Sep 11, 2017

rOpenSci HQ

Community Calls

We’ll have our next community call this week on September 13th, on rOpenSci Software Review and Onboarding.

https://github.com/ropensci/commcalls/issues/15

We hope past authors and reviewers will attend, as well as people considering volunteering to review rOpenSci packages or people considering submitting their package for review.

Discussion forum

Recently, on our discussion forum https://discuss.ropensci.org:

• What are good resources for someone starting to use BioConductor?

Software

New packages

• A new package jaod (v0.1.0) is on CRAN. jaod is an R client for the Directory of Open Access Journals API. Check out the jaod README to get started. Repository on GitHub
• A new package writexl (v0.1) is on CRAN. writexl is a portable, light-weight data frame to .xlsx exporter based on libxlsxwriter. No Java or Excel required! Check out the writexl README to get started. Repository on GitHub
• A new package spelling (v1.0) is on CRAN. spelling spell checks common document formats including latex, markdown, manual pages, and description files, and includes utilities to automate checking of documentation and vignettes as a unit test during R CMD check. Check out Jeroen’s recent blog post to get started. Repository on GitHub

Releases

• A new version (v1.3.1) of datapack is on CRAN. See the NEWS for details. Check out the datapack vignette to get started. Repository on GitHub
• A new version (v0.4.1) of robotstxt is on CRAN. See the NEWS for details. Check out the robotstxt vignette to get started. Repository on GitHub
• A new version (v1.4) of pdftools is on CRAN. See the release notes for details. Check out the README to get started. Repository on GitHub
• A new version (v0.4.2) of geojsonio is on CRAN. See the release notes for details. Check out the vignettes to get started. Repository on GitHub
• A new version (v1.3) of magick is on CRAN. See the release notes for details. Check out the vignette to get started. Repository on GitHub
• A new version (v1.4) of graphql is on CRAN. See the NEWS for details. Check out Jeroen’s blog post 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 package was recently submitted to our onboarding process:

• cRegulome > Gets texts from the Perseus Digital Library
  • Author: Mahmoud Shaaban
  • Issue: ropensci/onboarding#149
  • Reviewers: not assigned yet

On the blog

We’ve had five blog posts on our main blog in the past two weeks:

• rtimicropem: Using an R package as platform for harmonized cleaning of data from RTI MicroPEM air quality sensors by Maëlle Salmon
• Community Call - rOpenSci Software Review and Onboarding by Stefanie Butland
• How rOpenSci uses Code Review to Promote Reproducible Science by rOpenSci Editors
• Experiences as a first time rOpenSci package reviewer by Verena Haunschmid
• rOpenSci Software Review: Always Improving by rOpenSci Editors

We’ve also had two blog posts on our developer blog in the same timeframe:

• Spelling 1.0: quick and effective spell checking in R by Jeroen Ooms
• The writexl package: zero dependency xlsx writer for R by Jeroen Ooms

Use Cases

The following 7 works use/cite rOpenSci or rOpenSci software:

• Ben Baumer mentioned rOpenSci in his preprint A Grammar for Reproducible and Painless Extract-Transform-Load Operations on Medium Data ¹
• Leung et al. used taxize in their paper A quantitative-PCR based method to estimate ranavirus viral load following normalisation by reference to an ultraconserved vertebrate target ²
• Giroldo et al. used brranching in their paper Trait shifts associated with the subshrub life-history strategy in a tropical savanna ³
• Metzger et al. used nneo and Rocker (Docker containers for R) in their paper eddy4R 0.2.0: a DevOps model for community-extensible processing and analysis of eddy-covariance data based on R, Git, Docker, and HDF5 ⁴
• Ben Marwick, Carl Boettiger (of rOpenSci), and Lincoln Mullen mentioned rOpenSci in their preprint Packaging data analytical work reproducibly using R (and friends) ⁵
• A recent blog post Heat maps with Divvy data 2 by Austin Wehrwein uses our bikedata package ⁶
• A Shiny application called Ecological Event Miner, by Gabriel Muñoz, mines ecological events from published literature. It uses three rOpenSci packages: monkeylearn, fulltext, and taxize ⁷

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

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