Feb 8, 2021

rOpenSci HQ

Maëlle Salmon and Scott Chamberlain introduced the new HTTP Testing in R book: Learn All About HTTP Testing: Book Update

Stefanie Butland and Steffi LaZerte wrote a post on Introducing the rOpenSci Community Contributing Guide

Software 📦

CRAN: GitHub:

New packages

• The first version (v0.0.2) of tarchetypes is on CRAN - archetypes for targets. Checkout the docs to get started.
• The first version (v0.0.2) of targets is on CRAN - dynamic function-oriented make-like declarative workflows. Checkout the docs to get started.
• The first version (v0.13.5) of coder is on CRAN - deterministic categorization of items based on external code data. Checkout the docs to get started.

New Versions

• A new version (v1.1.1) of webchem is on CRAN - Chemical information from the web. See the release notes for changes. Checkout the docs to get started.
• A new version (v0.6.0) of ckanr is on CRAN - client for the CKAN API. See the release notes for changes. Checkout the docs to get started.
• A new version (v7.13.1) 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.
• A new version (v1.0.0) of ritis is on CRAN - an R client for ITIS (Integrated Taxonomic Information Service). See the release notes for changes. Checkout the docs to get started.
• A new version (v0.3.2) of grainchanger is on CRAN - Data aggregation methods for raster data. See the release notes for changes. Checkout the docs to get started.
• A new version (v1.0.6) of essurvey is on CRAN - data from the European Social Survey. See the release notes for changes. Checkout the docs to get started.
• A new version (v1.2.0) of rebird is on CRAN - client for the eBird database of bird observations. See the release notes for changes. Checkout the vignette to get started.
• A new version (v3.5.2) of rgbif is on CRAN - interface to the Global Biodiversity Information Facility API. See the release notes for changes. Checkout the docs to get started.
• A new version (v1.1.0) of gert is on CRAN - simple git client for R. See the release notes for changes. Checkout the docs to get started.
• A new version (v2.8) of assertr is on CRAN - Assertive Programming for R Analysis Pipelines. See the release notes for changes. Checkout the vignette to get started.
• A new version (v0.2.0) of rgnparser is on CRAN - parse scientific names using the Go tool gnparser. See the release notes for changes. Checkout the docs to get started.
• A new version (v3.0.0) of GSODR is on CRAN - Global Surface Summary of the Day (GSOD) Weather Data from R. See the release notes for changes. Checkout the docs to get started.
• A new version (v0.4.4) of nomisr is on CRAN - access UK official statistics from the Nomis database. See the release notes for changes. Checkout the docs to get started.
• A new version (v0.3.1) of git2rdata is on CRAN - store and retrieve data.frames in a Git repository. See the release notes for changes. Checkout the docs to get started.
• A new version (v0.7) of roadoi is on CRAN - find free versions of scholarly publications via Unpaywall. See the release notes for changes. Checkout the vignette to get started.
• A new version (v0.7.0) of rorcid is on CRAN - Interface to the Orcid.org API. See the release notes for changes. Checkout the vignette to get started.
• A new version (v1.4.0) of UCSCXenaTools is on CRAN - download and explore datasets from UCSC Xena data hubs. See the release notes for changes. Checkout the docs to get started.
• A new version (v3.1.5) of rfishbase is on CRAN - interface to Fishbase data. See the release notes for changes. Checkout the docs to get started.
• A new version (v0.3.0) of taxizedb is on CRAN - tools for working with taxonomic databases. See the release notes for changes. Checkout the docs to get started.
• A new version (v0.5.0) 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.
• A new version (v0.9.3) of hddtools is on CRAN - Hydrological Data Discovery Tools. See the release notes for changes. Checkout the docs to get started.
• A new version (v2.2.5) of ijtiff is on CRAN - comprehensive TIFF I/O with full support for ImageJ TIFF files. See the release notes for changes. Checkout the docs to get started.
• A new version (v0.4.2) of nodbi is on CRAN - the NoSQL database connector. See the release notes for changes. Checkout the README to get started.
• A new version (v3.1.4) of qualtRics is on CRAN - download Qualtrics survey data. See the release notes for changes. Checkout the docs to get started.
• A new version (v0.9.4) 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.
• A new version (v2.6.0) of magick is on CRAN - Advanced graphics and Image-Processing in R. See the release notes for changes. Checkout the docs to get started.
• A new version (v1.4.1) of cld3 is on CRAN - Bindings to Google’s Compact Language Detector 3. See the release notes for changes. Checkout the docs to get started.

