Mar 18, 2019

rOpenSci HQ

• Our next Community Call on Research Applications of rOpenSci Taxonomy and Biodiversity Tools is coming up next week! See our recent blog post for all the details.
• 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.
• Our citations Twitter bot @rocitations (src code) tweets new citations of rOpenSci software. You can now contribute citations. Citations live on GitHub at ropenscilabs/ropensci_citations. Here’s an example pull request demonstrating how it’s done: https://github.com/ropenscilabs/ropensci_citations/pull/1. If you just want to look at the citations, peruse the tsv file.

Software 📦

CRAN: GitHub:

New packages

• The first version (v0.2.0) of emld is on CRAN - ecological metadata as linked data. The package recently went through rOpenSci software review, check out the review. Checkout the vignette to get started.
• The first version (v0.2.1) of tacmagic is on CRAN - positron emission tomography time-activity curve analysis. The package recently went through rOpenSci software review, check out the review. Checkout the vignette to get started.

New Versions

• A new version (v0.25.1) 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.

  fixed significant warning from ‘R CMD check’

• A new version (v0.4.8) of iheatmapr is on CRAN - Interactive and complex heatmaps. See the release notes for changes. Checkout the docs to get started.

  fix for sample; fixes for add_col_groups, iheatmapr_event, show_colorbar, save_iheatmap

• A new version (v0.15.6) 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.

  fixes for writing to users dir; fixes to update_news()

• A new version (v0.1.7) of codemetar is on CRAN - Generate codemeta metadata for R packages. See the release notes for changes. Checkout the docs to get started.

  jsonld to Suggests; write_codemeta() gains new arg. use_githook; create_codemeta() & write_codemeta() gain new arg. use_filesize

• A new version (v3.0.3) of rfishbase is on CRAN - interface to Fishbase data. See the release notes for changes. Checkout the docs to get started.

  fix bug in sealifebase name resolution

• A new version (v2.1) of spelling is on CRAN - tools for spell checking. See the release notes for changes. Checkout the README to get started.

  pre-filter script/style/img tags when checking html files; treat input files in spell_check_files() as UTF-8 on all platforms; fix sorting bug in spell_check_files()

• A new version (v7.0.0) 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 breaking changes; some bug fixes; new features including DSL for generating large plans; many enhancements including a large speed boost

• A new version (v2.2) of pdftools is on CRAN - Text extraction, rendering and converting of PDF documents. See the release notes for changes. Checkout the README to get started.

  import new qpdf pkg; document new PPA for Ubuntu 16.04 and 18.04 with poppler 0.74

• A new version (v1.3.8) of MODIStsp is on CRAN - Automate Download and Preprocessing of MODIS Land Products Data. See the release notes for changes. Checkout the docs to get started.

  fix for incorrect application of scale/offset values on GDAL verions > 2.3; added support for more MODIS products

• A new version (v0.2.1) 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.

  change in deprivation_decile(); bug fix for fingertips_data()

• A new version (v1.1) of qpdf is on CRAN - Split, combine and compress PDF files. See the release notes for changes. Checkout the README to get started.

  add configure script to allow building with system libqpdf; fix solaris build

Archived

• The rdefra has been archived on CRAN - we’re hoping to get it back on CRAN soon.

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 two packagess were recently submitted:

• MtreeRing > A Shiny Application for Automatic Measurements of Tree-Ring Widths on Digital Images
  • Author: Jingning Shi
  • Issue: ropensci/onboarding#287
  • Reviewers: not yet assigned
• grainchanger > Moving-Window and Direct Data Aggregation
  • Author: Laura Jane Graham
  • Issue: ropensci/onboarding#289
  • Reviewers: not yet assigned

On the blog

Community calls

Stefanie Butland wrote about our upcoming community call: Community Call - Research Applications of rOpenSci Taxonomy and Biodiversity Tools.

Tech notes

Will Landau wrote about a new version (v7) of drake in a tech note drake transformed. drake is an R-focused pipeline toolkit for reproducibility and high-performance computing.

Use Cases

The following eight works use/cite rOpenSci software:

• Karger et al. used CoordinateCleaner in their article Why tree lines are lower on islands-Climatic and biogeographic effects hold the answer ¹
• Olsson-Collentine et al. used rcrossref in their paper The Prevalence of Marginally Significant Results in Psychology Over Time ²
• Poulin et al. used rentrez in their paper on Taxonomic and geographic bias in the genetic study of helminth parasites ³
• Piñar et al. used rgbif in their article A time travel story: metagenomic analyses decipher the unknown geographical shift and the storage history of possibly smuggled antique marble statues ⁴
• Dreyer et al. used rgbif in their article Ligustrum lucidum W. T. Aiton (broad-leaf privet) demonstrates climatic niche shifts during global-scale invasion ⁵
• Ludt et al. used rgbif in their paper Genomic, ecological, and morphological approaches to investigating species limits: A case study in modern taxonomy from Tropical Eastern Pacific surgeonfishes ⁶
• Peruffo used skimr in their thesis on Improving predictive maintenance classifiers of industrial sensors’ data using entropy. A case study ⁷
• Free et al. used rfishbase in their paper Impacts of historical warming on marine fisheries production ⁸

In The News

We’ve introduced a template in our UseCases category in our discussion forum to make it easy to share how folks are using rOpenSci tools. Check out a recent one by Sharla Gelfand #visdat, #skimr, and #assertr use case: Exploring and understanding a new data set to find top 5 causes for delays on the TTC subway and SRT in 2018.

Stephanie Hazlitt wrote a blog post using the rOpenSci package weathercan triggered by her fence being blown over!

Guangchuang Yu is writing a bookdown book wrote Data Integration, Manipulation and Visualization of Phylogenetic Trees, in which he includes a section of a chapter on the rOpenSci package treeio

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 three 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

We’ve got three packages 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
• rsnps: The current maintainer would like to hand it over to someone with more expertise in the domain. Please get in touch with Scott if you’re interested.
• rdpla: The current maintainer would like to hand it over to someone with more expertise in the domain. Please get in touch with Scott if you’re interested.

Keep up with rOpenSci

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Footnotes