rOpenSci HQ

Our next rOpenSci community call is coming up on January 31st. Find all the details for the upcoming and all past and future calls at http://communitycalls.ropensci.org/.


Nick Golding, rOpenSci Fellow, on enabling reproducible research in ecology with zoon and simple & scalable statistical modelling with greta



Software 📦

New packages

Releases



Software Review ✔

We accept community contributed packages via our onboarding 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 nine packages were recently submitted for review:



On the blog

.rprofile series

Our fourth post is out in our .rprofile series: .rprofile: Karthik Ram by Kelly O’Briant. Karthik on Twitter -> https://twitter.com/_inundata

Keep an eye out for more posts in this series.

main blog

Sam Albers wrote about his package tidyhydat and his experience with rOpenSci software review in a blog post: 5 Things I Learned Making a Package to Work with Hydrometric Data in R. Check out the review and shout out to the reviewers Laura DeCicco and Luke Winslow.

Our community manager Stefanie Butland wrote about our next community call Writing Packages to Support Research Communities - zoon & greta.



Use cases

If you’ve used rOpenSci software in a blog post or a paper, tell us on the discussion forum and we’ll share it with our community here.

The following 11 works use/cite rOpenSci or rOpenSci software:



In the news

The NRGI Institute links to an application they developed for extracting tables from PDFs using tabulizer (github repo) in this tweet :


Elin Waring wrote a great blog post Open Science, Skimr and Me


Aaron Tay wrote a post that referenced our package roadoi: Using oaDOI & Crossref event data API to calculate your institution’s open access citation advantage. We have a package for Crossref event data in the work - crevents - let us know what you think


Gergana Daskalova wrote a great post about working with species/specimen occurrence data Manipulation and visualisation of spatial and population data. She used our package for GBIF data rgbif.


Michael Warner wrote a nice post about using the gutenberger package: Gutenberg Text Mining Practice






Submit news to rOpenSci

Reach out to us with your news suggestions by sending us an email info@ropensci.org or by contacting us on Twitter @ropensci


Keep up with rOpenSci


Footnotes

  1. Matthews, A. E., Klimov, P. B., Proctor, H. C., Dowling, A. P. G., Diener, L., Hager, S. B., … Boves, T. J. (2017). Cophylogenetic assessment of New World warblers (Parulidae) and their symbiotic feather mites (Proctophyllodidae). Journal of Avian Biology. https://doi.org/10.1111/jav.01580 

  2. Roy, A., Ghosal, S., & Choudhury, K. R. (2017). High dimensional Single Index Bayesian Modeling of the Brain Atrophy over time. arXiv preprint arXiv:1712.06743. https://arxiv.org/abs/1712.06743 

  3. Sánchez-Tapia, A., de Siqueira, M., Lima, R., Barros, F., Gall, G., Gadelha, L., and da Silva, L. Model-R: A Framework for Scalable and Reproducible Ecological Niche Modeling. In High Performance Computing - Fourth Latin American Conference, CARLA 2017. Communications in Computer and Information Science, vol. 796. Springer, 2017 http://www.lncc.br/~lgadelha/publications/model-r-carla-2017.pdf 

  4. Drost, H.-G., Gabel, A., Liu, J., Quint, M., & Grosse, I. (2017). myTAI: evolutionary transcriptomics with R. Bioinformatics. https://doi.org/10.1093/bioinformatics/btx835 

  5. Van de Peer, T., Mereu, S., Verheyen, K., María Costa Saura, J., Morillas, L., Roales, J., … Muys, B. (2018). Tree seedling vitality improves with functional diversity in a Mediterranean common garden experiment. Forest Ecology and Management, 409, 614–633. https://doi.org/10.1016/j.foreco.2017.12.001 

  6. Albers, S. (2017). tidyhydat: Extract and Tidy Canadian Hydrometric Data. The Journal of Open Source Software, 2(20), 511. https://doi.org/10.21105/joss.00511 

  7. Dolnicar, S. (2017). Peer-to-Peer Accommodation Networks: Pushing the boundaries. http://www.oapen.org/download?type=document&docid=640674 

  8. Oldham, K. A., & Weeks, A. (2017). Varieties of Melampyrum Lineare (Orobanchaceae) Revisited. Rhodora. http://www.rhodorajournal.org/doi/abs/10.3119/16-13 

  9. Krawczyk, P. S., Lipinski, L., & Dziembowski, A. (2018). PlasFlow: predicting plasmid sequences in metagenomic data using genome signatures. Nucleic Acids Research. https://doi.org/10.1093/nar/gkx1321 

  10. Shoub, K. 2017. Shifting Debate to Shift Policy: How Frames Influence Policy. https://pdfs.semanticscholar.org/3997/a040748a3bb6a66085240bdf8b771a641efe.pdf 

  11. Vaidya, G. G. (2017). Taxonomic Checklists as Biodiversity Data: How Series of Checklists can Provide Information on Synonymy, Circumscription Change and Taxonomic Discovery (Doctoral dissertation, University of Colorado at Boulder). https://search.proquest.com/openview/e04ca58442fa1725c8bc31b2cc0abf0f/1?pq-origsite=gscholar&cbl=18750&diss=y