rOpenSci HQ


Software 📦

CRAN: GitHub:

New Versions

  • A new version (v0.3.1) 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. weathercan weathercan

    internal changes only

  • A new version (v3.0.10) of rotl is on CRAN - an interface to the Open Tree of Life API. See the release notes for changes. Checkout the vignettes to get started. rotl rotl

    internal changes & updated docs

  • A new version (v0.3.0) of nlrx is on CRAN - setup, run and analyze NetLogo model simulations. See the release notes for changes. Checkout the vignettes to get started. nlrx nlrx

    updated docs; two new vignettes; changes to simdesign_GenAlg, simdesign_GenSA, simdesign_simple, and download_netLogo

  • A new version (v0.9.0) of rnoaa is on CRAN - NOAA Weather Data from R. See the release notes for changes. Checkout the vignettes to get started. rnoaa rnoaa

    sea ice updates; new fxn lcd_cleanup; docs updates; many 🐞 fixes

  • A new version (v0.2.9) 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. fingertipsR fingertipsR

    fixed firewall issue

  • A new version (v0.4.0) of auk is on CRAN - eBird data extraction and processing. See the release notes for changes. Checkout the docs to get started. auk

    updated to 2019 eBird taxonomy; auk_observer() filter added

  • A new version (v1.4.1) of MtreeRing is on CRAN - a shiny application for automatic measurements of tree-ring widths on digital images. See the release notes for changes. Checkout the docs to get started. MtreeRing MtreeRing
  • A new version (v3.1.1) of qualtRics is on CRAN - download Qualtrics survey data. See the release notes for changes. Checkout the docs to get started. qualtRics qualtRics

    fix bug in infer_data_types(); improve docs; deprecate registerOptions(); make data import more robust

  • A new version (v0.2.20) of rglobi is on CRAN - R Interface to Global Biotic Interactions. See the release notes for changes. Checkout the vignette to get started. rglobi rglobi

    use readr pkg to avoid encoding issues on windows

  • A new version (v0.2.5) of tradestatistics is on CRAN - open trade statistics api wrapper and utility program. See the release notes for changes. Checkout the docs to get started. tradestatistics tradestatistics

    now requires R>=3.5; changes in ots_create_tidy_data()

  • A new version (v0.3.0) of nodbi is on CRAN - the NoSQL database connector. See the release notes for changes. Checkout the README to get started. nodbi nodbi

    new author Ralf Herold contributed SQLite/json1 integration for all pkg methods; docdb_update gains MongoDB method; etcd integration dropped

  • A new version (v0.3.1) of stplanr is on CRAN - sustainable transport planning. See the release notes for changes. Checkout the docs to get started. stplanr stplanr

    new logo; line_to_points() deprecated -> od2line(); line2pointsn() now works with sf objects; docs fixes

Package notes

The staff supported package etseed is now archived on CRAN. It was an R client for the key-value store etcd. After understanding the etcd product more, we decided it’s not something R users are reaching for.



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 package was recently submitted:



On the blog

Technical notes

Scott Chamberlain wrote a post on his new package, citecorp: citecorp: working with open citations. citecorp brings R user’s data from the OpenCitations Corpus; check it out if you are looking for citation data for any reason.


Jeroen Ooms dug into image suite packages in a recent blog post: Updates to the rOpenSci image suite: magick, tesseract, and av. To learn more about these and other rOpenSci packages, check out articles on https://docs.ropensci.org.



Use Cases

The following 23 works use/cite rOpenSci software:



  • In command line news, there’s a new shell in town - Nushell - that embraces the tabular world we live in. Listen to the latest Changelog podcast episode on Nushell; it’s a bit of work to install it right now, but it’s got lots of interesting ideas that may be of interest. Another interesting project is a command line tool - navi - that leverages pluggable cheatsheet files (and no, R package cheatsheets in pdf format will not work here).
  • Many readers are academics, and thus have perhaps deposited data with, or at least heard of, Dryad. We happen to maintain the R client for Dryad, rdryad. Dryad has just announced a refresh of their web services, among other things. Change to rdryad will be coming soon.
  • Regex crossword is a fun new (to us) way to learn regex through a crossword format; it’s good to know regex no matter what programming language(s) you use!



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.



In The News



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. Checkout our Contributing Guide for why and how to contribute to rOpenSci.

We’ve had six recent examples of maintainer transitions within rOpenSci:

We don’t have any packages looking for new maintainers - if you are a maintainer and want to hand over that role to someone else get in touch with us.






Keep up with rOpenSci


Footnotes

  1. Atickem, A., Stenseth, N. C., Fashing, P. J., Nguyen, N., Chapman, C. A., Bekele, A., … Kalbitzer, U. (2019). Build science in Africa. Nature, 570(7761), 297–300. https://doi.org/10.1038/d41586-019-01885-1 

  2. Collins, R. A., Bakker, J., Wangensteen, O. S., Soto, A. Z., Corrigan, L., Sims, D. W., … Mariani, S. (2019). Non‐specific amplification compromises environmental DNA metabarcoding with COI. Methods in Ecology and Evolution. https://doi.org/10.1111/2041-210x.13276 

  3. Van der Veer, C., Bruisten, S. M., van Houdt, R., Matser, A. A., Tachedjian, G., van de Wijgert, J. H. H. M., … van der Helm, J. J. (2019). Effects of an over-the-counter lactic-acid containing intra-vaginal douching product on the vaginal microbiota. BMC Microbiology, 19(1). https://doi.org/10.1186/s12866-019-1545-0 

  4. Petersen, A. H., & Ekstrøm, C. T. (2019). dataMaid: Your Assistant for Documenting Supervised Data Quality Screening in R. Journal of Statistical Software, 90(6). https://doi.org/10.18637/jss.v090.i06 

