rOpenSci HQ


Software 📦

CRAN: GitHub:

There’s very little activity in this section because CRAN submissions were closed for the last week and a half.

New Versions

  • A new version (v0.4.0) of webmockr is on CRAN - stubbing and setting expectations on HTTP requests. See the release notes for changes. Checkout the HTTP testing book to get started. webmockr webmockr

    fix link to package manual; fix single method request matching

  • A new version (v0.5.19) of aRxiv is on CRAN - Interface to the arXiv API. See the release notes for changes. Checkout the docs to get started. aRxiv aRxiv

    update vignette; add ORCIDs to DESCRIPTION



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.

The following package was recently submitted:

The following package recently went through our software-review process and has been approved:



Use Cases

The following 19 works use/cite rOpenSci software:



In the News

In a recent blog post Being a better programmer and scientist with rOpenSci Matt Boone of the Mablab at University of Florida (and an author on the refnet package under rOpenSci review) wrote about R and programming, and did a nice job of describing our software review system.


In an August 15th article in Forbes Restrict Twice-As-Deadly SUVs In U.K. Cities, Urge Transport Data Scientists, the data used was from the stplanr package maintained by Robin Lovelace and others. See also Robin’s tweet about the article.



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.

  • The Trafford Data Lab supports government decision-making in Trafford, Greater Manchester, UK. They shared use cases for ropenaq to retrieve air quality information from the Manchester Piccadilly monitoring station, fingertipsR to access public health data on the rate of antidepressant prescribing, and ghql to query linked data to map hot and cold spots of worklessness and improve public services.

fingertips_use_case



Call For Contributors

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. Checkout our Contributing Guide for why and how to contribute to rOpenSci.

We’ve had six recent examples of maintainer transitions within rOpenSci:

We don’t have any packages looking for new maintainers - if you are a maintainer and want to hand over that role to someone else get in touch with us.






Keep up with rOpenSci


Footnotes

  1. Yen, Y., Zhao, P., & Sohail, M. T. (2019). The morphology and circuity of walkable, bikeable, and drivable street networks in Phnom Penh, Cambodia. Environment and Planning B: Urban Analytics and City Science, 239980831985772. https://doi.org/10.1177/2399808319857726 

  2. Danella Figo, D., De Amicis, K., Neiva Santos de Aquino, D., Pomiecinski, F., Gadermaier, G., Briza, P., … Souza Santos, K. (2019). Cashew Tree Pollen: An Unknown Source of IgE-Reactive Molecules. International Journal of Molecular Sciences, 20(10), 2397. https://doi.org/10.3390/ijms20102397 

  3. Kanterakis, G., Skoulikaris, C., & Dimitriou, E. Assessment of hydrological modelling behaviour at basin scale on the number of delineated sub-basins. Proceedings of the Seventh International Conference on Environmental Management, Engineering, Planning & Economics https://www.researchgate.net/profile/Charalampos_Skoulikaris/publication/333652500_Assessment_of_hydrological_modelling_behaviour_at_basin_scale_on_the_number_of_delineated_sub-basins/links/5cfa46ba4585157d15991da1/Assessment-of-hydrological-modelling-behaviour-at-basin-scale-on-the-number-of-delineated-sub-basins.pdf 

  4. Petrik, C. M., Stock, C. A., Andersen, K. H., van Denderen, P. D., & Watson, J. R. (2019). Bottom-up drivers of global patterns of demersal, forage, and pelagic fishes. Progress in Oceanography, 176, 102124. https://doi.org/10.1016/j.pocean.2019.102124 

  5. Calderone, A. (2019). A Computational Analysis of Natural Languages to Build a Sentence Structure Aware Artificial Neural Network. arXiv preprint arXiv:1906.05491 https://arxiv.org/pdf/1906.05491.pdf 

  6. Uzma, Jiménez-Mejías, P., Amir, R., Hayat, M. Q., & Hipp, A. L. (2019). Timing and ecological priority shaped the diversification of sedges in the Himalayas. PeerJ, 7, e6792. https://doi.org/10.7717/peerj.6792 

