Jan 3, 2017

Software

New packages

• A new package finch (v0.1.0) is on CRAN. finch parses Darwin Core simple and archive directories/zip files. One major source of these kinds of data come from the Global Biodiversity Information Facility (GBIF). Check out the README to get started. p.s. depends on EML below :) Repository on GitHub
• A new package EML (v1.0.1) is on CRAN. EML parses and serializes Ecological Metadata Language (EML, see https://en.wikipedia.org/wiki/Ecological_Metadata_Language for more information) files into S4 objects. Check out the vignettes to get started. Repository on GitHub

Releases

• A new version (v3.1-1) of clifro is on CRAN. See release notes for changes. Repository on GitHub.
• A new version (v0.3.0) of rbhl is on CRAN. See release notes for changes. Repository on GitHub.
• A new version (v0.1.7-2) of stplanr is on CRAN. See release notes for changes. Repository on GitHub.
• Two new versions of git2r have hit CRAN since the last rOpenSci News: (v0.17.0) and (v0.18.0). git2r on CRAN. See release notes for v0.17.0 and v0.18.0 for changes. Repository on GitHub.
• A new version (v0.2.0) of crul is on CRAN. This version includes more documentation, fixed URL encoding, fixed parsing of request and response headers, and now supports multiple query parameters of the same name. See release notes for changes and links to issues. 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 and is undergoing review:

• JSTORr > Simple text mining and document clustering of JSTOR journal articles
  • Author: Ben Marwick
  • Issue: ropensci/onboarding#86
  • Reviewers:
    • Thomas Leeper

Use cases

Two blog posts and many new (and some old) papers cite rOpenSci packages:

• Kan Nishida wrote a nice blog post on Making Maps for Canada’s Provisions and Census Divisions in R, which included use of geojsonio, an rOpenSci package for working with GeoJSON data. ¹
• Tuja Sonkkila wrote a nice blog post on Semi-automatic IT at work, which used rAltmetric, an rOpenSci package for working with Altmetric.com data. Check out her code in her repository tts/finunipolicy. ²
• Gilles et al. cite and use rgbif in their paper RAINBIO: a mega-database of tropical African vascular plants distributions ³
• Lundgren & Christin cite and use rgbif in their paper Despite phylogenetic effects, C3-C4 lineages bridge the ecological gap to C4 photosynthesis ⁴
• Galata et al. cite and use taxize in their paper Comparing genome versus proteome-based identification of clinical bacterial isolates ⁵
• Hassall et al. cite and use bold in their paper Phenological shifts in hoverflies (Diptera: Syrphidae): linking measurement and mechanism ⁶
• Hampton et al. cite and use rentrez in their paper The Tao of open science for ecology ⁷
• Nguyen et al. cite and use rentrez in their paper Integrative Computational and Experimental Approaches to Establish a Post-Myocardial Infarction Knowledge Map ⁸
• Killen et al. cite and use rotl in their paper Do method and species lifestyle affect measures of maximum metabolic rate in fishes? ⁹
• Estrada-Peña & de la Fuente cite and use rotl in their paper Species interactions in occurrence data for a community of tick-transmitted pathogens ¹⁰
• Bauer et al. cite fulltext and rcrossref in their paper The Quality of Citations: Towards Quantifying Qualitative Impact in Social Science Research ¹¹
• Mackinnon et al. cite and use rsnps in their paper Environmental Correlation Analysis for Genes Associated with Protection against Malaria ¹²
• Söderholm cites and uses rsnps in his thesis The Complex Genetics of Multiple Sclerosis: A preliminary study of MS-associated SNPs prior to a larger genotyping project ¹³
• Kolb uses and cites geonames in his paper Visualizing GeoData with R ¹⁴

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.

Footnotes