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., & Schäfer, 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., Scharmüller, A., & Schäfer, 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. Fernández-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