Jul 18, 2017

rOpenSci HQ

Fellowships

In a recent blog post, Announcing the rOpenSci Fellowships Program, we discussed the rOpenSci fellowship program, designed to support individual researchers and collaborative efforts to help them do better science, build community around projects or best practices, or develop some tools as part of ongoing research that could impact one or more research domains. Check out the post for more information and to apply!

Postdoc

Stefanie and Karthik wrote a post Introducing our Postdoctoral Fellow, Dr. Dan Sholler. Dan intends to investigate what drives scientists to engage with or resist open science tools and communities.

Discussion forum

Recently, on our discussion form <> we’ve had a few interesting discussions:

• Peter Meissner asks about maintainer guidelines for R package updates
• A conversation linked to our post about our new postdoc Dan Sholler

Software

New packages

• A new package rcoreoa (v0.1.0) is on CRAN. rcoreoa is an R client for the CORE API (https://core.ac.uk/docs/). CORE (https://core.ac.uk) aggregates open access research outputs from repositories and journals worldwide and make them available to the public. Check out the rcoreoa vignette to get started. [Repository on GitHub][rcoreoa]
• A new package taxa (v0.1.0) is on CRAN. taxa provides taxonomic classes for groupings of taxonomic names both with and without data. Methods provided are taxonomically aware, in that they know about ordering of ranks, and methods that filter based on taxonomy also filter associated data. Check out the taxa vignette to get started. Repository on GitHub
• A new package patentsview (v0.1.0) is on CRAN. patentsview provides functions to work with the PatentsView API (http://www.patentsview.org/api/doc.html) for patents data. Check out the patentsview vignettes to get started. Repository on GitHub

Releases

• A new version (v0.1.3) of gutenbergr is on CRAN. See the NEWS for details. Check out the gutenbergr vignette to get started. Repository on GitHub
• A new version (v0.1.4) of taxizedb is on CRAN. See the release notes for details. Check out the taxizedb README to get started. Repository on GitHub
• A new version (v0.0.4) of osmdata is on CRAN. See the release notes for details. Check out the osmdata vignette to get started. Repository on GitHub
• A new version (v1.0.5) of lingtypology is on CRAN. See the release notes for details. Check out the lingtypology vignette to get started. Repository on GitHub
• A new version (v1.7.0) of neotoma is on CRAN. See the NEWS for details. Check out the neotoma README to get started. Repository on GitHub
• A new version (v0.9.2) of rzmq is on CRAN. See the NEWS for details. Check out the rzmq README to get started. Repository on GitHub
• A new version (v1.0.1) of plater is on CRAN. See the NEWS for details. Check out the vignette to get started. Repository on GitHub
• A new version (v2.6) of hunspell is on CRAN. See the release notes for details. Check out the vignette to get started. Repository on GitHub
• A new version (v0.3.0) of osmplotr is on CRAN. See the NEWS for details. Check out the vignettes to get started. Repository on GitHub
• A new version (v0.1.8) of getCRUCLdata is on CRAN. See the release notes for details. Check out the vignette to get started. Repository on GitHub
• A new version (v0.3.0) of USAboundaries is on CRAN. See the release notes for details. Check out the docs to get started. Repository on GitHub
• Two new versions of taxize have been released since last news: (v0.8.8, v0.8.9) ~ CRAN. taxize gains new functions ncbi_downstream and get_iucn, new data source (Wiki-pedia/-species/-data), and many other changes. See the release notes for details. Check out the vignettes to get started. Repository on GitHub
• A new version (v0.1.9) of stplanr is on CRAN. See the release notes for details. Check out the vignette to get started. Repository on GitHub
• A new version (v0.4.0) of robotstxt is on CRAN. See the NEWS for details. Check out the vignette to get started. Repository on GitHub
• A new version (v0.3.0) of roadoi is on CRAN. See the release notes for details. This isn’t the first version on CRAN, but is first version on CRAN after being accepted into rOpenSci! Check out the vignette to get started. Repository on GitHub
• A new version (v0.5.1) of biomartr is on CRAN. See the NEWS for details. Check out the vignettes to get started. Repository on GitHub

Onboarding

We accept community contributed packages via our onboarding system - a software review system, sorta like scholarly paper review, but way better. We’ll highlight new packages here that have come through this system. 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 we have a new form you can fill out, and we’ll ping you when there’s a submission that fits in your area of expertise.