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 approved:

• targets (Dynamic Function-Oriented Make-Like Declarative Workflows) & tarchetypes (Archetypes for Targets)
  • Author: William Landau
  • Issue: ropensci/software-review#401
  • Reviewers:
    • Samantha Oliver
    • TJ Mahr
• coder > Deterministic Categorization of Items Based on External Code Data
  • Author: Erik Bülow
  • Issue: ropensci/software-review#381
  • Reviewers:
    • Emily Zabor
    • David Robinson
• pixelclasser > A Package for Classifying Pixels by Colour
  • Author: Carlos Real
  • Issue: ropensci/software-review#406
  • Reviewers:
    • Quentin Rea
    • Jai Ranganathan
• osmextract > Download and Read OpenStreetMap Data Extracts
  • Author: Andrea Gilardi
  • Issue: ropensci/software-review#395
  • Reviewers:
    • Nicholas Potter
    • salvafern

The following packages were recently submitted:

• slopes > Calculate Slopes of Roads, Rivers and Trajectories
  • Author: Rosa Flx, Robin Lovelace
  • Issue: ropensci/software-review#420
  • Reviewers: not yet assigned
• aquamapsdata > Curated Data From AquaMaps.Org
  • Author: Markus Skyttner
  • Issue: ropensci/software-review#421
  • Reviewers: not yet assigned

On the blog

Maëlle Salmon and Scott Chamberlain introduced the HTTP Testing in R book: Learn All About HTTP Testing: Book Update.

Stefanie Butland and Steffi LaZerte wrote a post on Introducing the rOpenSci Community Contributing Guide.

Stefanie Butland and Emily Lescak wrote about How rOpenSci Runs Community Calls - arising from a presentation Stefanie gave to a Code for Science & Society Event.

Software review

Will Landau introduces his new packages targets - a new pipeline toolkit for R: targets: Democratizing Reproducible Analysis Pipelines. targets is the successor of drake, which succeeded remake.

Lluís Revilla Sancho introduces the package BaseSet that recently went through rOpenSci Software Review: Introducing BaseSet for mathematical sets

Tech notes

Jeroen Ooms wrote about updates to the magick package: Behind the magick: updates to imagemagick and beyond

Citations

The following 15 works use/cite rOpenSci software:

• Lucky et al. used refsplitr in their paper Gender, and Geography: changing demographics of a research community over thirty years ¹
• Bonnet et al. used rentrez in their paper Optimizing Literature Search: TEMAS, A New Text-Mining Algorithm-Assisted Search Tool ²
• Brightly et al. used rgbif and CoordinateCleaner in their paper High silicon concentrations in grasses are linked to environmental conditions and not associated with C4 photosynthesis ³
• Germani et al. used ijtiff in their paper SAPHIR: a Shiny application to analyze tissue section images ⁴
• Fastovich et al. used neotoma in their paper Spatial Fingerprint of Younger Dryas Cooling and Warming in Eastern North America ⁵
• Rycyk et al. used rnaturalearth in their paper Passive acoustic listening stations (PALS) show rapid onset of ecological effects of harmful algal blooms in real time ⁶
• Wenndt et al. used rnaturalearth in their paper Exploring aflatoxin contamination and household-level exposure risk in diverse Indian food systems ⁷
• Abbas et al. used rnaturalearth in their paper Biocontrol of aflatoxin in corn by inoculation with non-aflatoxigenicAspergillus flavusisolates ⁸
• Jacobs et al. used rnaturalearth in their paper Upwelling-induced trace gas dynamics in the Baltic Sea inferred from 8 years of autonomous measurements on a ship of opportunity ⁹
• Hotez et al. used rnaturalearth in their paper A new patient registry for Chagas disease ¹⁰
• Raut used rnaturalearth in their paper A computer vision approach to assess wood variability from whole-disk images of longleaf pine ¹¹
• Cramer et al. used rnaturalearth in their paper A spatiotemporal comparison of length-at-age in the coral reef fish Acanthurus nigrofuscus between marine reserves and fished reefs ¹²
• Winter-Billington et al. used rnaturalearth in their paper Evaluating the transferability of empirical models of debris-covered glacier melt ¹³
• Meng et al. used camsRad in their paper Data-driven inference of unknown tilt and azimuth of distributed PV systems ¹⁴
• Perez & Feeley used brranching in their paper Weak phylogenetic and climatic signals in plant heat tolerance ¹⁵

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.

Four new use cases were shared in the forum over the past month since our last newsletter:

• Gordon Shotwell: Using dittodb to test database queries - using the rOpenSci package dittodb
• Sharon Machlis: Shiny apps to search #rstudioglobal or #rstats tweets with rtweet, using the rtweet package
• Danielle Navarro: Use gert to scan all git repos in a directory, using the gert package
• Emilio Bruna: Mapping collaborations in Neotropical Taxonomy with refsplitr, using the refsplitr package

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. Check out our guidance for taking over maintenance of a package.

We’ve had eight 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
• webchem: now maintained by Erik Sapper
• mregions: now maintained by Lennert Schepers (VLIZ)
• rWBclimate: now maintained by Sergio Ibarra-Espinosa and Amanda Rehbein
• rinat: now maintained by Stéphane Guillou

Get involved with rOpenSci

We maintain a Contributing Guide that can help direct you to the right place, whether you want to make code contributions, non-code contributions, or other things like sharing use cases.

Keep up with rOpenSci

• Mailing list: Sign up with an email address to get this newsletter sent to your inbox -> https://news.ropensci.org/
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• rOpenSci on Twitter: @ropensci
• The rOpenSci blog at ropensci.org/blog - you can subscribe in any RSS aggregator, or manually via https://ropensci.org/index.xml. We also announce new blog posts on our Twitter account.

Footnotes