Aug 5, 2019

rOpenSci HQ

• Recording and notes and public discussion are up from our latest community call on Reproducible Research with R.

Software 📦

CRAN: GitHub:

New packages

• The first version (v1.7) of tidypmc is on CRAN - parse full text XML documents from PubMed Central. Checkout the vignettes to get started.
• The first version (v1.2.5) of UCSCXenaTools is on CRAN - download and explore datasets from UCSC Xena data hubs. Checkout the docs to get started.

New Versions

• A new version (v0.8.4) of crul is on CRAN - an R6 based HTTP client for R made for developers. See the release notes for changes. Checkout the docs to get started.

  (Windows users please do upgrade: no longer set cainfo curl option); improve parse method in HttpResponse class

• A new version (v1.22) of rtika is on CRAN - R Interface to Apache Tika. See the release notes for changes. Checkout the docs to get started.

  update Tika to 1.22

• A new version (v0.3.0) of stplanr is on CRAN - sustainable transport planning. See the release notes for changes. Checkout the docs to get started.

  new fxns: od_to_odmatrix(), odmatrix_to_od(), od_oneway(), and many new od_id*() fxns; new vignette

• A new version (v0.1.3) of gitignore is on CRAN - create useful .gitignore files for your project. See the release notes for changes. Checkout the docs to get started.

  fix cran check problems

• A new version (v1.0.0) 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.

  now much easier to download STATS19 data w/ dl_stats19()

• A new version (v0.5.0) of brranching is on CRAN - Fetch Phylogenies from Many Sources. See the release notes for changes. Checkout the vignette to get started.

  now using pkg conditionz to make messages less frequent when user does not have an API key for NCBI

• A new version (v0.1.2) of geoparser is on CRAN - interface to the Geoparser.io API. See the release notes for changes. Checkout the docs to get started.

  fix error caused by namespace issue; geoparser_key() fails better when no key avail.

• A new version (v0.0.3) of plotdap is on CRAN - easily visualize data from ERDDAP servers via the rerddap package. See the release notes for changes. Checkout the vignette to get started.
• A new version (v2.1) 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 docs site; many fixes

• A new version (v4.1) of tesseract is on CRAN - bindings to Tesseract, an OCR engine https://opensource.google.com/projects/tesseract. See the release notes for changes. Checkout the vignette to get started.

  fix memory leak in ocr_data; update to libtesseract 4.1.0

• A new version (v0.1.4) of phylocomr is on CRAN - Interface to Phylocom for analysis of phylogenetic community structure and character evolution. See the release notes for changes. Checkout the vignette to get started.

  fix some non-working examples; fixes to internal type checking; fix C lib error

• A new version (v0.3.0) of ckanr is on CRAN - R client for the CKAN API. See the release notes for changes. Checkout the docs to get started.

  big release, first in 4 years: new pkg maintainer; many new fxns; many fxns w/ changed params; fxn name changes

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 five packages were recently submitted:

• photosearcher > Queries the Flick API for photo images and metadata
  • Author: Nathan Fox
  • Issue: ropensci/onboarding#325
  • Reviewers:
    • Monica Gerber
    • other not assigned yet
• Rclean > A Tool for Writing Cleaner, More Transparent Code
  • Author: Matthew Lau
  • Issue: ropensci/onboarding#327
  • Reviewers: not yet assigned
• mapscanner > Print Maps, Draw on Them, Scan Them Back In
  • Author: Mark Padgham
  • Issue: ropensci/onboarding#330
  • Reviewers:
    • Nicholas Potter
    • other not assigned yet
• workloopR > Analysis of Work Loops and Other Data from Muscle Physiology Experiments
  • Author: Vikram Baliga
  • Issue: ropensci/onboarding#326
  • Reviewers: not yet assigned
• rmangal > An interface to the Mangal database https://mangal.io/#/
  • Author: Steve Vissault
  • Issue: ropensci/onboarding#332
  • Reviewers: not yet assigned

The following package recently went through our software-review process and has been approved:

• UCSCXenaTools > Download and Explore Datasets from UCSC Xena Data Hubs
  • Author: Shixiang Wang
  • Issue: ropensci/software-review#315
  • Reviewers:
    • Christine Stawitz
    • Carl Ganz

Use Cases

The following 15 works use/cite rOpenSci software:

• Wright et al. cite plotly in their paper Understanding microbial community dynamics to improve optimal microbiome selection ¹
• Meisner et al. used FedData in their paper Soil and climactic predictors of canine coccidioidomycosis seroprevalence in Washington State: an ecological cross‐sectional study> ²
• Tetzlaff et al. used rotl in their paper Effects of antipredator training, environmental enrichment, and soft release on wildlife translocations: A review and meta-analysis ³
• Alhajeri & Fourcade used rredlist and rgbif in their paper High correlation between species‐level environmental data estimates extracted from IUCN expert range maps and from GBIF occurrence data ⁴
• Boggs et al. used taxize in their paper Single Fragment or Bulk Soil DNA Metabarcoding: Which is Better for Characterizing Biological Taxa Found in Surface Soils for Sample Separation? ⁵
• Ros-Candeira et al. used rgbif in their paper Dataset of occurrence and incidence of pine processionary moth in Andalusia, south Spain ⁶
• Van Denderen et al. used rfishbase in their pre-print Little difference in average fish growth and maximum size across temperatures ⁷
• Bailey et al. used plotly in their paper Habitat selection can reduce effects of extreme climatic events in a long‐lived shorebird ⁸
• Palacios-Abrantes et al. used taxize in their paper A metadata approach to evaluate the state of ocean knowledge: Strengths, limitations, and application to Mexico ⁹
• McTavish cited rotl and rgbif in her abstract for the upcoming Biodiversity Next conference: Linking Biodiversity Data Using Evolutionary History ¹⁰
• Nyboer et al. used rfishbase and rredlist in their paper Assessing the vulnerability of Africa’s freshwater fishes to climate change: A continent-wide trait-based analysis ¹¹
• Krah & Heibl used phylotar in their paper rGUIDANCE – alignment confidence score computation in R ¹²
• Morelle et al. used osmdata in their paper Deathbed choice by ASF‐infected wild boar can help find carcasses ¹³
• Grattarola et al. used rredlist and taxize in their paper Biodiversidata: An Open-Access Biodiversity Database for Uruguay ¹⁴
• Kravchuk et al. used rotl in their paper Characterization of the 20S proteasome of the lepidopteran, Spodoptera frugiperda ¹⁵

In The News

Dan Quintana gives a short video demonstration of using europepmc, a package maintained by Najko Jahn

Ever wanted to visualize the popularity of a research topic over time? Here's how, using the 'europepmc' #Rstats package

YouTube link: https://t.co/fI5B6PLDco
Code: https://t.co/hSnYiBrUh8
Thread 👇 pic.twitter.com/Ezsh9jUJul

— Dan Quintana (@dsquintana) July 23, 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. 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