Software 📩

CRAN: GitHub:

New Versions

  • A new version (v0.2.0) of taxizedb is on CRAN - tools for working with taxonomic databases. See the release notes for changes. Checkout the docs to get started.
  • A new version (v2.1.4) of babette is on CRAN - control BEAST2 from R. See the release notes for changes. Checkout the docs to get started.
  • A new version (v0.4.0) of finch is on CRAN - parse Darwin Core files. See the release notes for changes. Checkout the README to get started.
  • A new version (v2.1) of mauricer is on CRAN - install BEAST2 packages. See the release notes for changes. Checkout the docs to get started.
  • A new version (v2.1.3) of beastier is on CRAN - Provides a way to call BEAST2 from R. See the release notes for changes. Checkout the docs to get started.
  • A new version (v2.3.7) of beautier is on CRAN - create BEAST2 input files programmatically. See the release notes for changes. Checkout the docs to get started.
  • A new version (v2.2.0) of ijtiff is on CRAN - comprehensive TIFF I/O with full support for ImageJ TIFF files. See the release notes for changes. Checkout the docs to get started.
  • A new version (v1.3.3) of UCSCXenaTools is on CRAN - download and explore datasets from UCSC Xena data hubs. See the release notes for changes. Checkout the docs to get started.
  • A new version (v1.1-3) of suppdata is on CRAN - downloading supplementary data from published manuscripts. See the release notes for changes. Checkout the vignette to get started.



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.



Citations

The following 22 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 nine 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. Connors, B., Malick, M. J., Ruggerone, G. T., Rand, P., Adkison, M., Irvine, J. R., 
 Gorman, K. (2020). Climate and competition influence sockeye salmon population dynamics across the Northeast Pacific Ocean. Canadian Journal of Fisheries and Aquatic Sciences, 77(6), 943–949. https://www.nrcresearchpress.com/doi/10.1139/cjfas-2019-0422 ↩

  2. Hesselbarth, M. H. 2020. Analysing and modelling spatial patterns to infer the influence of environmental heterogeneity using point pattern analysis, individual-based simulation modelling and landscape metrics. Dissertation https://bit.ly/2E0yuAx ↩

  3. Geller, J., Davis, S. D., & Peterson, D. (2020, May 23). Sans forgetica is not desirable for learning. https://doi.org/10.31234/osf.io/ku5bz ↩

  4. Biber‐Freudenberger, L., Ergeneman, C., Förster, J. J., Dietz, T., & Börner, J. (2020). Bioeconomy futures: Expectation patterns of scientists and practitioners on the sustainability of bio‐based transformation. Sustainable Development. https://doi.org/10.1002/sd.2072 ↩

  5. Siqueira, A. C., Morais, R. A., Bellwood, D. R., & Cowman, P. F. (2020). Trophic innovations fuel reef fish diversification. Nature Communications, 11(1). https://doi.org/10.1038/s41467-020-16498-w ↩

  6. D’Orazio, M., Bernardini, G., & Quagliarini, E. (2020). Sustainable and resilient strategies for touristic cities against COVID-19: an agent-based approach. arXiv preprint arXiv:2005.12547. https://arxiv.org/pdf/2005.12547.pdf ↩

  7. Stringham, O., Toomes, A., Kanishka, A. M., Mitchell, L., Heinrich, S., Ross, J. V., & Cassey, P. (2020). A guide to using the Internet to monitor and quantify the wildlife trade. https://ecoevorxiv.org/5yzw9/download?format=pdf ↩

  8. Morselli, D., Passini, S., & McGarty, C. (2020). Sos Venezuela: an analysis of the anti-Maduro protest movements using Twitter. Social Movement Studies, 1–22. https://doi.org/10.1080/14742837.2020.1770072 ↩

  9. Vogler, D., & SchĂ€fer, M. S. (2020). Growing Influence of University PR on Science News Coverage? A Longitudinal Automated Content Analysis of University Media Releases and Newspaper Coverage in Switzerland, 2003‒2017. International Journal of Communication, 14, 22. https://ijoc.org/index.php/ijoc/article/download/13498/3113 ↩