The following three packages were recently submitted to our onboarding process:

• codemetar > Generate CodeMeta Metadata for R Packages
  • Author: Carl Beottiger
  • Issue: ropensci/onboarding#130
  • Reviewers:
    • Toph Allen
    • Anna Krystalli
• data.world > Main Package for Working with ‘data.world’ Data Sets
  • Author: Rafael Pereira
  • Issue: ropensci/onboarding#133
  • Reviewers: not assigned yet
• geoops > GeoJSON Manipulation Operations
  • Author: Scott Chamberlain
  • Issue: ropensci/onboarding#134
  • Reviewers: not assigned yet

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

• bittrex > Client for the Bitrex Exchange
  • Author: Michael Kane
  • Issue: ropensci/onboarding#120
  • Reviewers:
    • Taylor Arnold
    • Noam Ross
• iheatmapr > Interactive Complex Heatmaps
  • Author: Alicia Schep
  • Issue: ropensci/onboarding#107
  • Reviewers:
    • Andee Kaplan
    • Carl Ganz
• rtimicropem > Supports the Analysis of RTI MicroPEM Output Files
  • Author: Maëlle Salmon
  • Issue: ropensci/onboarding#126
  • Reviewers:
    • Lucy D’Agostino McGowan
    • Kara Woo
• roadoi > Find Free Versions of Scholarly Publications via the oaDOI Service
  • Author: Najko Jahn
  • Issue: ropensci/onboarding#115
  • Reviewers:
    • Ross Mounce
    • Tuija Sonkkila
• refimpact > API Wrapper for the UK REF 2014 Impact Case Studies Database
  • Author: Perry Stephenson
  • Issue: ropensci/onboarding#78
  • Reviewers:
    • Najko Jahn
    • Kenneth Benoit

On the blog

We’ve been very busy on the rOpenSci blog!

• Noam Ross et al. got a blog post up about their #runconf17 project Tackling the Research Compendium at runconf17.
• Shannon Ellis wrote a really nice post about xxxx titled Hey! You there! You are welcome here.
• Becca Krouse et al. wrote a blog post about packagemetrics: packagemetrics - Helping you choose a package since runconf17.
• Stefanie and Karthik wrote a post Introducing our Postdoctoral Fellow, Dr. Dan Sholler. More up above in #ropensci HQ.
• Alicia Schep and Miles McBain wrote a post on Launching webrockets at runconf17.
• The great team that worked on skimr wrote a post on their project skimr for useful and tidy summary statistics.

Onboarding series

We’re doing a series of guest blog posts for packages that have gone through our software review process at ropensci/onboarding.

We’ll have more posts in this series coming out soon - keep an eye out.

Use Cases

The following two papers use/cite rOpenSci or rOpenSci software:

• Allen et al. used [rfishbase][rfishbase] in their paper Calling for more accurate information in aquarium trade: analysis of live-fish import permits in Costa Rica ¹
• Alfsnes et al. used rgbif and [spocc][spocc] in their paper Genome size in arthropods; different roles of phylogeny, habitat and life history in insects and crustaceans ²
• Lahti et al. referenced rOpenSci in their paper Alchemy and algorithms: perspectives on the philosophy and history of open science ³
• Araújo & Fontainha used our package [gender][gender] in their paper Big Missing Data: are scientific memes inherited differently from gendered authorship? ⁴
• Pedersen et al. used [rfishbase][rfishbase] in their paper Signatures of the collapse and incipient recovery of an overexploited marine ecosystem ⁵
• Mulder used [helminthR][helminthR] in his paper Pathogenic helminths in the past: Much ado about nothing ⁶
• Ram et al. discuss rOpenSci in their paper Lightning talk: A model for peer review and onboarding research software ⁷
• Smith et al. reference rOpenSci in their paper Journal of Open Source Software (JOSS): design and first-year review ⁸
• Lou Woodley cited rOpenSci in her post Considering Community: What types of community are there? (Part one, science edition) ⁹

Submit news to rOpenSci

Reach out to us with your news suggestions by sending us an email [email protected] or by contacting us on Twitter @ropensci

Keep up with rOpenSci news

There are a number of ways to keep up with what rOpenSci is doing:

• Mailing list: Sign up with an email address to get new blog posts sent to your inbox -> ropensci.org/#subscribe
• rOpenSci on Twitter: we’re @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.
• rOpenSci news. XML feed at https://news.ropensci.org/feed.xml - JSON feed at https://news.ropensci.org//feed.json

Footnotes