Apr 1, 2019

rOpenSci HQ

• More than 50 people attended our Community Call on Research Applications of rOpenSci Taxonomy and Biodiversity Tools. Video, slides, and code are available: https://ropensci.org/commcalls/2019-03-27/. Thank you to our speakers: Kathryn Turner, Zachary Foster, Kari Norman, Margaret Siple, Scott Chamberlain and Ciera Martinez.
• We’re planning a Community Call on Security for R with Ildi Czeller & Bob Rudis. Create Your Own Security Adventure by telling us what you want to know about the topic.

Software 📦

CRAN: GitHub:

New packages

• The first version (v1.0.1) of cyphr is on CRAN - high level encryption wrappers. See the release notes for changes. Checkout the vignettes to get started.
• The first version (v0.1.0) of nlrx is on CRAN - setup, run and analyze NetLogo model simulations. See the release notes for changes. Checkout the vignettes to get started.

New Versions

• A new version (v0.15.7) of DataPackageR is on CRAN - construct reproducible analytic data sets as R packages. See the release notes for changes. Checkout the vignettes to get started.

  fix test/vignette bugs related to upcoming version of usethis

• A new version (v0.7.4) of crul is on CRAN - an R6 based HTTP client for R made for developers. See the release notes for changes. Checkout the docs to get started.

  request/response hooks now supported; improve $parse behavior; Paginator gains progress bar option

• A new version (v0.2.18) of rglobi is on CRAN - R Interface to Global Biotic Interactions. See the release notes for changes. Checkout the vignette to get started.

  update cypher query endpoint after server upgrade to neo4j

• A new version (v0.5) of ssh is on CRAN - Secure shell (SSH) client for R. See the release notes for changes. Checkout the vignette to get started.

  use key management fxns from credentials pkg; refactor password callback; rename ssh_info() to ssh_session_info()

• A new version (v0.4.0) of tidyhydat is on CRAN - Water Survey of Canada hydrometric data. See the release notes for changes. Checkout the vignettes to get started.

  all fxns now return either “hy” or “realtime” class with associated print and plot methods; fxns now fail with an informative error message

• A new version (v0.4.2) of Rpolyhedra is on CRAN - polyhedra database from various sources as R6 objects and visualizing capabilities. See the release notes for changes. Checkout the vignette to get started.

  calculates & normalizes polyhedra size using geometry::convhulln instead of bounding box; a polyhedron now applies internal transformation matrix

• A new version (v0.2.8) of stplanr is on CRAN - sustainable transport planning. See the release notes for changes. Checkout the docs to get started.

  STATS19 fxns such as dl_stats19() split-out into the new package stats19; new fxns route_dodgr(), overline2() … a substantial refactoring operation has begun

• A new version (v0.5.0) of bomrang is on CRAN - Australian government Bureau of Meteorology (BOM) data. See the release notes for changes. Checkout the docs to get started.

  some new print methods; new aliases for some fxns; new default image when image failed to download

• A new version (v2.0-8) 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.

  moved vignettes to online documentation; added an area column to the countryref dataset

• A new version (v0.0.10) 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.

  bug fix for vectorized lists of values in add_osm_feature; bug fix to ensure all sf data.frame objects have stringsAsFactors = FALSE

• A new version (v3.2-2) of clifro is on CRAN - easily download and visualise climate data from CliFlo. See the release notes for changes. Checkout the vignettes to get started.

  fixed error in cf_find_station() fxn when searching for CliFlo stations based on geog. proximity & when using a datatype

• A new version (v0.25.2) of git2r is on CRAN - an interface to the libgit2 library, a pure C implementation of the Git core methods. See the release notes for changes. Checkout the README to get started.

  improved build configuration script

• A new version (v0.6.3) of rdhs is on CRAN - Client for Demographic and Health Survey (DHS) Data. See the release notes for changes. Checkout the docs to get started.

  new delabel_df() fxn for converting labelled data frames to characters

Un-Archived

• rdefra was archived on CRAN for a bit - Now it’s back up.

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:

• tidypmc > Parse full text XML documents from PMC
  • Author: Chris Stubben
  • Issue: ropensci/onboarding#290
  • Reviewers: not yet assigned

Use Cases

The following 12 works use/cite rOpenSci software:

• Phelps et al. used rentrez in their paper on Bat Research Networks and Viral Surveillance: Gaps and Opportunities in Western Asia ¹
• Angel & Markus used rnoaa in their article Frequency Distributions of Heavy Precipitation in Illinois: Updated Bulletin 70 ²
• Mitchell & Moseley used RSelenium in their paper Deriving Accurate Lipid Classification based on Molecular Formula ³
• Solt used tabulizer in their work on Measuring Income Inequality Across Countries and Over Time: The Standardized World Income Inequality Database ⁴
• Michalak et al. used plotly in their article ComplexBrowser: a tool for identification and quantification of protein complexes in large scale proteomics datasets ⁵
• Su et al. used plotly in their article TCC-GUI: a Shiny-based application for differential expression analysis of RNA-Seq count data ⁶
• König et al. used taxize in their article Biodiversity data integration–The significance of data resolution and domain ⁷
• Ravenhall et al. used plotly in their article SV-Pop: population-based structural variant analysis and visualization ⁸
• Higino & Vital used taxize in their paper Mapping and understanding the digital biodiversity knowledge about vertebrates in the Atlantic Rainforest ⁹
• Ahmed et al. wrote a paper about their package colocr in the rOpenSci suite: colocr: An R package for conducting co-localization analysis on fluorescence microscopy images ¹⁰
• Jo et al. used taxize in their paper SoEM: a novel PCR-free biodiversity assessment method based on small-organelles enriched metagenomics ¹¹
• Shefferson et al. used rotl in their paper Does evolutionary history determine specificity in broad ecological interactions? ¹²

In The News

Erik Gahner Larsen and Zoltán Fazekas have a bookdown book titled Quantitative Politics with R in which they include Chapter 4: Get existing data with a section on the European Social Survey using the rOpenSci package esssurvey, maintained by Jorge Cimentada.

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 five 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

We’ve got only one package in need of new maintainers:

• webchem: The current maintainer of webchem, Eduard Szöcs, is looking for a new maintainer. See issue #155. Do ping Eduard in that issue and/or email us at info@ropensci.org

Keep up with rOpenSci

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Footnotes