Feb 27, 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.

Software 📦

New packages

• A new package cRegulome (v0.1.0) is on CRAN. cRegulome lets you obtain and visualize regulome-gene expression correlations in cancer. Check out the cRegulome vignettes to get started. Repository on GitHub

Releases

• A new version (v0.3.0) of ijtiff is on CRAN - this isn’t the first version of the package on CRAN, but is the first version on CRAN under rOpenSci. See the release notes for details. Check out the ijtiff vignette to get started. Repository on GitHub
• A new version (v0.2.12) of rglobi is on CRAN. See the release notes for details. Check out the rglobi vignette to get started. Repository on GitHub
• A new version (v1.9) of tesseract is on CRAN. See the tesseract NEWS for details. Check out the tesseract README to get started. Repository on GitHub
• A new version (v0.0.6) of osmdata is on CRAN. See the osmdata release notes for details. Check out the tesseract vignettes to get started. Repository on GitHub
• A new version (v0.5.2) of crul is on CRAN. See the crul release notes for details. Check out the crul vignettes to get started. Repository on GitHub
• A new version (v1.7) of magick is on CRAN. See the magick release notes for details. Check out the magick 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 four packages recently went through our onboarding process and has been approved!

• ijtiff > TIFF I/O for ImageJ Users
  • Author: Rory Nolan
  • Issue: ropensci/onboarding#164
  • Reviewers:
    • Jeroen Ooms
    • John Clayden
• rdflib > Tools to Manipulate and Query Semantic Data
  • Author: Carl Boettiger
  • Issue: ropensci/onboarding#169
  • Reviewers:
    • Anna Krystalli
    • Bryce Mecum
• onekp > Retrieve Data from the 1000 Plants Initiative (1KP)
  • Author: Zebulun Arendsee
  • Issue: ropensci/onboarding#178
  • Reviewers:
    • Jessica Minnier
    • Zachary Foster
• bowerbird > Keep a Collection of Sparkly Data Resources
  • Author: Ben Raymond
  • Issue: ropensci/onboarding#139
  • Reviewers:
    • Miles McBain
    • Leah Wasser

The following package was recently submitted for review:

• antanym > Antarctic Geographic Place Names
  • Author: Ben Raymond
  • Issue: ropensci/onboarding#198
  • Reviewers: not assigned yet

On the blog

main blog

The other week we announced our new cohort of four rOpenSci fellows: Introducing the 2018 rOpenSci Research Fellows!.

They are:

• Sam Tyner
• Zachary Foster
• Kelly Hondula
• Jon Zelner

rOpenSci has supported one fellow so far (see our most recent community call).

Our community manager Stefanie Butland wrote about rOpenSci Vancouver Community Meetup: Transforming science through open data and software. If you’ll be in Vancouver on March 12 join us.

technotes

We’ve had two posts by rOpenSci developers in the last few weeks.

The first Support for hOCR and Tesseract 4 in R by Jeroen Ooms discusses a new version of the rOpenSci package tesseract (R bindings to Google’s open source optical character recognition (OCR) engine Tesseract).

The second post webmockr: mock HTTP requests by Scott Chamberlains is an overview of the rOpenSci package webmockr, including lots of new features and fixes.

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:

• Krotov & Tennyson used the rOpenSci package pdftools in their paper Scraping Financial Data from the Web Using R Language (the url is https://doi.org/10.2308/jeta-52063 but it doesn’t resolve, not sure what happened) ¹
• Gogleva et al. used the rOpenSci package biomartr in their paper SecretSanta: flexible pipelines for functional secretome prediction ²
• Chen et al. used rentrez in their paper miRToolsGallery: a tag-based and rankable microRNA bioinformatics resources database portal ³

In the news

Suzan Baert used rOpenSci’s pdftools package to extract text from PDFs to make Galentine’s Day Cards in R:

Happy Galentine's day #rladies!!! 🎉 New blog post featuring some short #tidytext analysis on parks and recreation! #rstatshttps://t.co/HUGlngDBe3 pic.twitter.com/6kDhc7hKaa

— Suzan Baert (@SuzanBaert) February 13, 2018

In a blog post Katie Jolly used the rOpenSci package magick to manipulate images to create Valentine’s Day cards in R:

#rstats blog post! @yung__pip and I made valentines for our friends with markovifyR, magick, and ponyexpress 😊 Feeling extra appreciation for #ropensci this week! https://t.co/Y8mEpFnUQr pic.twitter.com/vcy3SNZVwS

— Katie Jolly (@katiejolly6) February 19, 2018

In a blog post Jesse Tweedle used the rOpenSci package ckanr to audit some open data:

I try to audit @OpenGovCan's open data API with #rstats: https://t.co/izCIzJBDcX #opendata #opendatacan #gcdigital

— tweedle🦑⦩ (@tweed1e) February 19, 2018

Neil Gilbert was pretty happy to find out about one of our packages:

Me, 2 hours ago: hmm I wonder if there's an R package to deal with taxonomy stuff

Me, now: woooww taxize is awesomehttps://t.co/iIbptlC2Jg #rstats pic.twitter.com/zhoy2UorT2

— Neil Gilbert (@n_a_gilbert) February 21, 2018

Our software engineer Maëlle Salmon wrote about on her blog how to use magick to combine your hex stickers:

New #rstats post in which I learn how to use @rOpenSci @opencpu magick 🎩✨🐇 package to combine HEX STICKERS for my imaginary laptop!https://t.co/dGjbbCmBMa pic.twitter.com/f0dqsQYpI4

— Maëlle Salmon 🐟 (@ma_salmon) February 22, 2018

In a post from almost exactly one year ago Manuela Gonzalez and Luis Verde wrote about cleaning taxonomic names using our package taxize.

Damiano Oldoni did a tutorial for a LifeWatch meeting on our package rgbif (among other things):

Yesterday my 1st presentation about #rgbif as member of the @LifeWatchINBO team at #VLIZ. Proud of it!Thks @LifeWatchVLIZ for organization! https://t.co/BYCR0rZsYT #OpenData #gbif #lifewatch

— Damiano Oldoni (@damianozingaro) January 27, 2018

Keep up with rOpenSci

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Footnotes