Software 📦

CRAN: GitHub:

New packages

  • A new package rdflib (v0.1.0) is on CRAN. rdflib is a high level wrapper around the redland package for common rdf applications. This package recently went through rOpenSci review. Check out the rdflib docs to get started.
  • A new package landscapetools (v0.3.0) is on CRAN. landscapetools provides utility functions to complete tasks involved in most landscape analysis. This package recently went through rOpenSci review. Check out the landscapetools docs to get started.
  • A new package essurvey (v1.0.0) is on CRAN. essurvey lets you download data from the European Social Survey. This package recently went through rOpenSci review. Check out the essurvey docs to get started.

Releases

  • A new version (v0.4.0) of webchem is on CRAN. See the webchem NEWS for details. Check out the webchem README to get started.

    Lots a 🐞 fixes!!!

  • A new version (v3.0.4) of rotl is on CRAN. See the release notes for details. Check out the rotl vignettes to get started.
  • A new version (v1.0.2) of skimr is on CRAN. See the skimr NEWS for details. Check out the skimr vignettes to get started.

    You can create skimmers with the formula syntax from `rlang!

  • A new version (v0.6.0) of geojsonio is out - see the release notes for details. Check out the geojsonio vignettes to get started.

    You can now control the object name output for topojson_write, and there’s now an analog of geojson_sp for sf (geojson_sf)`

  • A new version (v1.2.0) of GSODR is out. See the GSODR NEWS for details. Check out the GSODR vignettes to get started.

    package slimmed down with move of sp/sf/rgdal from Imports to Suggests

  • A new version (v0.3.1) of USAboundaries is on CRAN. See the release notes for details. Check out the USAboundaries docs to get started.

    a new vignette - woop woop

  • A new version (v0.5.0) of wellknown is on CRAN. See the release notes for details. Check out the wellknown vignette to get started.

    added wkt<–>wkb awesome sauce, and overhaul of wkt2geojson and geojson2wkt

  • A new version (v0.2.1) of tokenizers is on CRAN. See the release notes for details. Check out the tokenizers docs to get started.
  • A new version (v0.3.0) of microdemic is on CRAN. See the release notes for details. Check out the microdemic README to get started.

    changed base url, make sure to get a new API 🔑

  • A new version (v1.6) of pdftools is on CRAN. See the pdftools NEWS for details. Check out the pdftools README to get started.



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 packages recently went through our onboarding process and has been approved!

The following two packages were recently submitted:



On the blog

main blog

Miles McBain was kind enough to cross-post a reflection on the value of software peer review from his personal blog: Where is the value in package peer review?.


As part of our series of posts on packages that have gone through rOpenSci onboarding Konstantinos Vantas wrote a post (ὕδωρ + σκοπῶ = water + observe) about his package hydroscoper for interacting with the Greek National Data Bank for Hydrometeorological Information.


As part of our series of posts on packages that have gone through rOpenSci onboarding Daniel Münch wrote a post (DoOR - The Database of Odorant Responses) about his packages DoOR.functions and DoOR.data for interacting with the Database of Odorant Responses.



Use cases

The following 18 works use/cite rOpenSci software:



In the news

Jorge Cimentada wrote a blog post RSelenium and scraping Catalan educational data using, you guessed it, our RSelenium package.


Caryn Johansen and Ciera Martinez of the Cabinet of Curiosity blog wrote a blog post on Exploring Neotoma Part 2: Extinct Mammal Distributions using our neotoma package


Juan Mayorga wrote a nice blog post about mapping fisheries, while using our rnaturalearth package


Daniela Vázquez wrote a blog post Scrapeando las Sesiones Parlamentarias de Uruguay (english title: Scraping the Parliamentary Sessions of Uruguay) - and used rOpenSci packages pdftools and robotstxt






Keep up with rOpenSci


Footnotes

  1. Tang, Y. (2018). Autoplotly-Automatic Generation of Interactive Visualizations for Popular Statistical Results. arXiv preprint arXiv:1803.08424. https://arxiv.org/pdf/1803.08424 

  2. Dion, Michelle L., Jane L. Sumner, and Sara McLaughlin Mitchell. “Gendered Citation Patterns across Political Science and Social Science Methodology Fields.”, Forthcoming, Political Analysis. See also the Appendix for the paper and the replication materials.” http://www.saramitchell.org/DSM2018PAfinal.pdf 

