Dec 18, 2017

rOpenSci HQ

Maëlle Salmon, an editor with our rOpenSci onboarding software review team, represented rOpenSci at a hackathon event in Ghent, Belgium recently. The event (hashtag #EAB2017) was a event centered around doing software things in R with an ecology focus. Find out more about the event at https://methodsblog.wordpress.com/2017/11/16/hackathon-challenges/. Maëlle gave a talk on tips for developing R packages, of which she’s made many. She wrote up a blog post on her talk: How to develop good #rstats packages (for open science)

Carl Boettiger and Scott Chamberlain participated in a codefest/hackathon last week centered around Phenoscape - a knowledebase of computable phenotypes for studies of evolution and genetics. Check out the repo at https://github.com/phenoscape/KB-DataFest-2017/, the project ideas, and the teams. There’s a small but informative set of tweets on the event at the hashtag #phenohack. Carl and Scott worked on NeXML/JSON-LD interoperability with a great team including Mark Holder, Gaurav Vaidya, Matt Yoder, and Rutger Vos. There’s a in progress implementation for going between NeXML and JSON-LD at cboettig/nexld.

Software 📦

New packages

• A new package tidyhydat (v0.3.1) is on CRAN. Check out the tidyhydat vignette to get started. You can read the rOpenSci software review at https://github.com/ropensci/onboarding/issues/152. Repository on GitHub
• A new version (v1.0) of cleanEHR is on CRAN. Check out the cleanEHR vignettes to get started. This isn’t the first version of this package on CRAN, but is the first version on CRAN under rOpenSci. You can read the rOpenSci software review at https://github.com/ropensci/onboarding/issues/102. Repository on GitHub

Releases

• A new version (v0.4.3) of iheatmapr is on CRAN. See the NEWS for details. Check out the iheatmapr docs to get started. Repository on GitHub
• A new version (v0.2) of europepmc is on CRAN. See the release notes for details. Check out the europepmc vignettes to get started. Repository on GitHub
• A new version (v0.1.1) of bomrang is on CRAN. See the NEWS for details. Check out the bomrang docs to get started. Repository on GitHub
• A new version (v2.5.0) of FedData is on CRAN. See the NEWS for details. Check out the FedData docs to get started. Repository on GitHub
• A new version (v1.0.10) of lingtypology is on CRAN. See the release notes for details. Check out the lingtypology docs to get started. Repository on GitHub
• A new version (v1.1.2) of GSODR is on CRAN. See the NEWS for details. Check out the GSODR vignettes to get started. Repository on GitHub
• A new version (v0.2.2) of getCRUCLdata is on CRAN. See the NEWS for details. Check out the getCRUCLdata docs to get started. Repository on GitHub
• A new version (v2.9) of hunspell is on CRAN. See the release notes for details. Check out the hunspell vignette to get started. Repository on GitHub
• A new version (v0.20.0) of git2r is on CRAN. See the NEWS for details. Check out the git2r README to get started. Repository on GitHub
• A new version (v1.1) of spelling is on CRAN. See the NEWS for details. Check out the spelling README to get started. Repository on GitHub

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.

The following package recently went through our onboarding process and has been approved!

• cleanEHR > The Critical Care Clinical Data Processing Tools
  • Author: Sinan Shi
  • Issue: ropensci/onboarding#102
  • Reviewers:
    • Hao Zhu
    • Andrew MacDonald

The following two packages were recently submitted for review:

• fingertipsR > Fingertips Data for Public Health
  • Author: Sebastian Fox
  • Issue: ropensci/onboarding#168
  • Reviewers:
    • Carl Ganz
    • Duncan Garmonsway
• rdflib > Tools to Manipulate and Query Semantic Data
  • Author: Carl Boettiger
  • Issue: ropensci/onboarding#169
  • Reviewers: not assigned yet

On the blog

.rprofile series

Our third post is out in our .rprofile series: .rprofile: Jenny Bryan by Kelly O’Briant. Jenny on Twitter -> https://twitter.com/JennyBryan

Keep an eye out for more posts in this series.

main blog

David Ranzolin wrote about his package rpersues and his experience with rOpenSci software review in a blog post: Exploratory Data Analysis of Ancient Texts with rperseus. Check out the review and shout out to the reviewers Ildikó Czeller and François Michonneau.

Use cases

If you’ve used rOpenSci software in a blog post or a paper, tell us on the discussion forum and we’ll share it with our community here.

The following three works use/cite rOpenSci or rOpenSci software:

• Ramasubramanian and Albrecht used stplanr in their book chapter Placemaking: Why Everything Is Local in the book The Urban Book Series ¹
• Marx et al. used pdftools in their white paper Synthesis Report on Disaster Risk Reduction and Climate Change Adaptation in Germany ²
• Armstrong et al. used monkeylearn in a book The 2016 Presidential Election: The Causes and Consequences of a Political Earthquake. We can’t link to an open access version but there is a screenshot showing discussion of the use of the package. ³

In the news

There was a nice tweet about our rfishbase package:

#rstats package rfishbase is making my day. https://t.co/tNWNWkfGl0 @BrentBHughes @ecophyte

— Wendel Raymond (@wendel_raymond) December 8, 2017

Najko Jahn, maintainer of the rOpenSci packages europepmc and roadoi presented a nice use case with europepmc in a vignette in said package

Finally on CRAN, including @ma_salmon great function to avoid an #evergreenreviewgraph
Use-case:https://t.co/4iNQMkp4WU https://t.co/HOaNw6R1Ak

— Najko Jahn (@najkoja) December 11, 2017

Submit news to rOpenSci

Reach out to us with your news suggestions by sending us an email info@ropensci.org or by contacting us on Twitter @ropensci

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Footnotes