rOpenSci HQ

Contributing Guide Release 🚀

https://contributing.ropensci.org/

The purpose of the guide is to welcome you to rOpenSci and help you recognize yourself as a potential contributor. It will help you figure out what you might gain by giving your time, expertise, and experience; match your needs with things that will help rOpenSci’s mission; and connect you with resources to help you along the way. Is there something you might like to contribute that isn’t addressed there? Open an issue in the GitHub repository for the Guide.

Software 📦

CRAN: GitHub:

New Versions

  • A new version (v3.2-3) of clifro is on CRAN - easily download and visualise climate data from CliFlo. See the release notes for changes. Checkout the docs to get started. clifro clifro
  • A new version (v2.0-17) of CoordinateCleaner is on CRAN - automated cleaning of occurrence records from biological collections. See the release notes for changes. Checkout the docs to get started. CoordinateCleaner CoordinateCleaner
  • A new version (v0.4.0) of rsnps is on CRAN - fetch SNP (Single-Nucleotide Polymorphism) data from the web. See the release notes for changes. Checkout the docs to get started. rsnps rsnps
  • A new version (v0.7.0) 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 (v0.5.0) of traits is on CRAN - species trait data from around the web. See the release notes for changes. Checkout the docs to get started. traits traits
  • A new version (v0.3.0) of ccafs is on CRAN - client for Climate Change, Agriculture, & Food Security (CCAFS) General Circulation Models. See the release notes for changes. Checkout the docs to get started. ccafs ccafs
  • A new version (v0.7.4) of DataSpaceR is on CRAN - interface to the CAVD DataSpace. See the release notes for changes. Checkout the docs to get started. DataSpaceR DataSpaceR
  • A new version (v1.2.0) of dbparser is on CRAN - DrugBank database XML parser. See the release notes for changes. Checkout the docs to get started. dbparser dbparser
  • A new version (v7.12.5) 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 (v0.2.2) of taxizedb is on CRAN - tools for working with taxonomic databases. See the release notes for changes. Checkout the docs to get started. taxizedb taxizedb
  • A new version (v1.3.1) of writexl is on CRAN - a portable, light-weight data frame to xlsx exporter. See the release notes for changes. Checkout the docs to get started. writexl writexl



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.


No new submissions or approved submissions.



On the blog

It’s time for another installment of … 2 Months in 2 Minutes - rOpenSci News, February 2020 - if you want a brief summary of the last 2 months of these newsletters, these blog posts are for you (written by Stefanie Butland)


Software Review:

Jonathan Keane wrote about their recently rOpenSci reviewed package dittodb: Developing dittodb. Jonathan discusses the motivation behind the package, some of the technical challenges, and the story behind the name of the package.


Tech notes

Scott Chamberlain wrote a post on Scientific Name Parsing: rgnparser and namext, covering the rgnparser and namext packages.



Citations

The following 18 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.


A new use case was shared in the forum over the past two weeks 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:



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. Ordynets, A., Liebisch, R., Lysenko, L., Scherf, D., Volobuev, S., Saitta, A., … Langer, E. (2020). Morphologically similar but not closely related: the long-spored species of Subulicystidium (Trechisporales, Basidiomycota). Mycological Progress, 19(7), 691–703. https://doi.org/10.1007/s11557-020-01587-3 

  2. Ye, J. (2020). Independent and dependent possessive person forms. Studies in Language, 44(2), 363–406. https://doi.org/10.1075/sl.19020.ye 

  3. Monaco, C. J., Bradshaw, C. J. A., Booth, D. J., Gillanders, B. M., Schoeman, D. S., & Nagelkerken, I. (2020). Dietary generalism accelerates arrival and persistence of coral‐reef fishes in their novel ranges under climate change. Global Change Biology. https://doi.org/10.1111/gcb.15221 

  4. Tennant, W. S. D., Tildesley, M. J., Spencer, S. E. F., & Keeling, M. J. (2020). Climate drivers of plague epidemiology in British India, 1898–1949. Proceedings of the Royal Society B: Biological Sciences, 287(1928), 20200538. https://doi.org/10.1098/rspb.2020.0538 

