May 8, 2017

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Software

New packages

• A new package crminer (v0.1.0) is on CRAN. crminer focuses on getting the user full text via the Crossref search API, depending on the full text links provided by publishers in the Crossref search API. See also rcrossref Check out the crminer README to get started. Repository on GitHub
• A new package taxizedb (v0.1.0) is on CRAN. taxizedb is a suite of functions to help users download, load into SQL, and query taxonomic databases. The goal is to make it easy to handle a lot of queries - sometimes making lots of web requests (e.g. with taxize) is just too slow. Support thus far for: Integrated Taxonomic Information Service, Catalogue of Life, ThePlantList, and GBIF backbone taxonomy (more to come). This package is likely to have a number of bugs on various platform/database combinations, so please do report bugs. Check out the taxizedb README to get started. Repository on GitHub
• A new package antiword (v1.1) is on CRAN. antiword wraps the AntiWord utility to extract text from Microsoft Word documents. The utility only supports the old doc format, not the new xml based docx format. Check out the antiword README to get started. Repository on GitHub

Releases

• A new version (v0.1.2) of binomen is on CRAN. This version includes a fix for new dplyr coming out soon. See release notes for details. Repository on GitHub
• A new version (v0.4.0) of rerddap is on CRAN. This version adds a new and very thorough vignette, replaces some internals, changes to using https for many URLS in servers(), and improves docs. Note that rerddap has been archived temporarily but will be back soon - you can always install from GitHub. See release notes for details. Repository on GitHub
• A new version (v4.6.0) of plotly is on CRAN. This version adds significant support for multiple linked views, adds highlight() function, support for animation, added support for more ggplot2 geoms, and much more. See the NEWS for details. Repository on GitHub
• A new version (v1.0.3) of EML is on CRAN. This version migrates from XML to xml2, and improves performance for displaying and serializing XML. See the NEWS for details. Repository on GitHub
• A new version (v0.4.0) of rebird is on CRAN. See the NEWS for details. Repository on GitHub
• A new version (v0.2.0) of ropenaq is on CRAN. See the NEWS for details. Repository on GitHub
• A new version (v0.7.0) of rcrossref is on CRAN. This version breaks off text mining functionality into new package crminer; all Crossref API requests now using https; now using crul for HTTP requests; many bug fixes. See release notes for details. Repository on GitHub
• A new version (v0.5.16) of aRxiv is on CRAN. See release notes for details. Repository on GitHub
• A new version (v2.4) of hunspell is on CRAN. See release notes for details. Repository on GitHub
• A new version (v0.7.0) of rnoaa is on CRAN. This version adds new params to isd(); new functions for the Climate Prediction Center, and for Africa Rainfall Climatology version 2; many NOAA services now switched to using https; many bug fixes. See release notes for details. 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 packages were recently submitted to our onboarding process:

• patentsview > An R Client to the PatentsView API
  • Author: Christopher Baker
  • Issue: ropensci/onboarding#112
  • Reviewers:
    • Verena Haunschmid
    • Paul Oldham
• gitlabr > Access to the Gitlab API
  • Author: Jirka Lewandowski
  • Issue: ropensci/onboarding#113
  • Reviewers: not assigned yet
• cyphr > High Level Enryption Wrappers
  • Author: Rich FitzJohn
  • Issue: ropensci/onboarding#114
  • Reviewers: not assigned yet

The following package recently went through our onboarding process and has been approved:

• lingtypology > Linguistic Typology and Mapping
  • Author: George Moroz
  • Issue: ropensci/onboarding#95
  • Reviewers:
    • Kent Russell
    • Taras Zakharko
    • languageSpaceLabs

On the blog

Since last rOpenSci news we’ve had three blog posts.

First, we wrote a post about our awesome interns. Check it out: Welcome to our rOpenSci interns

Second, our community manager Stefanie Butland wrote a post about where you can catch up and chat with rOpenSci team members: Chat with the rOpenSci team at upcoming meetings

Last, Ken Benoit wrote up a summary of the recent rOpenSci affiliated Text Analysis Package Developers’ Workshop that happened in London. Our own Jeroen Ooms attended, in addition to many other great folks in the text analysis R community. Check it out: Text Analysis R Developers’ Workshop 2017

Onboarding series

We’re doing a series of guest blog posts for packages that have gone through our software review process at ropensci/onboarding.

7th: Thomas Leeper on his package tabulizer - Release ‘open’ data from their PDF prisons using tabulizer.

6th: Tony Fischetti on his package assertr - Data validation with the assertr package.

5th: Adam Sparks on his package GSODR - Everybody talks about the weather.

4th: Lukas Lundstrom on his package camsRad - camsRad, satellite-based time series of solar irradiation.

3rd: Claudia Vitolo on her package hddtools - Discover hydrological data using the hddtools R package.

2nd: Maëlle Salmon on her package ropenaq - ropenaq, a breath of fresh air/R.

1st: Sean Hughes on his package plater - From a million nested ifelses to the plater package.

We’ll have more posts in this series coming out soon - keep an eye out.

Use Cases

The following five papers use/cite rOpenSci or rOpenSci software:

• Andruszkiewicz et al. used our package taxize in their paper Biomonitoring of marine vertebrates in Monterey Bay using eDNA metabarcoding ¹
• Na and Ye used our package rAltmetric in their paper Content Analysis of Scholarly Discussions of Psychological Academic Articles on Facebook ²
• Lahti et al. cited rOpenSci in their paper Retrieval and Analysis of Eurostat Open Data with the eurostat package ³
• Perez-Escobar et al. used and cited spocc in their paper A new species of Telipogon (Oncidiinae; Orchidaceae) from the paramos of Colombia ⁴
• Singh used and cited our package helminthR in their paper Evaluating two freely available geocoding tools for geographical inconsistencies and geocoding errors ⁵

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 feed at https://news.ropensci.org/feed.xml

Footnotes