rOpenSci HQ

Our own Maëlle Salmon was featured in an US-RSE Stories podcast. The US-RSE is The United States (US) Research Software Engineer Association. This is a great chance to learn more about Maëlle and some of the work she does.

Community Calls

Our next Community Call will cover Statistical Software Peer Review. The date is not yet set. See the link for more details.

Code of Conduct

Make sure to read our two recent posts on our Code of Conduct: rOpenSci Code of Conduct Annual Review and rOpenSci 2020 Code of Conduct Transparency Report



Software 📦

CRAN: GitHub:

New Versions

  • A new version (v1.2.1) of cld2 is on CRAN - R wrapper for Google’s Compact Language Detector 2. See the release notes for changes. Checkout the docs to get started. cld2 cld2
  • A new version (v1.4.1) of cld3 is on CRAN - Bindings to Google’s Compact Language Detector 3. See the release notes for changes. Checkout the docs to get started. cld3 cld3
  • A new version (v0.28.0) 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 docs to get started. git2r git2r
  • A new version (v4.9.3) of plotly is on CRAN - Create Interactive Web Graphics via plotly.js. See the NEWS for changes. Checkout the plotly book to get started. plotly plotly
  • A new version (v0.3.0) of PostcodesioR is on CRAN - API wrapper for Postcodes.io. See the release notes for changes. Checkout the docs to get started. PostcodesioR PostcodesioR
  • A new version (v1.3.0) of rnoaa is on CRAN - NOAA Weather Data from R. See the release notes for changes. Checkout the docs to get started. rnoaa rnoaa
  • A new version (v0.8.1) of stplanr is on CRAN - sustainable transport planning. See the release notes for changes. Checkout the docs to get started. stplanr stplanr
  • A new version (v0.7.2) of wellknown is on CRAN - Convert between WKT and GeoJSON. See the release notes for changes. Checkout the docs to get started. wellknown wellknown
  • A new version (v1.0.3) of plater is on CRAN - read, tidy, and display data from microtiter plates. See the release notes for changes. Checkout the docs to get started. plater plater
  • A new version (v3.4.2) of rgbif is on CRAN - interface to the Global Biodiversity Information Facility API. See the release notes for changes. Checkout the docs to get started. rgbif rgbif
  • A new version (v1.2.0) of spocc is on CRAN - an interface to many species occurrence data sources. See the release notes for changes. Checkout the docs to get started. spocc spocc
  • A new version (v7.13.0) 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. drake drake
  • A new version (v1.1-6) of suppdata is on CRAN - downloading supplementary data from published manuscripts. See the release notes for changes. Checkout the docs to get started. suppdata suppdata



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

Software review

Tech notes



Citations

The following 25 works use/cite rOpenSci software:



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.


Two new use cases were shared in the forum over the past month since our last newsletter:



Call For Maintainers

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. Check out our guidance for taking over maintenance of a package.

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

We’ve got three packages in need of a new maintainer. The current maintainer of all three packages is looking for new maintainers. Email Scott if you’re interested. If a new maintainer is not found these packages will be archived.

  • traits: species trait data from around the web
  • getlandsat: download Landsat 8 data
  • originr: Fetch species origin data from the web



Get involved with rOpenSci

We maintain a Contributing Guide that can help direct you to the right place, whether you want to make code contributions, non-code contributions, or other things like sharing use cases.






Keep up with rOpenSci


Footnotes

  1. Grattarola, F., & Rodríguez-Tricot, L. (2020). Mammals of Paso Centurión, an area with relicts of Atlantic Forest in Uruguay. Neotropical Biology and Conservation, 15(3), 267–283. https://doi.org/10.3897/neotropical.15.e53062 

  2. Calderón Franco, D. (2020). Hi-C pipeline development for linking resistome and mobilome to the microbiome of wastewater samples https://bit.ly/3i7Q59d 

  3. Hansen, E. R., & Jansa, J. M. (2020). Complexity, Resources, and Text Borrowing in State Legislatures. https://bit.ly/3nvLK0R 

  4. Ilík, B. V. High-throughput sequencing as a tool for studying strongylid nematode communities in primates. Thesis. https://is.muni.cz/th/vg2vb/DP_Ilik_Vladislav.pdf 

  5. Walton, S., Livermore, L., Bánki, O., Cubey, R., Drinkwater, R., Englund, M., … Wu, Z. (2020). Landscape Analysis for the Specimen Data Refinery. Research Ideas and Outcomes, 6. https://doi.org/10.3897/rio.6.e57602 

  6. Ossola, A., Hoeppner, M. J., Burley, H. M., Gallagher, R. V., Beaumont, L. J., & Leishman, M. R. (2020). The Global Urban Tree Inventory: A database of the diverse tree flora that inhabits the world’s cities. Global Ecology and Biogeography, 29(11), 1907–1914. https://doi.org/10.1111/geb.13169 

  7. Atwood, T. B., Valentine, S. A., Hammill, E., McCauley, D. J., Madin, E. M. P., Beard, K. H., & Pearse, W. D. (2020). Herbivores at the highest risk of extinction among mammals, birds, and reptiles. Science Advances, 6(32), eabb8458. https://doi.org/10.1126/sciadv.abb8458 

