Feb 17, 2020

Software 📦

CRAN: GitHub:

New Versions

• A new version (v0.9.0) of geojsonio is on CRAN - Convert Data from and to GeoJSON or TopoJSON. See the release notes for changes. Checkout the vignettes to get started.

  geojson_sf()/geojson_sp() now accept strings; replace httr with crul & rgdal replaced with sf

• A new version (v0.4.0) of geojsonlint is on CRAN - Tools for Validating GeoJSON. See the release notes for changes. Checkout the docs to get started.

  geojson_lint() defunct - the geojsonlint.com API is down

• A new version (v2.1.0) of rgbif is on CRAN - interface to the Global Biodiversity Information Facility API. See the release notes for changes. Checkout the occurrence manual to get started.

  occ_download() bug fix for within predicates for geometry queries; occ_spellcheck() now defunct

• A new version (v4.9.2) of plotly is on CRAN - Create Interactive Web Graphics via plotly.js. See the release notes for changes. Checkout the plotly book to get started.

  upgrade plotly.js to v1.52.2

• A new version (v0.9.92) of taxize is on CRAN - taxonomic toolbelt for R. See the release notes for changes. Checkout the taxize book to get started.

  all Catalogue of Life functions removed (get in touch if you need help); new fxn gn_parse() for Global Names name parser

• A new version (v1.0.8) of spocc is on CRAN - an interface to many species occurrence data sources. See the release notes for changes. Checkout the docs to get started.
• A new version (v1.1.1) of lingtypology is on CRAN - linguistic typology and mapping. See the release notes for changes. Checkout the docs to get started.

  update glottolog from v2.7 to v4.1; some fxns removed

• A new version (v0.3.0) of scrubr is on CRAN - clean biological occurrence records. See the release notes for changes. Checkout the docs to get started.

  new fxn fix_names(); new fxn eco_region to filter data by ecoregions; new fxns coord_imprecise()/coord_uncertain() to clean coordinates

• A new version (v1.0.2) of fingertipsR is on CRAN - Fingertips data for public health http://fingertips.phe.org.uk/. See the release notes for changes. Checkout the vignettes to get started.

  bug fix for fingertips_data()

• A new version (v0.1.3) of osmdata is on CRAN - import OpenStreetMap data as simple features or spatial objects. See the release notes for changes. Checkout the docs to get started.

  osmdata_pbf() function removed; remove deprecated add_feature() - replaced by add_osm_feature()

• A new version (v2.0.2) of EML is on CRAN - read and write ecological metadata language files. See the release notes for changes. Checkout the docs to get started.
• A new version (v0.4.1) of nlrx is on CRAN - setup, run and analyze NetLogo model simulations. See the release notes for changes. Checkout the vignettes to get started.
• A new version (v0.2.0.8) of opentripplanner is on CRAN - client for OpenTripPlanner for journey planning. See the release notes for changes. Checkout the docs to get started.
• A new version (v0.6.4) of rorcid is on CRAN - Interface to the Orcid.org API. See the release notes for changes. Checkout the vignette to get started.

  recursive parameter removed from orcid(); orcid_search() loses some parameters; orcid() gains additional fields to query, e.g., peer-review-type

• A new version (v2.7) of assertr is on CRAN - Assertive Programming for R Analysis Pipelines. See the release notes for changes. Checkout the vignette to get started.

  added “inverse” option to predicates

• A new version (v0.4.0) of emld is on CRAN - ecological metadata as linked data. See the release notes for changes. Checkout the vignette to get started.

  fixed serialization bug in references attribute; fixed validation bugs

• A new version (v0.3.3) of weathercan is on CRAN - Download weather data from the Environment and Climate Change Canada website. See the release notes for changes. Checkout the docs to get started.

  update internal datasets

• A new version (v1.7.7) of RSelenium is on CRAN - R client for Selenium Remote WebDriver. See the release notes for changes. Checkout the docs to get started.

  re-submission to CRAN after archiving

Software Review ✔

We accept community contributed packages via our software review 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 packages were recently submitted:

• mcbette > Model Comparison Using babette
  • Author: Richard Bilderbeek
  • Issue: ropensci/onboarding#360
  • Reviewers:
    • Vikram Baliga
    • bjoelle
• dittodb > A Test Environment for DB Requests
  • Author: Jonathan Keane
  • Issue: ropensci/onboarding#366
  • Reviewers: not yet assigned
• circle > R client package for the Circle CI API
  • Author: Patrick Schratz
  • Issue: ropensci/onboarding#356
  • Reviewers: not yet assigned

On the blog

• Steph Stammel wrote about OzUnconf 2019 ~> The Fun of Building Things and the Challenge of Learning - the rOpenSci OzUnconf 2019. Steph does a really nice job of explaining the motivation behind the unconf and dives into some of the projects explored at the event.

