Software 📦

CRAN: GitHub:

New packages

  • A new version (v2.1.0) of phylogram is on CRAN - a tool for developing phylogenetic trees as deeply-nested lists known as “dendrogram” objects. Check out the vignette to get started. This is not the first version on CRAN - but it just completed our software review process and is now in the rOpenSci family - welcome Shaun! phylogram phylogram
  • A new version (v1.2.2) of skynet is on CRAN - A flexible tool that allows generating bespoke air transport statistics for urban studies based on publicly available data from the Bureau of Transport Statistics (BTS) in the United States. Check out the skynet vignette to get started. This is not the first version on CRAN - but it just completed our software review process and is now in the rOpenSci family - welcome Filipe! skynet skynet

Releases

  • A new version (v5.2.1) of drake is on CRAN - A Pipeline Toolkit for Reproducible Computation at Scale. Check out the drake docs to get started. drake drake

    tests changes

  • A new version (v0.3.0) of brranching is on CRAN - grab plant phylogenies from Phylomatic. See the release notes for changes. Check out the brranching README to get started. brranching brranching

    new fxn bladj 🌲 - crul now for http requests

  • A new version (v0.2.0) of googleLanguageR is on CRAN - call Google’s Natural Language, Cloud Translation, Cloud Speech and Cloud Text-to-Speech API’s. See the release notes for changes. Check out the googleLanguageR docs to get started. googleLanguageR googleLanguageR

    new example Shiny app for Speech API, new fxn gl_talk() for Google text to speech

  • A new version (v0.8.4) of elastic is on CRAN - the best R client for Elasticsearch. See the release notes for changes. Check out the elastic vignettes to get started. elastic elastic

    new fxn docs_bulk_update, many docs_bulk fixes/improvements

  • A new version (v0.8.0) of biomartr is on CRAN - genomic data retrieval with R. See the biomartr NEWS for changes. Check out the biomartr docs to get started. biomartr biomartr

    new fxn getCollection, lots of new functionality in existing functions

  • A new version (v1.1) of cld3 is on CRAN - bindings to Google’s Compact Language Detector 3. See the cld3 NEWS for changes. Check out the cld3 README to get started. cld3 cld3
  • A new version (v0.4.2) of gistr is on CRAN - work with GitHub gists API from R. See the release notes for changes. Check out the gistr vignette to get started. gistr gistr

    better failure behavior; gist() can now fetch a specific revision



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 four packages recently went through our onboarding process and have been approved!

The following three packages were recently submitted:



On the blog

rOpenSci Unconference

There will be a series of posts from teams at our recent rOpenSci Unconference. Here’s the first:

The roomba team (Amanda Dobbyn, Jim Hester, Laura DeCicco, Christine Stawitz, Isabella Velasquez) wrote about their roomba package: A package for tidying nested lists

Software Review / Onboarding

We’re excited to announce two new editors for rOpenSci software review: Anna Krystalli and Lincoln Mullen. Read the details: Announcing new software review editors: Anna Krystalli and Lincoln Mullen.

rOpenSci HQ

Chat with the rOpenSci team at upcoming meetings - check out where various rOpenSci team members will be. We’d love to chat with you.



Use cases

The following 14 works use/cite rOpenSci software:



In the news


Lorenzo Busetto wrote a blog post about a new version of his package MODIStsp

Adam Sparks highlights a use of his package GSODR in the wild

Hal Snyder shared a Jupyter Notebook with use of our package rrricanes

Jose Vera used pdftools in a blog post

Lucy D’Agostino McGowan wrote a post using opencage: Bringing the family together: Finding the center of geographic points in R


Steven Mortimer wrote a blog post: Scraping responsibly with R in which he uses our package robotstxt






Keep up with rOpenSci


Footnotes

  1. Venkat, A. (2018). Sub-basin Valuation of Agriculture: A Crop-specific Assessment of Groundwater Footprints and Value in California (Masters thesis, Tufts University). https://search.proquest.com/docview/2054012866 

  2. Jaspers, S., De Troyer, E., & Aerts, M. (2018). Machine learning techniques for the automation of literature reviews and systematic reviews in EFSA. EFSA Supporting Publications, 15(6), 1427E. https://doi.org/10.2903/sp.efsa.2018.EN-1427 

  3. Hsu, Lawrence. 2018. Linking Traditional Chinese Medicinal Herbs to Cancer Related Pathways. Scholar Archive. 4054. https://digitalcommons.ohsu.edu/etd/4054 

  4. Krogsgaard, L. R., Andersen, L. O. ‘Brien, Johannesen, T. B., Engsbro, A. L., Stensvold, C. R., Nielsen, H. V., & Bytzer, P. (2018). Characteristics of the bacterial microbiome in association with common intestinal parasites in irritable bowel syndrome. Clinical and Translational Gastroenterology, 9(6). https://doi.org/10.1038/s41424-018-0027-2 

  5. Mienna, I. M. (2018). Patterns and Drivers of Phylogenetic Diversity and Endemism in the Norwegian Vascular Flora (Master’s thesis, NTNU). https://brage.bibsys.no/xmlui/bitstream/handle/11250/2502355/17650_FULLTEXT.pdf?sequence=1 

  6. Morais, R. A., & Bellwood, D. R. (2018). Global drivers of reef fish growth. Fish and Fisheries. https://doi.org/10.1111/faf.12297 

  7. Schwalie, P. C., Dong, H., Zachara, M., Russeil, J., Alpern, D., Akchiche, N., … Deplancke, B. (2018). A stromal cell population that inhibits adipogenesis in mammalian fat depots. Nature. https://doi.org/10.1038/s41586-018-0226-8 

  8. Ondei, S., Brook, B. W., & Buettel, J. C. (2018). Nature’s untold stories: an overview on the availability and type of on-line data on long-term biodiversity monitoring. Biodiversity and Conservation. https://doi.org/10.1007/s10531-018-1582-2 

  9. Hendrickson, P. J. (2018). Ecological Characterization of the Kuparuk River Aufeis Field, North Slope Alaska (Doctoral dissertation, University of Colorado at Boulder). https://search.proquest.com/docview/2056852840 

  10. Sanford, T., Gadzinski, A. J., Gaither, T., Osterberg, E. C., Murphy, G. P., Carroll, P. R., & Breyer, B. N. (2018). Effect of Oscillation on Perineal Pressure in Cyclists: Implications for Micro-Trauma. Sexual Medicine. https://doi.org/10.1016/j.esxm.2018.05.002 

  11. Mioduchowska, M., Czyż, M. J., Gołdyn, B., Kur, J., & Sell, J. (2018). Instances of erroneous DNA barcoding of metazoan invertebrates: Are universal cox1 gene primers too “universal”? PLOS ONE, 13(6), e0199609. https://doi.org/10.1371/journal.pone.0199609 

  12. Casey, Jerome (2018). Text Analytics Techniques in the Digital World: a Sentiment Analysis Case Study of the Coverage of Climate Change on US News Networks. Irish Communication Review: Vol. 16: Iss. 1, Article 7. https://arrow.dit.ie/icr/vol16/iss1/7 

  13. Koc, A., Henriksson, T., & Chawade, A. (2018). Specalyzer—an interactive online tool to analyze spectral reflectance measurements. PeerJ, 6, e5031. https://doi.org/10.7717/peerj.5031 

  14. Devlin, J. C., Battaglia, T., Blaser, M. J., & Ruggles, K. V. (2018). WHAM!: a web-based visualization suite for user-defined analysis of metagenomic shotgun sequencing data. BMC Genomics, 19(1). https://doi.org/10.1186/s12864-018-4870-z