  3. Gearty, W., McClain, C. R., & Payne, J. L. (2018). Energetic tradeoffs control the size distribution of aquatic mammals. Proceedings of the National Academy of Sciences, 201712629. https://doi.org/10.1073/pnas.1712629115 

  4. Nolan, R., & Padilla-Parra, S. (2018). ijtiff: An R package providing TIFF I/O for ImageJ users. Journal of Open Source Software, 3(23), 633. https://doi.org/10.21105/joss.00633 

  5. Gershanov, S., Toledano, H., Michowiz, S., Barinfeld, O., Pinhasov, A., Goldenberg-Cohen, N., & Salmon-Divon, M. (2018). MicroRNA–mRNA expression profiles associated with medulloblastoma subgroup 4. Cancer Management and Research, Volume 10, 339–352. https://doi.org/10.2147/cmar.s156709 

  6. Peters, I., Kraker, P., Lex, E., Gumpenberger, C., & Gorraiz, J. I. (2017). Zenodo in the Spotlight of Traditional and New Metrics. Frontiers in Research Metrics and Analytics, 2. https://doi.org/10.3389/frma.2017.00013 

  7. Tierney, N. (2017). visdat: Visualising Whole Data Frames. The Journal of Open Source Software, 2(16), 355. https://doi.org/10.21105/joss.00355 

  8. Mullen, L., Benoit, K., Keyes, O., Selivanov, D., & Arnold, J. (2018). Fast, Consistent Tokenization of Natural Language Text. Journal of Open Source Software, 3(23), 655. https://doi.org/10.21105/joss.00655 

  9. Sales, L. P., Ribeiro, B. R., Hayward, M. W., Paglia, A., Passamani, M., & Loyola, R. (2017). Niche conservatism and the invasive potential of the wild boar. Journal of Animal Ecology, 86(5), 1214–1223. https://doi.org/10.1111/1365-2656.12721 

  10. Essl, A., Ortner, A., Haas, R., & Hettegger, P. (2017). Machine learning analysis for a flexibility energy approach towards renewable energy integration with dynamic forecasting of electricity balancing power. 2017 14th International Conference on the European Energy Market (EEM). https://doi.org/10.1109/eem.2017.7981877 

  11. Grosser, S., Scofield, R. P., & Waters, J. M. (2017). Multivariate skeletal analyses support a taxonomic distinction between New Zealand and Australian Eudyptula penguins (Sphenisciformes: Spheniscidae). Emu - Austral Ornithology, 117(3), 276–283. https://doi.org/10.1080/01584197.2017.1315310 

  12. Bowser, M., Morton, J., Hanson, J., Magness, D., & Okuly, M. (2017). Arthropod and oligochaete assemblages from grasslands of the southern Kenai Peninsula, Alaska. Biodiversity Data Journal, 5, e10792. https://doi.org/10.3897/bdj.5.e10792 

  13. Divoll, T. J., Brown, V. A., Kinne, J., McCracken, G. F., & O’Keefe, J. M. (2018). Disparities in second-generation DNA metabarcoding results exposed with accessible and repeatable workflows. Molecular Ecology Resources. https://doi.org/10.1111/1755-0998.12770 

  14. Cravens, Z. M., Brown, V. A., Divoll, T. J., & Boyles, J. G. (2017). Illuminating prey selection in an insectivorous bat community exposed to artificial light at night. Journal of Applied Ecology, 55(2), 705–713. https://doi.org/10.1111/1365-2664.13036 

  15. Fox, S., Flowers, J., Thelwall, S., Flint, D., & Hain, D. (2017). fingertipsR: an R package for accessing population health information in England. https://doi.org/10.1101/189167 

  16. ȚÎRU, A. M., & NECULA, M. (2017). rTempo–an R package to access the TEMPO-Online database. Romanian Statistical Review, (4). http://www.revistadestatistica.ro/wp-content/uploads/2017/11/RRS-4_2017_A04.pdf 

  17. Manlove, K. R., & Belou, R. M. (2018). Authors and editors assort on gender and geography in high-rank ecological publications. PLOS ONE, 13(2), e0192481. https://doi.org/10.1371/journal.pone.0192481 

  18. Bennett, D. J., Hettling, H., Silvestro, D., Zizka, A., Bacon, C. D., Faurby, S., … Antonelli, A. (2018). phylotaR: An automated pipeline for retrieving orthologous DNA sequences from GenBank in R. https://doi.org/10.20944/preprints201804.0047.v1