  5. Runge, C. A., Hausner, V. H., Daigle, R. M., & Monz, C. A. (2020). Pan-Arctic analysis of cultural ecosystem services using social media and automated content analysis. Environmental Research Communications, 2(7), 075001. https://doi.org/10.1088/2515-7620/ab9c33 

  6. Swetnam, D. M., Stuart, J. B., Young, K., Maharaj, P. D., Fang, Y., Garcia, S., … Coffey, L. L. (2020). Movement of St. Louis encephalitis virus in the Western United States, 2014- 2018. PLOS Neglected Tropical Diseases, 14(6), e0008343. https://doi.org/10.1371/journal.pntd.0008343 

  7. Walker, P. G. T., Whittaker, C., Watson, O. J., Baguelin, M., Winskill, P., Hamlet, A., … Ghani, A. C. (2020). The impact of COVID-19 and strategies for mitigation and suppression in low- and middle-income countries. Science, eabc0035. https://doi.org/10.1126/science.abc0035 

  8. McDonald, S. (2020). Applying Geographic Information Systems to the Study of Honey Bee Diseases and Pests (Doctoral dissertation). https://bit.ly/34Ox33c 

  9. Ficcadenti, V., Cerqueti, R., Ausloos, M., & Dhesi, G. (2020). Words ranking and Hirsch index for identifying the core of the hapaxes in political texts. Journal of Informetrics, 14(3), 101054. https://doi.org/10.1016/j.joi.2020.101054 

  10. Hierink, F., Bolon, I., Durso, A. M., Ruiz de Castañeda, R., Zambrana-Torrelio, C., Eskew, E. A., & Ray, N. (2020). Forty-four years of global trade in CITES-listed snakes: Trends and implications for conservation and public health. Biological Conservation, 248, 108601. https://doi.org/10.1016/j.biocon.2020.108601 

  11. Pal Negi, A., Singh, R., Sharma, A., & Negi, V. S. (2020). Insights into high mobility group A (HMGA) proteins from Poaceae family: An in silico approach for studying homologs. Computational Biology and Chemistry, 87, 107306. https://doi.org/10.1016/j.compbiolchem.2020.107306 

  12. Puerta, P., Laguna, L., Vidal, L., Ares, G., Fiszman, S., & Tárrega, A. (2020). Co-occurrence networks of Twitter content after manual or automatic processing. A case-study on “gluten-free.” Food Quality and Preference, 86, 103993. https://doi.org/10.1016/j.foodqual.2020.103993 

  13. Anton, C. B., Smith, D. W., Suraci, J. P., Stahler, D. R., Duane, T. P., & Wilmers, C. C. (2020). Gray wolf habitat use in response to visitor activity along roadways in Yellowstone National Park. Ecosphere, 11(6). https://doi.org/10.1002/ecs2.3164 

  14. Loewen, C. J. G., Strecker, A. L., Gilbert, B., & Jackson, D. A. (2020). Climate warming moderates the impacts of introduced sportfish on multiple dimensions of prey biodiversity. Global Change Biology, 26(9), 4937–4951. https://doi.org/10.1111/gcb.15225 

  15. Siregar, E., & Prawisudatama, A. Improving data literacy using liteRate: an R Shiny Apps for visualizing and exploring data published on BPS-Statistics Indonesia’s Website https://bit.ly/2ELTyuZ 

  16. Bisbee, J., & Honig, D. (2020). Flight to Safety: 2020 Democratic Primary Election Results and COVID-19. Covid Economics, 3(10), 54-84. https://bit.ly/2YRiWWP 

  17. Hobert, A., Jahn, N., Mayr, P., Schmidt, B., & Taubert, N. C. (2020). Open Access Uptake in Germany 2010-18: Adoption in a diverse research landscape. https://bit.ly/3bt1LjP 

  18. Webb, T. J., Lines, A., & Howarth, L. M. (2020). Occupancy‐derived thermal affinities reflect known physiological thermal limits of marine species. Ecology and Evolution, 10(14), 7050–7061. https://doi.org/10.1002/ece3.6407