Sep 30, 2019

rOpenSci HQ

• What would you like to hear about in an rOpenSci Community Call? We are soliciting your “votes” and new ideas for Community Call topics and speakers. Find out how you can influence us by checking out our new Community Calls repository.
• Recording and notes are up from our latest community call on Reproducible Workflows at Scale with drake.
• Help wanted! We encourage rOpenSci package authors to help us help you get more contributors to your package. If you label an issue “help wanted” (no hyphen or emojis), those issues can be found in a search of the rOpenSci organization; and on the rOpenSci GitHub landing page https://github.com/ropensci the number of open help wanted issues is highlighted for each package that has them.

Software 📦

CRAN: GitHub:

New Versions

• A new version (v0.3.1) of weathercan is on CRAN - Download weather data from the Environment and Climate Change Canada website. See the release notes for changes. Checkout the docs to get started.

  internal changes only

• A new version (v3.0.10) 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.

  internal changes & updated docs

• A new version (v0.3.0) of nlrx is on CRAN - setup, run and analyze NetLogo model simulations. See the release notes for changes. Checkout the vignettes to get started.

  updated docs; two new vignettes; changes to simdesign_GenAlg, simdesign_GenSA, simdesign_simple, and download_netLogo

• A new version (v0.9.0) of rnoaa is on CRAN - NOAA Weather Data from R. See the release notes for changes. Checkout the vignettes to get started.

  sea ice updates; new fxn lcd_cleanup; docs updates; many 🐞 fixes

• A new version (v0.2.9) of fingertipsR is on CRAN - Fingertips data for public health http://fingertips.phe.org.uk/. See the release notes for changes. Checkout the vignettes to get started.

  fixed firewall issue

• A new version (v0.4.0) of auk is on CRAN - eBird data extraction and processing. See the release notes for changes. Checkout the docs to get started.

  updated to 2019 eBird taxonomy; auk_observer() filter added

• A new version (v1.4.1) of MtreeRing is on CRAN - a shiny application for automatic measurements of tree-ring widths on digital images. See the release notes for changes. Checkout the docs to get started.
• A new version (v3.1.1) of qualtRics is on CRAN - download Qualtrics survey data. See the release notes for changes. Checkout the docs to get started.

  fix bug in infer_data_types(); improve docs; deprecate registerOptions(); make data import more robust

• A new version (v0.2.20) of rglobi is on CRAN - R Interface to Global Biotic Interactions. See the release notes for changes. Checkout the vignette to get started.

  use readr pkg to avoid encoding issues on windows

• A new version (v0.2.5) of tradestatistics is on CRAN - open trade statistics api wrapper and utility program. See the release notes for changes. Checkout the docs to get started.

  now requires R>=3.5; changes in ots_create_tidy_data()

• A new version (v0.3.0) of nodbi is on CRAN - the NoSQL database connector. See the release notes for changes. Checkout the README to get started.

  new author Ralf Herold contributed SQLite/json1 integration for all pkg methods; docdb_update gains MongoDB method; etcd integration dropped

• A new version (v0.3.1) of stplanr is on CRAN - sustainable transport planning. See the release notes for changes. Checkout the docs to get started.

  new logo; line_to_points() deprecated -> od2line(); line2pointsn() now works with sf objects; docs fixes

Package notes

The staff supported package etseed is now archived on CRAN. It was an R client for the key-value store etcd. After understanding the etcd product more, we decided it’s not something R users are reaching for.

Software Review ✔

We accept community contributed packages via our software review 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:

• eia > API Wrapper for ‘US Energy Information Administration’ Open Data
  • Author: Matthew Leonawicz
  • Issue: ropensci/onboarding#342
  • Reviewers:
    • David Ranzolin
    • not assigned yet

On the blog

Technical notes

Scott Chamberlain wrote a post on his new package, citecorp: citecorp: working with open citations. citecorp brings R user’s data from the OpenCitations Corpus; check it out if you are looking for citation data for any reason.

Jeroen Ooms dug into image suite packages in a recent blog post: Updates to the rOpenSci image suite: magick, tesseract, and av. To learn more about these and other rOpenSci packages, check out articles on https://docs.ropensci.org.