  7. Baylis, A. M. M., Tierney, M., Orben, R. A., Warwick-Evans, V., Wakefield, E., Grecian, W. J., … Brickle, P. (2019). Important At-Sea Areas of Colonial Breeding Marine Predators on the Southern Patagonian Shelf. Scientific Reports, 9(1). https://doi.org/10.1038/s41598-019-44695-1 

  8. Nourbakhsh, M., Mansoor, A., Koro, K., Zhang, Q., & Minoo, P. (2019). Expression Profiling Reveals Involvement of WNT Pathway in the Malignant Progression of Sessile Serrated Adenomas. The American Journal of Pathology. https://doi.org/10.1016/j.ajpath.2019.05.009 

  9. Waller, J. (2019). Data Location Quality at GBIF. Biodiversity Information Science and Standards, 3. https://doi.org/10.3897/biss.3.35829 

  10. Shackleton, M. E., Rees, G. N., Watson, G., Campbell, C., & Nielsen, D. (2019). Environmental DNA reveals landscape mosaic of wetland plant communities. Global Ecology and Conservation, 19, e00689. https://doi.org/10.1016/j.gecco.2019.e00689 

  11. Nelli, L., Ferguson, H. M., & Matthiopoulos, J. (2019). Achieving explanatory depth and spatial breadth in infectious disease modelling: Integrating active and passive case surveillance. Statistical Methods in Medical Research, 096228021985638. https://doi.org/10.1177/0962280219856380 

  12. Glicksberg, B. S., Oskotsky, B., Thangaraj, P. M., Giangreco, N., Badgeley, M. A., Johnson, K. W., … Butte, A. J. (2019). PatientExploreR: an extensible application for dynamic visualization of patient clinical history from electronic health records in the OMOP common data model. Bioinformatics. https://doi.org/10.1093/bioinformatics/btz409 

  13. Brown, E. E., Rashidi‐Ranjbar, N., Caravaggio, F., Gerretsen, P., Pollock, B. G., … Mulsant, B. H. (2019). Brain Amyloid PET Tracer Delivery is Related to White Matter Integrity in Patients with Mild Cognitive Impairment. Journal of Neuroimaging. https://doi.org/10.1111/jon.12646 

  14. Koppelstaetter, C., Leierer, J., Rudnicki, M., Kerschbaum, J., Kronbichler, A., Melk, A., … Perco, P. (2019). Computational Drug Screening Identifies Compounds Targeting Renal Age-associated Molecular Profiles. Computational and Structural Biotechnology Journal, 17, 843–853. https://doi.org/10.1016/j.csbj.2019.06.019 

  15. Calero Valdez A., Ziefle M. (2019) Trends and Changes in the Field of HCI the Last Decade from the Perspective of HCII Conference. In: Kurosu M. (eds) Human-Computer Interaction. Perspectives on Design. HCII 2019. Lecture Notes in Computer Science, vol 11566. Springer, Cham https://doi.org/10.1007/978-3-030-22646-6_3 

  16. Alfaro, M. E., Karan, E., Schwartz, S. T., & Shultz, A. J. (2019). The Evolution of Color Pattern in Butterflyfishes (Chaetodontidae). Integrative and comparative biology. https://academic.oup.com/icb/advance-article-abstract/doi/10.1093/icb/icz119/5530961 

  17. Butterfield, B. J., Holmgren, C. A., Anderson, R. S., & Betancourt, J. L. (2019). Life history traits predict colonization and extinction lags of desert plant species since the Last Glacial Maximum. Ecology. https://doi.org/10.1002/ecy.2817 

  18. Kovalenko, K. E., Johnson, L. B., Brady, V. J., Ciborowski, J. J. H., Cooper, M. J., Gathman, J. P., … Uzarski, D. G. (2019). Hotspots and bright spots in functional and taxonomic fish diversity. Freshwater Science, 000–000. https://doi.org/10.1086/704713 

  19. Ferraz, M. de A. M. M., Carothers, A., Dahal, R., Noonan, M. J., & Songsasen, N. (2019). Oviductal extracellular vesicles interact with the spermatozoon’s head and mid-piece and improves its motility and fertilizing ability in the domestic cat. Scientific Reports, 9(1). https://doi.org/10.1038/s41598-019-45857-x