  5. Watson, O. J., Sumner, K. M., Janko, M., Goel, V., Winskill, P., Slater, H. C., … Parr, J. B. (2019). False-negative malaria rapid diagnostic test results and their impact on community-based malaria surveys in sub-Saharan Africa. BMJ Global Health, 4(4), e001582. https://doi.org/10.1136/bmjgh-2019-001582 

  6. Piper, A. M., Batovska, J., Cogan, N. O. I., Weiss, J., Cunningham, J. P., Rodoni, B. C., & Blacket, M. J. (2019). Prospects and challenges of implementing DNA metabarcoding for high-throughput insect surveillance. GigaScience, 8(8). https://doi.org/10.1093/gigascience/giz092 

  7. Macip Sancho, G. 2019. Deciphering host-pathogen interactions at the biomembrane interface, key to target therapeutical approaches against Mycoplasma genitalium. Masters Thesis. Universitat Oberta de Catalunya. http://hdl.handle.net/10609/97806 

  8. Sobreiro, J. F. F. 2019. Vegetation multitemporal responses to hydroclimate variations in the Espinhaço Range (Brazil). Masters Thesis. (link broken: http://hdl.handle.net/11449/183096) 

  9. Brionne, A., Juanchich, A., & Hennequet-Antier, C. (2019). ViSEAGO: a Bioconductor package for clustering biological functions using Gene Ontology and semantic similarity. BioData Mining, 12(1). https://doi.org/10.1186/s13040-019-0204-1 

  10. Fernandez-Basso, C., Ruiz, M. D., Delgado, M., & Martin-Bautista, M. J. (2019, August). A comparative analysis of tools for visualizing association rules: A proposal for visualising fuzzy association rules. In 2019 Conference of the International Fuzzy Systems Association and the European Society for Fuzzy Logic and Technology (EUSFLAT 2019). Atlantis Press. https://download.atlantis-press.com/article/125914842.pdf 

  11. Zanin, M., Bergamaschi, C. L., Ferreira, J. R., Mendes, S. L., & Oliveira Moreira, D. (2019). Dog days are just starting: the ecology invasion of free-ranging dogs (Canis familiaris) in a protected area of the Atlantic Forest. European Journal of Wildlife Research, 65(5). https://doi.org/10.1007/s10344-019-1303-5 

  12. Luc, A., Lê, S., & Philippe, M. (2019). Nudging consumers for relevant data using Free JAR profiling: an application to product development. Food Quality and Preference, 103751. https://doi.org/10.1016/j.foodqual.2019.103751 

  13. Lennox, R. J., Veríssimo, D., Twardek, W. M., Davis, C. R., & Jarić, I. (2019). Sentiment analysis as a measure of conservation culture in scientific literature. Conservation Biology. https://doi.org/10.1111/cobi.13404 

  14. da Conceição António, N. M. (2019). Hotel Revenue Management: Using Data Science to Predict Booking Cancellations (Doctoral dissertation, ISCTE-IUL). http://bit.ly/2nWX50I 

  15. Han, T., Zheng, Q., Onstein, R. E., Rojas‐Andrés, B. M., Hauenschild, F., Muellner‐Riehl, A. N., & Xing, Y. (2019). Polyploidy promotes species diversification of Allium through ecological shifts. New Phytologist. https://doi.org/10.1111/nph.16098 

  16. Dawson, A., Paciorek, C. J., Goring, S. J., Jackson, S. T., McLachlan, J. S., & Williams, J. W. (2019). Quantifying trends and uncertainty in prehistoric forest composition in the upper Midwestern United States. Ecology. https://doi.org/10.1002/ecy.2856 

  17. O’Farrell, S., Chollett, I., Sanchirico, J. N., & Perruso, L. (2019). Classifying fishing behavioral diversity using high-frequency movement data. Proceedings of the National Academy of Sciences, 201906766. https://doi.org/10.1073/pnas.1906766116 

  18. Hayden, B., Palomares, M. L. D., Smith, B. E., & Poelen, J. H. (2019). Biological and environmental drivers of trophic ecology in marine fishes - a global perspective. Scientific Reports, 9(1). https://doi.org/10.1038/s41598-019-47618-2 

  19. Neugebauer, K., El‐Serehy, H. A., George, T. S., McNicol, J. W., Moraes, M. F., Sorreano, M. C. M., & White, P. J. (2019). The influence of phylogeny and ecology on root, shoot and plant ionomes of fourteen native Brazilian species. Physiologia Plantarum. https://doi.org/10.1111/ppl.13018 

  20. Wagner, J. (2019). Using Advanced Analytics to Predict Risk for Grants Oversight. Masters Thesis. https://jscholarship.library.jhu.edu/bitstream/handle/1774.2/61849/Wagner%2C%20Jennifer.pdf?sequence=1&isAllowed=y 

  21. Pender, J. E., Hipp, A. L., Hahn, M., Kartesz, J., Nishino, M., & Starr, J. R. (2019). How sensitive are climatic niche inferences to distribution data sampling? A comparison of Biota of North America Program (BONAP) and Global Biodiversity Information Facility (GBIF) datasets. Ecological Informatics, 100991. https://doi.org/10.1016/j.ecoinf.2019.100991 

  22. Park, A. W. (2019). Food web structure selects for parasite host range. Proceedings of the Royal Society B: Biological Sciences, 286(1908), 20191277. https://doi.org/10.1098/rspb.2019.1277 

  23. Sánchez-Páez, D. A., & Ortega, J. A. (2019). Reported patterns of pregnancy termination from Demographic and Health Surveys. PLOS ONE, 14(8), e0221178. https://doi.org/10.1371/journal.pone.0221178