Use Cases

The following 23 works use/cite rOpenSci software:

• Atickem et al. used rnaturalearth in their paper Build science in Africa ¹
• Collins et al. used rgbif, bold and rfishbase in their paper Non‐specific amplification compromises environmental DNA metabarcoding with COI ²
• Veer et al. used plotly in their paper Effects of an over-the-counter lactic-acid containing intra-vaginal douching product on the vaginal microbiota ³
• Petersen & Ekstrøm used assertr in their paper dataMaid: Your Assistant for Documenting Supervised Data Quality Screening in R ⁴
• Watson et al. used rdhs in their paper False-negative malaria rapid diagnostic test results and their impact on community-based malaria surveys in sub-Saharan Africa ⁵
• Piper et al. used fulltext and rentrez and bold in their paper Prospects and challenges of implementing DNA metabarcoding for high-throughput insect surveillance ⁶
• Macip Sancho used rentrez in their paper Deciphering host-pathogen interactions at the biomembrane interface, key to target therapeutical approaches against Mycoplasma genitalium ⁷
• Sobreiro used MODIStsp in their paper Vegetation multitemporal responses to hydroclimate variations in the Espinhaço Range (Brazil) (link broken: http://hdl.handle.net/11449/183096) ⁸
• Brionne et al. used plotly in their paper ViSEAGO: a Bioconductor package for clustering biological functions using Gene Ontology and semantic similarity ⁹
• Fernandez-Basso et al. used plotly in their paper A comparative analysis of tools for visualizing association rules: A proposal for visualising fuzzy association rules ¹⁰
• Zanin et al. used MODIStools in their paper Dog days are just starting: the ecology invasion of free-ranging dogs (Canis familiaris) in a protected area of the Atlantic Forest ¹¹
• Luc et al. used hunspell and spelling in their paper Nudging consumers for relevant data using Free JAR profiling: an application to product development ¹²
• Lennox et al. used rredlist and taxize in their paper Sentiment analysis as a measure of conservation culture in scientific literature ¹³
• Conceição António used skimr in their paper Hotel Revenue Management: Using Data Science to Predict Booking Cancellations ¹⁴
• Han et al. used chromer in their paper Polyploidy promotes species diversification of Allium through ecological shifts ¹⁵
• Dawson et al. used rredlist in their paper Quantifying trends and uncertainty in prehistoric forest composition in the upper Midwestern United States ¹⁶
• O’Farrell et al. used rerddap in their paper Classifying fishing behavioral diversity using high-frequency movement data ¹⁷
• Hayden et al. used rgbif and rfishbase in their paper Biological and environmental drivers of trophic ecology in marine fishes - a global perspective ¹⁸
• Neugebauer et al. used rentrez in their paper The influence of phylogeny and ecology on root, shoot and plant ionomes of fourteen native Brazilian species ¹⁹
• Wagner used pdftools in their paper Using Advanced Analytics to Predict Risk for Grants Oversight ²⁰
• Pender et al. used spocc, rgbif and CoordinateCleaner in their paper How sensitive are climatic niche inferences to distribution data sampling? A comparison of Biota of North America Program (BONAP) and Global Biodiversity Information Facility (GBIF) datasets ²¹
• Park used rotl in their paper Food web structure selects for parasite host range ²²
• Sánchez-Páez & Ortega used rdhs in their paper Reported patterns of pregnancy termination from Demographic and Health Surveys ²³

Related News

• In command line news, there’s a new shell in town - Nushell - that embraces the tabular world we live in. Listen to the latest Changelog podcast episode on Nushell; it’s a bit of work to install it right now, but it’s got lots of interesting ideas that may be of interest. Another interesting project is a command line tool - navi - that leverages pluggable cheatsheet files (and no, R package cheatsheets in pdf format will not work here).
• Many readers are academics, and thus have perhaps deposited data with, or at least heard of, Dryad. We happen to maintain the R client for Dryad, rdryad. Dryad has just announced a refresh of their web services, among other things. Change to rdryad will be coming soon.
• Regex crossword is a fun new (to us) way to learn regex through a crossword format; it’s good to know regex no matter what programming language(s) you use!

From the Forum

We have a discussion forum (using Discourse) for the rOpenSci community. It’s a really nice way to have conversations on the internet. From time to time we’ll highlight recent discussions of interest.

• Arvi Sreenivasan filed a use case on how to Use rnaturalearth to get a background map in sf format for plotting with ggplot. The rnaturalearth package is maintained by Andy South.
• Amanda Dobbyn wrote about using our drake package maintained by Will Landau: drake use case involving fires! - check out her slides at https://aedobbyn.github.io/nyc-fires/index.html

In The News

• Dmytro Perepølkin wrote a blog post about using ourpackage magick to play with images, fonts and such: Miracles with magick and bunny
• Jennifer Cooper wrote a post on using our package tabulizer: PDF Scraping in R with tabulizer
• Ethan White and company used our package spocc in their Data Carpentry workshop for biologists: Working with Spatial Data

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. Checkout our Contributing Guide for why and how to contribute to rOpenSci.

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.

Keep up with rOpenSci

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Footnotes