Sep 16, 2019

rOpenSci HQ

• Join us for our next community call on Reproducible Workflows at Scale with drake on Sep 24th, 2019. The speaker is drake developer Will Landau.
• 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 packages

• The first version (v0.4.1) of cde is on CRAN - download data from the Catchment Data Explorer. Checkout the docs to get started.
• The first version (v0.1.0) of citecorp is on CRAN - client for the Open Citations Corpus. Checkout the docs to get started.
• The first version (v0.1.1) of PostcodesioR is on CRAN - API wrapper for Postcodes.io. Checkout the docs to get started.

New Versions

• A new version (v0.6) of roadoi is on CRAN - find free versions of scholarly publications via Unpaywall. See the release notes for changes. Checkout the vignette to get started.

  new data fields in Unpaywall data; minor fixes

• A new version (v7.6.1 & v7.6.2) of drake is on CRAN - a pipeline toolkit for reproducible computation at scale. See the release notes for changes. Checkout the docs to get started.

  docs now at https://docs.ropensci.org/drake/; many bug fixes

• A new version (v0.8.0 & v0.8.2) of pangaear is on CRAN - Client for the Pangaea database. See the release notes for changes. Checkout the vignette to get started.

  new object pg_cache to manage file caching; pg_data() now includes parsed metadata; bug fixes for pg_data()

• A new version (v0.1.5) of gutenbergr is on CRAN - Download and process public domain works from Project Gutenberg. See the release notes for changes. Checkout the vignette to get started.

  replace data_frame() w/ tibble()

• A new version (v0.2.8) 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.

  better failure behavior: throw informative message when no API response

• A new version (v1.1.2) of nasapower is on CRAN - NASA POWER API Client. See the release notes for changes. Checkout the docs to get started.

  correct citation; suppress APSIM::createMetFile() console output

• A new version (v0.3.0) of oai is on CRAN - general purpose OAI-PMH services client. See the release notes for changes. Checkout the docs to get started.

  id() gains as param; update_providers() fix; small changes

• A new version (v1.2.6) of UCSCXenaTools is on CRAN - download and explore datasets from UCSC Xena data hubs. See the release notes for changes. Checkout the docs to get started.

  update pkg citation

• A new version (v0.3.7) of jstor is on CRAN - read data from JSTOR/DfR. See the release notes for changes. Checkout the docs to get started.

  tidyr compatability; remove defunct fxns

• A new version (v2.0.0) 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() now using https rather than FTP; objects now returned as data.table objects; minor changes

• A new version (v0.2.0) of jaod is on CRAN - Directory of Open Access Journals client. See the release notes for changes. Checkout the docs to get started.

  new vignette; docs changes

• A new version (v0.3.1) of getCRUCLdata is on CRAN - use and explore CRU CL v. 2.0 climatology elements. See the release notes for changes. Checkout the docs to get started.

  fix documentation bug in an example

• A new version (v0.2.3) 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.

  fixes for testthat

• A new version (v1.0.14) of lingtypology is on CRAN - linguistic typology and mapping. See the release notes for changes. Checkout the docs to get started.

  some dependencies moved to Suggests; new fxns uralex.feature() and ggmap.feature()

• A new version (v2.2) of magick is on CRAN - Advanced graphics and Image-Processing in R. See the release notes for changes. Checkout the vignette to get started.

  new fxns image_read_video(), image_separate(), image_combine(); improve RStudio auto preview

• A new version (v2.0.3) of ijtiff is on CRAN - Comprehensive TIFF I/O with full support for ImageJ TIFF files. See the release notes for changes. Checkout the docs to get started.

  add libjpeg needs to SystemRequirements

• A new version (v0.3) of av is on CRAN - working with audio and video. See the release notes for changes. Checkout the docs to get started.

  major refactor; new fxns av_video_convert(), av_audio_convert(), av_video_images()

• A new version (v0.7.2) of DataSpaceR is on CRAN - interface to the CAVD DataSpace. See the release notes for changes. Checkout the docs to get started.

  fix broken and invalid URLs

• A new version (v0.3.0) 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.

  re-recording cassettes now works, see docs about setting a re-record interval; fixes to request body matching

• A new version (v0.2.0) of handlr is on CRAN - Convert among citation formats. See the release notes for changes. Checkout the README to get started.

  new fxn handl_to_df() (and associated method $as_df() on HandlClient) to convert a handl object to a data.frame

• A new version (v0.5.0) of rnassqs is on CRAN - access the NASS Quick Stats API. See the release notes for changes. Checkout the docs to get started.

  change how queries are specified; simplified token management; docs improved

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 three packages were recently submitted:

• baRcodeR > Label Creation for Tracking and Collecting Data from Biological Samples
  • Author: Yihan Wu
  • Issue: ropensci/onboarding#338
  • Reviewers:
    • Rayna Harris
    • Lluís Revilla
• ruODK > An R Client for the ODK Central API
  • Author: Florian Mayer
  • Issue: ropensci/onboarding#335
  • Reviewers: not yet assigned
• parzer > Parse Coordinates
  • Author: Scott Chamberlain
  • Issue: ropensci/onboarding#341
  • Reviewers: not yet assigned

The following two packages recently went through our software-review process and have been approved:

• rmangal > An interface to the Mangal database https://mangal.io/#/
  • Author: Steve Vissault
  • Issue: ropensci/onboarding#332
  • Reviewers:
    • Thomas Pedersen
    • Anna Willoughby
• c14bazAAR > Download and Prepare C14 Dates from Different Source Databases
  • Author: Clemens Schmid
  • Issue: ropensci/onboarding#333
  • Reviewers:
    • Ben Marwick
    • Enrico Crema

