rOpenSci HQ

Our own community manager Stefanie Butland, and one of our software review editors Brooke Anderson, are remotely speaking at an R-Ladies East Lansing meetup on Thursday, October 22nd: rOpenSci - open tools for open science. If you’d like to attend, see “Who could join?” on the R-Ladies East Lansing page.


Software 📦

CRAN: GitHub:

New Packages

New Versions

  • A new version (v3.3.0) of rgbif is on CRAN - interface to the Global Biodiversity Information Facility API. See the release notes for changes. Checkout the occurrence manual to get started. rgbif rgbif
  • A new version (v0.3.0) of pubchunks is on CRAN - Fetch Sections of XML Scholarly Articles. See the release notes for changes. Checkout the README to get started. pubchunks pubchunks
  • A new version (v0.7.2) 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 (v0.7.13) of robotstxt is on CRAN - robots.txt parser and Webbot/Spider/Crawler permissions checker. See the release notes for changes. Checkout the docs to get started. robotstxt robotstxt
  • A new version (v2.0.2) of MODIStsp is on CRAN - Automate Download and Preprocessing of MODIS Land Products Data. See the release notes for changes. Checkout the docs to get started. MODIStsp MODIStsp
  • A new version (v0.4.0) 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
  • 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 (v0.1.5) of virtuoso is on CRAN - interface to Virtuoso using ODBC. See the release notes for changes. Checkout the docs to get started. virtuoso virtuoso



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 19 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. Li, D., Olden, J. D., Lockwood, J. L., Record, S., McKinney, M. L., & Baiser, B. (2020). Changes in taxonomic and phylogenetic diversity in the Anthropocene. Proceedings of the Royal Society B: Biological Sciences, 287(1929), 20200777. https://doi.org/10.1098/rspb.2020.0777 

  2. James, S., Pagliari, S., & Young, K. L. (2020). The internationalization of European financial networks: a quantitative text analysis of EU consultation responses. Review of International Political Economy, 1–28. https://doi.org/10.1080/09692290.2020.1779781 

  3. Drost, H.-G. (2020). LTRpred: de novo annotation of intact retrotransposons. Journal of Open Source Software, 5(50), 2170. https://doi.org/10.21105/joss.02170 

  4. Granados, J. E., Ros-Candeira, A., Pérez-Luque, A. J., Moreno-Llorca, R., Cano-Manuel, F. J., Fandos, P., … Zamora, R. (2020). Long-term monitoring of the Iberian ibex population in the Sierra Nevada of the southeast Iberian Peninsula. Scientific Data, 7(1). https://doi.org/10.1038/s41597-020-0544-1 

  5. Brazeau, N. (2020). The Molecular, Spatial, and Genetic Epidemiology of Malaria in the Democratic Republic of the Congo. https://cdr.lib.unc.edu/downloads/7s75dj87g 

  6. Pacifico, R., Almeda, F., Frota, A., & Fidanza, K. (2020). Areas of endemism on Brazilian mountaintops revealed by taxonomically verified records of Microlicieae (Melastomataceae). Phytotaxa, 450(2), 119–148. https://doi.org/10.11646/phytotaxa.450.2.1 

  7. Hanes, C., Wotton, M., Woolford, D. G., Martell, D. L., & Flannigan, M. (2020). Preceding Fall Drought Conditions and Overwinter Precipitation Effects on Spring Wildland Fire Activity in Canada. Fire, 3(2), 24. https://www.mdpi.com/2571-6255/3/2/24/pdf 

  8. Burda, P.-C., Crosskey, T., Lauk, K., Zurborg, A., Söhnchen, C., Liffner, B., … Gilberger, T.-W. (2020). Structure-Based Identification and Functional Characterization of a Lipocalin in the Malaria Parasite Plasmodium falciparum. Cell Reports, 31(12), 107817. https://doi.org/10.1016/j.celrep.2020.107817 

  9. Corput, D. V. D. (2020). Locked in Syndrome Machine Learning Classification using Sentence Comprehension EEG Data. arXiv preprint arXiv:2006.12336 https://arxiv.org/pdf/2006.12336.pdf 

  10. Stephens, M. (2020). A geospatial infodemic: Mapping Twitter conspiracy theories of COVID-19. Dialogues in Human Geography, 10(2), 276–281. https://doi.org/10.1177/2043820620935683 

  11. Green, J., Edgerton, J., Naftel, D., Shoub, K., & Cranmer, S. J. (2020). Elusive consensus: Polarization in elite communication on the COVID-19 pandemic. Science Advances, 6(28), eabc2717. https://doi.org/10.1126/sciadv.abc2717 

  12. Jayawardhana, W. G. N. N., & Chathurange, V. M. I. (2020). Investigate the sensitivity of the satellite-based agricultural drought indices to monitor the drought condition of paddy and introduction to enhanced multi-temporal agricultural drought indices. J Remote Sens GIS, 9, 271. https://bit.ly/2RoRprZ 

  13. Da Silva, R. G., Ribeiro, M. H. D. M., Mariani, V. C., & Coelho, L. dos S. (2020). Forecasting Brazilian and American COVID-19 cases based on artificial intelligence coupled with climatic exogenous variables. Chaos, Solitons & Fractals, 139, 110027. https://doi.org/10.1016/j.chaos.2020.110027 

  14. Sacchi, R., Cancian, S., Ghia, D., Fea, G., & Coladonato, A. (2020). Colour variation in signal crayfish Pacifastacus leniusculus. Current Zoology. https://academic.oup.com/cz/advance-article/doi/10.1093/cz/zoaa031/5865267 

  15. Charalampopoulos, I. (2020). The R Language as a Tool for Biometeorological Research. Atmosphere, 11(7), 682. https://doi.org/10.3390/atmos11070682 

  16. Oh, S., Yeom, J., Cho, H. J., Kim, J.-H., Yoon, S.-J., Kim, H., … Kim, H. S. (2020). Integrated pharmaco-proteogenomics defines two subgroups in isocitrate dehydrogenase wild-type glioblastoma with prognostic and therapeutic opportunities. Nature Communications, 11(1). https://doi.org/10.1038/s41467-020-17139-y 

  17. Sun, M., Folk, R. A., Gitzendanner, M. A., Soltis, P. S., Chen, Z., Soltis, D. E., & Guralnick, R. P. (2020). Recent accelerated diversification in rosids occurred outside the tropics. Nature Communications, 11(1). https://doi.org/10.1038/s41467-020-17116-5 

  18. Griffiths, D. (2020). Foraging habitat determines predator–prey size relationships in marine fishes. Journal of Fish Biology. https://doi.org/10.1111/jfb.14451 

  19. Kurose, D., Pollard, K. M., & Ellison, C. A. (2020). Chloroplast DNA analysis of the invasive weed, Himalayan balsam (Impatiens glandulifera), in the British Isles. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-67871-0