Feb 12, 2018

rOpenSci HQ

rOpenSci Unconference 2018

We’ve announced our 2018 unconference in a recent blog post Apply to attend rOpenSci unconf 2018!. You’ll find all the details in the post.

rOpenSci Community Calls

Video is up for our most recent community call https://vimeo.com/255094144. Find out more about past and upcoming rOpenSci community calls at http://communitycalls.ropensci.org/.

Software 📦

New packages

• A new package codemetar (v0.1.4) is on CRAN. The Codemeta Project defines a JSON-LD format for describing software metadata, as detailed at https://codemeta.github.io. codemetar provides utilities to generate, parse, and modify codemeta.json files automatically for R packages, as well as tools and examples for working with codemeta.json JSON-LD more generally. Check out the codemetar vignettes to get started. Repository on GitHub
• A new package fingertipsR (v0.1.5) is on CRAN - this isn’t the first version of the package on CRAN, but is the first version on CRAN under rOpenSci. Fingertips (http://fingertips.phe.org.uk/) contains data for many indicators of public health in England. The underlying data is now more easily accessible by making use of the API. Check out the fingertipsR vignettes to get started. Repository on GitHub

Releases

• A new version (v1.0.1) of fulltext is on CRAN. See the release notes for details. Check out the fulltext manual to get started. Repository on GitHub
• A new version (v0.2.0) of patentsview is on CRAN. See the release notes for details. Check out the patentsview docs to get started. Repository on GitHub
• A new version (v0.6.0) of robotstxt is on CRAN. See the NEWS for details. Check out the robotstxt vignette to get started. Repository on GitHub
• A new version (v0.4.0) of rorcid is on CRAN. See the release notes for details. Check out the rorcid vignette to get started. Repository on GitHub
• A new version (v1.2.0) of rentrez is on CRAN. See the release notes for details. Check out the rentrez vignette 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 six packages recently went through our onboarding process and has been approved!

• DoOR.functions > Integrating Heterogeneous Odorant Response Data into a Common Response Model: A DoOR to the Complete Olfactomes
  • Author: Daniel Münch
  • Issue: ropensci/onboarding#34
  • Reviewers:
    • Remko Duursma
• DoOR.data > Data Package for DoOR.functions
  • Author: Daniel Münch
  • Issue: ropensci/onboarding#35
  • Reviewers:
    • Remko Duursma
• weathercan > Download Weather Data from the Environment and Climate Change Canada Website
  • Author: Steffi LaZerte
  • Issue: ropensci/onboarding#160
  • Reviewers:
    • Charles Gray
    • Joe Thorley
• fingertipsR > Fingertips Data for Public Health
  • Author: Sebastian Fox
  • Issue: ropensci/onboarding#168
  • Reviewers:
    • Carl Ganz
    • Duncan Garmonsway
• drake > A solution for reproducible code and high-performance computing.
  • Author: William Landau
  • Issue: ropensci/onboarding#156
  • Reviewers:
    • Julia Stewart Lowndes
    • Ben Marwick
    • Peter Slaughter
• auk > eBird Data Extraction with AWK
  • Author: Matthew Strimas-Mackey
  • Issue: ropensci/onboarding#136
  • Reviewers:
    • Auriel Fournier
    • Edmund Hart

The following four packages were recently submitted for review:

• nomisr > Access Nomis UK Labour Market Data with R
  • Author: Evan Odell
  • Issue: ropensci/onboarding#190
  • Reviewers:
    • Christophe Dervieux
    • Pablo
• rtika > R Interface to ‘Apache Tika’
  • Author: Sasha Goodman
  • Issue: ropensci/onboarding#191
  • Reviewers:
    • Julia Silge
    • David Gohel
• qualtRics > Download Qualtrics Survey Data Directly into R
  • Author: Jasper Ginn
  • Issue: ropensci/onboarding#192
  • Reviewers:
    • Jesse Maegan
    • not assigned yet
• suppdata > Downloading Supplementary Data from Published Manuscripts
  • Author: William Pearse
  • Issue: ropensci/onboarding#195
  • Reviewers: not assigned yet

On the blog

.rprofile series

Our fifth post is out in our .rprofile series: .rprofile: Julia Stewart Lowndes by Kelly O’Briant. Julia on Twitter -> https://twitter.com/juliesquid

Keep an eye out for more posts in this series.

main blog

We have a nice blog post up from a recently onboarded package called drake: The prequel to the drake R package.

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 seven works use/cite rOpenSci or rOpenSci software:

• Santorelli et al. used rotl in their paper Most species are not limited by an Amazonian river postulated to be a border between endemism areas ¹
• Emer et al. used taxize in their paper Seed-dispersal interactions in fragmented landscapes - a metanetwork approach ²
• Srivastava et al. used taxize in their pre-print Patterns of microsatellite distribution reflect the evolution of biological complexity ³
• Khorramdelazad et al. used taxize in their paper Transcriptome profiling of lentil (Lens culinaris) through the first 24 hours of Ascochyta lentis infection reveals key defence response genes ⁴
• Ruano et al. used rAltmetric in their paper The differential impact of scientific quality, bibliometric factors, and social media activity on the influence of systematic reviews and meta-analyses about psoriasis ⁵
• Claypool and Patel used rentrez in their pre-print A transcript-wide association study in physical activity intervention implicates molecular pathways in chronic disease ⁶
• Vitolo et al. used rdefra in their paper Modelling air pollution, climate and health data using Bayesian Networks: a case study of the English regions ⁷

In the news

Callum Taylor used rOpenSci’s RSelenium package and Rocker to extract information from the WHO Snake Antivenom database:

Using RSelenium, rvest, and a bit of purrr for webscraping in R, looking at the WHO Snake Antivenom Database. You can ignore the bits that look like the owl!#rstats #tidyversehttps://t.co/t6ObV6J9zD pic.twitter.com/tCezYMKJaj

— Callum Taylor (@CallumGWT) February 1, 2018

Emma Vestesson tweeted about using the rOpenSci osmdata package to generate a map to help decide where to eat:

Sick of going to the same place for lunch every day? I created a random eatery generator using #osmdata and #shiny https://t.co/qBFJ39pNA8 #leaflet #rstats #londonfoodie

— Emma Vestesson (@Gummifot) February 6, 2018

Mara Averick tweeted about a blog post by Timothée Giraud that used the rOpenSci package osmdata to make maps exploring Paris:

ICYMI, code to 🗺 the nearest 🍺!
"Cartographic Explorations of OpenStreetMap DB w/ R" https://t.co/mJOkCOFLSs via @hypothesesorg #rstats #maps #dataviz pic.twitter.com/gB3Af3N3CF

— Mara Averick (@dataandme) February 7, 2018

Submit news to rOpenSci

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Footnotes