On the blog

Stefanie Butland wrote the second of a semi-monthly summary of the rOpenSci Newsletter including software reviews, packages on CRAN, use cases, posts from staff and community, and events - 2 Months in 2 Minutes - rOpenSci News, August 2019

Sam Tyner wrote a post describing her free online book on forensic science in R. This work was funded by a 2018 rOpenSci Research Fellowship. Read the post here: Introducing Open Forensic Science in R

Tiffany Timbers in a recent post Using rOpenSci Software Peer Review Guidelines for Teaching wrote about the Collaborative Software Development course she teaches at University of British Columbia. In this course, they recommend students use our book rOpenSci Packages: Development, Maintenance, and Peer Review; and the students and teachers use our Review Template when submitting and reviewing assignments.

Software Review

Aldo Compagnoni wrote a post on his package that recently went through review, popler: Synthesizing population time-series data from the USA Long Term Ecological Research Network. Aldo talks about the motivation for making the package and the database behind the package.

Use Cases

The following 24 works use/cite rOpenSci software:

• Saxena et al. used tesseract in their paper Feature Boosting in Natural Image Classification ¹
• Pilogallo et al. used MODIStsp in their paper Investigating Urban Growth Dynamic – Land Surface Temperature Relationship ²
• Sang used neotoma in their paper No-analog ecological communities since the last glacial maximum inferred from fossil pollen records for North America ³
• Xia et al. used plotly in their paper GEDS: A Gene Expression Display Server for mRNAs, miRNAs and Proteins ⁴
• Burkett used plotly in their paper Who Is Ready To Retire: Your Average Life Expectancy And The Savings Needed To Support You ⁵
• Valdez & Mandrekar used rfishbase in their paper Assessing the Species in the CARES Preservation Program and the Role of Aquarium Hobbyists in Freshwater Fish Conservation ⁶
• Correia et al. used rgbif in their paper Using ignorance scores to explore biodiversity recording effort for multiple taxa in the Caatinga ⁷
• Lin et al. used hunspell in their paper Projection Word Embedding Model With Hybrid Sampling Training for Classifying ICD-10-CM Codes: Longitudinal Observational Study ⁸
• Stöver et al. used RNeXML in their paper JPhyloIO: a Java library for event-based reading and writing of different phylogenetic file formats through a common interface ⁹
• Myers et al. used spocc in their paper Environmental Heterogeneity and Not Vicariant Biogeographic Barriers Generate Community Wide Population Structure in Desert Adapted Snakes ¹⁰
• Van Schaik et al. used fingertipsR in their paper Explainable statistical learning in public health for policy development: the case of real-world suicide data ¹¹
• Hagen et al. used taxize in their paper Mountain building, climate cooling and the richness of cold‐adapted plants in the Northern Hemisphere ¹²
• Carlström et al. used plotly in their paper Therapeutic efficacy of dimethyl fumarate in relapsing-remitting multiple sclerosis associates with ROS pathway in monocytes ¹³
• Dag et al. used plotly in their paper GMDH2: Binary Classification via GMDH-Type Neural Network Algorithms—R Package and Web-Based Tool ¹⁴
• Wüest et al. used CoordinateCleaner in their paper Macroecology in the age of Big Data – Where to go from here? ¹⁵
• Saunders et al. used rnoaa in their paper A Regionalisation Approach for Rainfall based on Extremal Dependence ¹⁶
• Collins et al. used rentrez in their paper Non‐specific amplification compromises environmental DNA metabarcoding with COI ¹⁷
• Elsner & Schroder used USABoundaries in their paper Tornado damage ratings estimated with cumulative logistic regression ¹⁸
• Abhilash & Sheeba used plotly in their paper RhythmicAlly: Your R and Shiny–Based Open-Source Ally for the Analysis of Biological Rhythms ¹⁹
• Peters et al. used rotl in their paper Immunosenescence in wild animals: meta‐analysis and outlook ²⁰
• Die et al. used rentrez in their paper geneHummus: an R package to define gene families and their expression in legumes and beyond ²¹
• Saadi et al. used FedData in their paper Random Forest Ability in Regionalizing Hourly Hydrological Model Parameters ²²
• Jaganathan & Dalrymple used rgbif in their paper Internal Seed Structure of Alpine Plants and Extreme Cold Exposure ²³
• Alhajeri et al. used taxize in their paper Habitat productivity is a poor predictor of body size in rodents ²⁴

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.

• Noam Ross wrote about Using rorcid to generate a website CV. The rorcid package, made by rOpenSci, is a client for ORCID data.
• Tim Williams wrote about using our rdflib package (a high level wrapper around the redland package for common rdf applications): Converting MedDRA Terminology to Linked Data using rdflib.

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

• Mailing list: Sign up with an email address to get this newsletter sent to your inbox -> ropensci.org/#subscribe
• Alternatively, you can subscribe to this newsletter via our XML feed at https://news.ropensci.org/feed.xml or our JSON feed at https://news.ropensci.org/feed.json
• rOpenSci on Twitter: @ropensci
• The rOpenSci blog at ropensci.org/blog - you can subscribe in any RSS aggregator, or manually via https://ropensci.org/feed.xml. We also announce new blog posts on our Twitter account.

Footnotes