  10. Szöcs, E., Stirling, T., Scott, E. R., ScharmĂŒller, A., & SchĂ€fer, R. B. (2020). webchem: An R Package to Retrieve Chemical Information from the Web. Journal of Statistical Software, 93(1), 1-17. https://www.jstatsoft.org/article/view/v093i13/v93i13.pdf ↩

  11. Manning, F., Curtis, P. J., Walker, I., & Pither, J. (2020, June 2). An experimental test of the capacity for long-distance dispersal of freshwater diatoms adhering to waterfowl plumage. https://doi.org/10.32942/osf.io/h97pw ↩

  12. Greco, F., & La Rocca, G. (2020). The Topics-scape of the Pandemic Crisis: The Italian Sentiment on Political Leaders. Culture e Studi del Sociale, 5(1, Special), 335-346. http://www.cussoc.it/index.php/journal/article/view/134 ↩

  13. FernĂĄndez-Ruiz, N., & Estrada-Peña, A. (2020). Could climate trends disrupt the contact rates between Ixodes ricinus (Acari, Ixodidae) and the reservoirs of Borrelia burgdorferi s.l.? PLOS ONE, 15(5), e0233771. https://doi.org/10.1371/journal.pone.0233771 ↩

  14. Santana, V. M., Alday, J. G., Adamo, I., Alloza, J. A., & Baeza, M. J. (2020). Climate, and not fire, drives the phylogenetic clustering of species with hard-coated seeds in Mediterranean Basin communities. Perspectives in Plant Ecology, Evolution and Systematics, 45, 125545. https://doi.org/10.1016/j.ppees.2020.125545 ↩

  15. Sales, L., Culot, L., & Pires, M. M. (2020). Climate niche mismatch and the collapse of primate seed dispersal services in the Amazon. Biological Conservation, 247, 108628. https://doi.org/10.1016/j.biocon.2020.108628 ↩

  16. Barrios‐O’Neill, D. (2020). Focus and social contagion of environmental organization advocacy on Twitter. Conservation Biology. https://doi.org/10.1111/cobi.13564 ↩

  17. Gaynor, M. L., Fu, C., Gao, L., Lu, L., Soltis, D. E., & Soltis, P. S. (2020). Biogeography and ecological niche evolution in Diapensiaceae inferred from phylogenetic analysis. Journal of Systematics and Evolution. https://doi.org/10.1111/jse.12646 ↩

  18. Liu, L., Huang, J., Xiong, Q., Zhang, H., Song, P., Huang, Y., 
 Wang, X. (2020). Optimal MODIS data processing for accurate multi-year paddy rice area mapping in China. GIScience & Remote Sensing, 57(5), 687–703. https://doi.org/10.1080/15481603.2020.1773012 ↩

  19. Estrada-Peña, A., Nava, S., Tarragona, E., de la Fuente, J., & Guglielmone, A. A. (2020). A community approach to the Neotropical ticks-hosts interactions. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-66400-3 ↩

  20. Trinka, J., Haghbin, H., & Maadooliat, M. (2020). Multivariate Functional Singular Spectrum Analysis Over Different Dimensional Domains. arXiv preprint arXiv:2006.03933. https://arxiv.org/pdf/2006.03933 ↩

  21. McKnelly, K. J., Howitz, W. J., Lam, S., & Link, R. D. (2020). Extraction on Paper Activity: An Active Learning Technique to Facilitate Student Understanding of Liquid–Liquid Extraction. Journal of Chemical Education, 97(7), 1960–1965. https://doi.org/10.1021/acs.jchemed.9b00975 ↩

  22. Davis, Z. (2020). Leaf the kids outdoors: approaches and enquiries in quantifying natural environments for health (Doctoral dissertation, University of British Columbia). https://open.library.ubc.ca/collections/ubctheses/24/items/1.0391841 ↩