  8. Morgan, M., & Lovelace, R. (2020). Travel flow aggregation: Nationally scalable methods for interactive and online visualisation of transport behaviour at the road network level. Environment and Planning B: Urban Analytics and City Science, 239980832094277. https://doi.org/10.1177/2399808320942779 

  9. Carroll, L. M., Huisman, J. S., & Wiedmann, M. (2020). Twentieth-century emergence of antimicrobial resistant human- and bovine-associated Salmonella enterica serotype Typhimurium lineages in New York State. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-71344-9 

  10. Whitmer, S. L. M., Lo, M. K., Sazzad, H. M. S., Zufan, S., Gurley, E. S., Sultana, S., … Klena, J. D. (2020). Inference of Nipah virus Evolution, 1999-2015. Virus Evolution. https://doi.org/10.1093/ve/veaa062 

  11. Ettinger, C. L., & Eisen, J. A. (2020). Fungi, bacteria and oomycota opportunistically isolated from the seagrass, Zostera marina. PLOS ONE, 15(7), e0236135. https://doi.org/10.1371/journal.pone.0236135 

  12. Grassl, P., Schraffenberger, H., Zuiderveen Borgesius, F., & Buijzen, M. (2020, July 21). Dark and bright patterns in cookie consent requests. https://doi.org/10.31234/osf.io/gqs5h 

  13. Scott, T. A., Ulibarri, N., & Perez Figueroa, O. (2020). NEPA and National Trends in Federal Infrastructure Siting in the United States. Review of Policy Research. https://doi.org/10.1111/ropr.12399 

  14. López Galán, A., Chung, W.-S., & Marshall, N. J. (2020). Dynamic Courtship Signals and Mate Preferences in Sepia plangon. Frontiers in Physiology, 11. https://doi.org/10.3389/fphys.2020.00845 

  15. Brandão, L. A. C., Agrelli, A., Bernardo, L., Paparella, F., Moura, R., & Crovella, S. (2020). PlatCOVID: A Novel Web Tool to Analyze, Curate and Share COVID-19 Literature. https://doi.org/10.21203/rs.3.rs-42169/v1 

  16. Wang, S., Xiong, Y., Gu, K., Zhao, L., Li, Y., Zhao, F., … Liu, X.-S. (2020). UCSCXenaShiny: An R Package for Exploring and Analyzing UCSC Xena Public Datasets in Web Browser. https://doi.org/10.20944/preprints202007.0179.v1 

  17. Obradovich, N., Özak, Ö., Martín, I., Ortuño-Ortín, I., Awad, E., Cebrián, M., … Cuevas, Á. (2020). Expanding the Measurement of Culture with a Sample of Two Billion Humans. National Bureau of Economic Research. https://doi.org/10.3386/w27827 

  18. Gutiérrez-Hernández, O. (2020). Fenología de los ecosistemas de alta montaña en Andalucía: Análisis de la tendencia estacional del SAVI (2000-2019). Pirineos, 175, 055. https://doi.org/10.3989/pirineos.2020.175005 

  19. Hazlett, M. A., Henderson, K. M., Zeitzer, I. F., & Drew, J. A. (2020). The geography of publishing in the Anthropocene. Conservation Science and Practice, 2(10). https://doi.org/10.1111/csp2.270 

  20. Mothes, C. C., Stemle, L. R., Fonseca, T. N., Clements, S. L., Howell, H. J., & Searcy, C. A. (2020). Protect or perish: Quantitative analysis of state‐level species protection supports preservation of the Endangered Species Act. Conservation Letters. https://doi.org/10.1111/conl.12761 

  21. Falconi, N., Fuller, T. K., DeStefano, S., & Organ, J. F. (2020). An open-access occurrence database for Andean bears in Peru. Ursus, 2020(31e11), 1. https://doi.org/10.2192/ursus-d-19-00012.1 

  22. Costanzi, S., Slavick, C. K., Hutcheson, B. O., Koblentz, G. D., & Cupitt, R. T. (2020). Lists of Chemical Warfare Agents and Precursors from International Nonproliferation Frameworks: Structural Annotation and Chemical Fingerprint Analysis. Journal of Chemical Information and Modeling, 60(10), 4804–4816. https://doi.org/10.1021/acs.jcim.0c00896 

  23. Batista, E., Lopes, A., & Alves, A. (2020). Botryosphaeriaceae species on forest trees in Portugal: diversity, distribution and pathogenicity. European Journal of Plant Pathology, 158(3), 693–720. https://doi.org/10.1007/s10658-020-02112-8 

  24. Rasher, D. B., Steneck, R. S., Halfar, J., Kroeker, K. J., Ries, J. B., Tinker, M. T., … Estes, J. A. (2020). Keystone predators govern the pathway and pace of climate impacts in a subarctic marine ecosystem. Science, 369(6509), 1351–1354. https://doi.org/10.1126/science.aav7515 

  25. Kuchta, R., Řehulková, E., Francová, K., Scholz, T., Morand, S., & Šimková, A. (2020). Diversity of monogeneans and tapeworms in cypriniform fishes across two continents. International Journal for Parasitology, 50(10-11), 771–786. https://doi.org/10.1016/j.ijpara.2020.06.005