Software Review:

• Kari Norman wrote about her recently rOpenSci reviewed package taxadb: taxadb: A High-Performance Local Taxonomic Database Interface. Kari discusses the motivation for and design of the package, and how to use taxadb.

Use Cases

The following 13 works use/cite rOpenSci software:

• Næss used rnaturalearth in their paper From hunter-gatherers to nomadic pastoralists: forager bands do not tell the whole story of the evolution of human cooperation ¹
• Wang et al. used UCSCXenaTools in their paper Antigen presentation and tumor immunogenicity in cancer immunotherapy response prediction ²
• Thorson used rfishbase in their paper Predicting recruitment density dependence and intrinsic growth rate for all fishes worldwide using a data‐integrated life‐history model ³
• Geary et al. used taxize in their paper Predator responses to fire: A global systematic review and meta‐analysis ⁴
• Hong et al. used FedData in their paper Visualizing Urban Microclimate and Quantifying its Impact on Building Energy Use in San Francisco ⁵
• Lange et al. used biomartR in their paper RST1 and RIPR connect the cytosolic RNA exosome to the Ski complex in Arabidopsis ⁶
• Báez et al. used spocc in their paper Ensemble modeling of the potential distribution of the whale shark in the Atlantic Ocean ⁷
• Estrada-Peña et al. used MODIStsp and rotl in their paper Species occurrence of ticks in South America, and interactions with biotic and abiotic traits ⁸
• Lecocq et al. used rfishbase in their paper TOFF, a database of traits of fish to promote advances in fish aquaculture ⁹
• Reis used rgbif in their paper Uma perspectiva macroecológica sobre o risco de extinção em mamíferos ¹⁰
• Yagli et al. used camsRad in their paper Can we justify producing univariate machine-learning forecasts with satellite-derived solar irradiance? ¹¹
• Li et al. used UCSCXenaTools in their paper The SMART App: an interactive web application for comprehensive DNA methylation analysis and visualization ¹²
• Fu & Hughey used rcrossref and rentrez in their paper Releasing a preprint is associated with more attention and citations for the peer-reviewed article ¹³

From the Forum

We have a discussion forum (using Discourse) for the rOpenSci community. It’s a really nice way to have conversations on the internet. From time to time we’ll highlight recent discussions of interest.

Two use cases have been reported in the forum recently:

• Mark Padgham shared a use case for his osmdata package: osmdata use case: Wall Art
• Ivan Leung shared a use case for the pdftools package: pdftools for parsing .pdf from a URL - public data mining

Call For Maintainers

Part of the mission of rOpenSci is making sustainable software that users can rely on. Some software maintainers need to give up maintenance due to a variety of circumstances. When that happens we try to find new maintainers. Checkout our Contributing Guide for why and how to contribute to rOpenSci.

We’ve had six recent examples of maintainer transitions within rOpenSci:

• RSelenium: now maintained by Ju Kim
• chromer: now maintained by Paula Andrea
• qualtRics: now maintained by Julia Silge
• rsnps: now maintained by Julia Gustavsen and Sina Rüeger
• rdpla: now maintained by Alyssa Columbus
• webchem: now maintained by Erik Sapper
• mregions: in process of moving to maintenance by VLIZ

We don’t have any packages looking for new maintainers - if you are a maintainer and want to hand over that role to someone else get in touch with us.

Keep up with rOpenSci

• Mailing list: Sign up with an email address to get this newsletter sent to your inbox -> ropensci.org/#subscribe
• Alternatively, you can subscribe to this newsletter via our XML feed at https://news.ropensci.org/feed.xml or our JSON feed at https://news.ropensci.org/feed.json
• rOpenSci on Twitter: @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