Apr 15, 2019

rOpenSci HQ

• Our next Community Call on Security for R with Ildi Czeller & Bob Rudis is coming up next Tuesday (May 7th). Create Your Own Security Adventure by telling us what you want to know about the topic.

Software 📦

CRAN: GitHub:

New packages

• The first version (v1.1-1) of suppdata is on CRAN - downloading supplementary data from published manuscripts. Checkout the vignette to get started.
• The first version (v0.1.0) of conditionz is on CRAN - control how many times conditions are thrown. Checkout the README to get started.

New Versions

• A new version (v0.2.19) of rglobi is on CRAN - R Interface to Global Biotic Interactions. See the release notes for changes. Checkout the vignette to get started.

  show informative messages when internet not up

• A new version (v0.3.0) of finch is on CRAN - parse Darwin Core files. See the release notes for changes. Checkout the README to get started.

  fix to unit tests for new EML version

• A new version (v0.7.0) 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.

  geo2topo/topojson_write fxns gain new parameter quantization; fixes related to sf package

• A new version (v0.1.0) 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.

  new fxn osm_elevation; new vignette

• A new version (v2.0-11) of CoordinateCleaner is on CRAN - automated cleaning of occurrence records from biological collections. See the release notes for changes. Checkout the docs to get started.

  changes to the description file

• A new version (v2.0.0) 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 ground-up rewrite of EML; primary difference is it’s now built on S3 instead of S4; most high level functions are preserved

• A new version (v0.1.8) of codemetar is on CRAN - Generate codemeta metadata for R packages. See the release notes for changes. Checkout the docs to get started.

  address internet timeout issue

• A new version (v2.5.7) of FedData is on CRAN - get geospatial data from several federated government data sources. See the release notes for changes. Checkout the README to get started.

  skip tests on CRAN that require internet

• A new version (v0.2.1) of smapr is on CRAN - acquisition and processing of NASA Soil Moisture Active-Passive (SMAP) data. See the release notes for changes. Checkout the docs to get started.

  skip tests on CRAN that require internet; updated SMAP data versions

• A new version (v0.2) of tradestatistics is on CRAN - open trade statistics api wrapper and utility program. See the release notes for changes. Checkout the docs to get started.
• A new version (v7.2.0) of drake is on CRAN - a pipeline toolkit for reproducible computation at scale. See the release notes for changes. Checkout the docs to get started.

  many changes, see release notes

• A new version (v1.1.1) of nasapower is on CRAN - NASA POWER API Client. See the release notes for changes. Checkout the docs to get started.

  fixes for tests; fixes for NA’s and a documentation fix

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 package was recently submitted:

• opentripplanner > OpenTripPlanner for R
  • Author: Malcolm Morgan
  • Issue: ropensci/onboarding#295
  • Reviewers: not yet assigned

On the blog

Main blog

Stefanie Butland, Nick Golding, Chris Grieves, Hugo Gruson, Thomas White and Hao Ye wrote a post jointly published on our blog as well as the Methods in Ecology and Evolution blog: When Standards Go Wild - Software Review for a Manuscript.

Tech notes

Jeroen Ooms wrote about an update to the pdftools package: Join, split, and compress PDF files with pdftools.

Scott Chamberlain wrote about a new package called conditionz: conditionz: control how many times conditions are thrown.

Use Cases

The following 11 works use/cite rOpenSci software:

• Chakroborty et al. used plotly in their paper An unbiased in vitro screen for activating epidermal growth factor receptor mutations ¹
• van Zonneveld et al. used rgbif in their pre-print Understanding patterns of abiotic and biotic stress resilience to unleash the potential of crop wild relatives for climate-smart legume breeding ²
• Axtner et al. used taxize in their paper An efficient and robust laboratory workflow and tetrapod database for larger scale environmental DNA studies ³
• Blakey et al. used rnoaa in their paper Bats in a changing landscape: Linking occupancy and traits of a diverse montane bat community to fire regime ⁴
• Miranda et al. used rgbif in their paper Climate change impact on ecosystem functions provided by birds in southeastern Amazonia ⁵
• Rodrigues et al. used skimr in their paper Transitioning from recruit to officer: An investigation of how stress appraisal and coping influence work engagement> ⁶
• Sanger & Warin used textreuse in their paper Dataset of Jaccard similarity indices from 1,597 European political manifestos across 27 countries (1945–2017) ⁷
• Van de Perre et al. used rgbif and rredlist in their paper Paleoclimate, ecoregion size, and degree of isolation explain regional biodiversity differences among terrestrial vertebrates within the Congo Basin> ⁸
• Chileen used neotoma in their thesis Vegetation response to wildfire and climate forcing in a Rocky Mountain lodgepole pine forest over the past 2,500 years ⁹
• Medury et al. used FedData in their paper Pedestrian Count Expansion Methods: Bridging the Gap between Land Use Groups and Empirical Clusters ¹⁰
• Conde et al. used taxize in their paper Data gaps and opportunities for comparative and conservation biology ¹¹

In The News

Tuija Sonkkila wrote about working with altmetrics data in her post Everyday altmetrics, and used our package crevents to get Crossref Event data for a Shiny app. Source code: https://github.com/tts/aaltoced/blob/master/getdata.R

Call For Contributors

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. 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: we’ve found a maintainer, but we’re still finalizing details

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.

Related News

• Brett Cannon, a Python Core developer, broke down/explained an XKCD comic about Python. It’s not about R, but still an interesting read. And there’s probably lots of R users that read XKCD. Find the post at https://snarky.ca/deconstructing-xkcd-com-1987/

Keep up with rOpenSci

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Footnotes