May 9, 2016

rOpenSci HQ

• We’ve completely updated all our tutorials at ropensci.org/tutorials - and we’ve added many new ones. Keep an eye out as we’ll add even more soon.

Software

• A new package originr (v0.1.0) is on CRAN. originr gets species origin data (whether species is native/invasive) from the following sources on the web: Encyclopedia of Life, Flora Europaea, Global Invasive Species Database, the Native Species Resolver, and Integrated Taxonomic Information Service. For an introduction to the package see the README. Repository on GitHub.
• A new version (0.3.2) of robotstxt is on CRAN. The package provides a simple ‘robotstxt’ class and accompanying methods to parse and check ‘robots.txt’ files. Data fields are provided as data frames and vectors. Permissions can be checked by providing path character vectors and optional bot names. See the vignette for an introduction to the package. Repository on GitHub.
• A new version (3.0.0) of rotl is on CRAN. See release notes for changes. Repository on GitHub.
• A new version (0.1.7) of lawn is on CRAN. See release notes for changes. Repository on GitHub.
• A new version (0.5.6) of rnoaa is on CRAN. See release notes for changes - this version has a bunch of bug fixes, make sure to upgrade. Repository on GitHub.
• A new version (1.5.1) of neotoma is on CRAN. See the NEWS for changes. Repository on GitHub.
• A new version (0.2.0) of pangaear is on CRAN. See release notes for changes. 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 pacakages 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!

The following are rOpenSci packages that have recently gone through our onboarding process:

• opencage
  • Author: Maëlle Salmon
  • Review: ropensci/onboarding#36
• ropenaq
  • Author: Maëlle Salmon
  • Review: ropensci/onboarding#24
• rgeospatialquality
  • Author: Javier Otegui
  • Review: ropensci/onboarding#28
• robotstxt
  • Author: Peter Meissner
  • Review: ropensci/onboarding#36

Use cases

Six recent papers cite and/or use rOpenSci software (or reference rOpenSci):

• Iraola and Naya cite and use taxize (the taxonomic toolbelt for R) in their paper Wedding higher taxonomic ranks with metabolic signatures coded in prokaryotic genomes ¹
• Perez-Riveral et al. cite rOpenSci in general and RNeXML specifically in their paper Ten Simple Rules for Taking Advantage of git and GitHub ²
• Jacobs et al. cite rfigshare and dvn in their paper Integrating Research Data Management into Geographical Information Systems ³
• Schwery, O., & O’Meara cite and use taxize in their paper MonoPhy: a simple R package to find and visualize monophyly issues ⁴
• Dafforn et al. reference rOpenSci in their paper Big data opportunities and challenges for assessing multiple stressors across scales in aquatic ecosystems ⁵
• Bachelot et al. cite and use taxize in their paper Long‐lasting effects of land use history on soil fungal communities in second‐growth tropical rain forests ⁶

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 http://ropensci.org/feed.xml. We also announce new blog posts on our Twitter account.

Footnotes