.

  ft_get() gains progress param; can now set cache path with full_path param in cache_options_set(); ft_chunks/ft_tabularize defunct (see pubchunks); ft_get_si defunct (see suppdata); replace httr with crul

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.

No new submissions or approved submissions.

On the blog

Software Review

OJ Watson wrote about his recently reviewed package rdhs Interacting with The Demographic and Health Surveys (DHS) Program data, including the motivation for the package, what the package does, and some lessons from the process.

The rOpenSci editors wrote changes in our software review: first, “rOpenSci onboarding” has been changed to “rOpenSci Software Review”; new editors; changes in standards; issue templates to better direct the different types of submissions; and the new bookdown book “rOpenSci Packages: Development, Maintenance, and Peer Review”. Read the the post: rOpenSci Software Peer Review: Still Improving.

rOpenSci is excited to welcome two new editors: Announcing new software peer review editors: Melina Vidoni and Brooke Anderson.

Use Cases

The following 20 works use/cite rOpenSci software:

• Farache et al. used rnaturalearth in their paper The unknown followers: Discovery of a new species of Sycobia Walker (Hymenoptera: Epichrysomallinae) associated with Ficus benjamina L. (Moraceae) in the Neotropical region ¹
• Shen & Spruit used plotly in their paper A Systematic Review of Open Source Clinical Software on GitHub for Improving Software Reuse in Smart Healthcare ²
• Łącki et al. used plotly in their paper masstodon: A tool for assigning peaks and modeling electron transfer reactions in top-down mass spectrometry ³
• Shang & Ghriga used plotly in their paper Exploring social media analytics on community development practices ⁴
• Duft used crul and rjsonapi in their dissertation Development of a generic concept to process questionnaire result data in different statistical applications ⁵
• Pettersen et al. used rotl in their paper Linking life-history theory and metabolic theory explains the offspring size-temperature relationship ⁶
• Waltz et al used plotly in their paper Small is big in Arabidopsis mitochondrial ribosome ⁷
• Dağ used plotly in their dissertation Binary Classification via GMDH-Type Neural Network Algorithm ⁸
• Hofmann et al. used plotly in their paper A convenient tool for bivariate data analysis and bar graph plotting with R ⁹
• Lovelace et al. cited stplanr in their paper stats19: A package for working with open road crash data ¹⁰
• Zuquim et al. used spocc in their paper The importance of soils in predicting the future of plant habitat suitability in a tropical forest ¹¹
• Kim et al. used iheatmapr in their paper Distinct gut virome profile of pregnant women with type 1 diabetes in the ENDIA study ¹²
• Lee et al. used rgbif in their paper REDLISTR: Tools for the IUCN Red Lists of Ecosystems and Threatened Species in R ¹³
• Krah et al. used RSelenium in their paper rMyCoPortal - an R package to interface with the Mycology Collections Portal ¹⁴
• Mankevich et al. used RSelenium in their conference paper Why Zlatan Ibrahimović is Bigger Than Manchester United: Investigating Digital Traces in Co-branding Processes on Social Media Platforms ¹⁵
• Muñoz et al. used taxize in their paper Biodiversity Observations Miner: A web application to unlock primary biodiversity data from published literature ¹⁶
• Smith et al. used taxize in their paper Metabolic rates of prokaryotic microbes may inevitably rise with global warming ¹⁷
• Ladwig et al. used rgbif in their paper Extreme winter warm event causes exceptionally early bud break for many woody species ¹⁸
• Pimiento et al. used rfishbase in their paper Evolutionary pathways toward gigantism in sharks and rays ¹⁹
• Halsey & White used rotl in their paper Terrestrial locomotion energy costs vary considerably between species: no evidence that this is explained by rate of leg force production or ecology ²⁰

In The News

We’re elated Halley Froehlich found rnoaa to be useful.

Um 'rnoaa' package is an absolute game changer. Thanks @juliesquid @openscapes for the intro! 🤯https://t.co/OdcwDKatd7

— Halley E. Froehlich 🐟 (@DocFroehlich) January 17, 2019

rcrossref is coming in handy for librarians 👌

Life as a Research Support Manager. (Report from EPrints, get DOIs, edit them up in gVim, then feed them through rcrossref with code kindly provided by @preater to get desired publication metadata). pic.twitter.com/qTmXGcwBbV

— Kevin Sanders (@moananddrone) January 24, 2019

#librarydirectorlife I've learned some new and useful things about error handling in GNU R and used rcrossref to work with the @CrossrefOrg API a bit more. One for schol comms / research support folk to check out. https://t.co/762ogGkDkC

— Andrew Preater (@preater) January 24, 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 three 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 (since our previous newsletter!)

We’ve got two packages in need of a new maintainer:

• webchem: The current maintainer of webchem, Eduard Szöcs, is looking for a new maintainer. See issue #155. Do ping Eduard in that issue and/or email us at info@ropensci.org
• rsnps: The current maintainer would like to hand it over to someone with more expertise in the domain. Please get in touch with Scott if you’re interested.

Related News

• A recent blog post Recursion vs. Looping in Python has a thorough overview of recursion vs. looping; it’s not in R, but the principles still apply.
• In a recent podcast episode on Podcast.__init__, Counteracting Code Complexity With Wily there’s a nice disussion of counteracting code complexity. Again, not in R, but still useful.
• In another recent podcast episode on Podcast.__init__, What You Need To Know About Open Source Licenses And Intellectual Property, there’s a relatively easy to understand discussion about licenses, copyright, patents, CLA’s, and trademarks - relevant to any programming language community.
• NumFOCUS has partnered with Code for Science & Society to do some qualitative research on the systemic challenges to sustainability for data driven tooling in science and scholarship. They would appreciate your participation in a short questionnaire: https://goo.gl/forms/Qk7TJslrMHP388tq1. Additional details about the project can be found on the Code for Science & Society blog

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Footnotes