rOpenSci HQ

  • What would you like to hear about in an rOpenSci Community Call? We are soliciting your “votes” and new ideas for Community Call topics and speakers. Find out how you can influence us by checking out our new Community Calls repository.
  • One of our next Community Calls will be about testing. Tell us what you want to know about it or who you’d like to hear from by commenting in our new Community Calls repository.
  • Help wanted! We encourage rOpenSci package authors to help us help you get more contributors to your package. If you label an issue “help wanted” (no hyphen or emojis), those issues can be found in a search of the rOpenSci organization; and on the rOpenSci GitHub landing page https://github.com/ropensci the number of open help wanted issues is highlighted for each package that has them.


Software 📦

CRAN: GitHub:

New Packages

  • The first version (v0.1.2) of chlorpromazineR is on CRAN - convert antipsychotic doses to chlorpromazine equivalents. Checkout the docs to get started. This package recently went through rOpenSci software review. chlorpromazineR chlorpromazineR
  • The first version (v2.0.0) of rmangal is on CRAN - interface to the Mangal database of ecological networks. Checkout the docs to get started. This package recently went through rOpenSci software review. rmangal rmangal

New Versions

  • A new version (v0.4.0) of stplanr is on CRAN - sustainable transport planning. See the release notes for changes. Checkout the docs to get started. stplanr stplanr

    family of new fxns for adding new nodes to routes, route networks and sfNetwork objects; other new fxns

  • A new version (v0.4.0) of ckanr is on CRAN - R client for the CKAN API. See the release notes for changes. Checkout the docs to get started. ckanr ckanr

    ^^ improvements to ckan_fetch fxn (thanks Sharla Gelfand)

  • A new version (v0.3.0) of emld is on CRAN - ecological metadata as linked data. See the release notes for changes. Checkout the vignette to get started. emld emld

    now supports EML v2.2; fixed xml parsing issue; eml_validate change

  • A new version (v1.2.7) 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. UCSCXenaTools UCSCXenaTools

    vignette updated; new datasets added; bug fixes

  • A new version (v1.4.2) of MtreeRing is on CRAN - a shiny application for automatic measurements of tree-ring widths on digital images. See the release notes for changes. Checkout the docs to get started. MtreeRing MtreeRing

    Update GitHub links in ring_app_launch function



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:



On the blog

There’s a new version of the rOpenSci Dev Guide out. The software review editors wrote up a post describing the accumulated changes since v0.2: rOpenSci Dev Guide 0.3.0: Updates. Some highlights:

Technical notes

Scott Chamberlain wrote a post on updates to the cran checks API. The API now has a route to get CRAN check results by maintainer, badges for CRAN checks with a number of different scenarios, and gives access to recent (30 day), and older (back to December 2018) checks data.



Use Cases

The following 18 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.



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’ve got one package in need of a new maintainer:






Keep up with rOpenSci


Footnotes

  1. Ayodele Benjamin, E., Vincent, E., Claudius, A., Olatomiwa, L., & Dickson, E. (2019). Data-based investigation on the performance of an independent Gas turbine for electricity generation using real power measurements and other closely related parameters. Data in Brief, 104444. https://doi.org/10.1016/j.dib.2019.104444 

  2. Mendes, G., Paiva, J. G. S., & Schwartz, W. R. (2019, July). Point-Placement Techniques and Temporal Self-Similarity Maps for Visual Analysis of Surveillance Videos. In 2019 23rd International Conference Information Visualisation (IV) (pp. 127-132). IEEE. https://ieeexplore.ieee.org/iel7/8798596/8811888/08811966.pdf 

  3. Stewart, D. B., Wright, J. R., Fowler, M., McLimans, C. J., Tokarev, V., Amaniera, I., … Lamendella, R. (2019). Integrated Meta-omics Reveals a Fungus-Associated Bacteriome and Distinct Functional Pathways in Clostridioides difficile Infection. mSphere, 4(4). https://doi.org/10.1128/msphere.00454-19 

  4. Lewis, M. J., Barnes, M. R., Blighe, K., Goldmann, K., Rana, S., Hackney, J. A., … Pitzalis, C. (2019). Molecular Portraits of Early Rheumatoid Arthritis Identify Clinical and Treatment Response Phenotypes. Cell Reports, 28(9), 2455–2470.e5. https://doi.org/10.1016/j.celrep.2019.07.091 

  5. Esperon‐Rodriguez, M., Power, S. A., Tjoelker, M. G., Beaumont, L. J., Burley, H., Caballero‐Rodriguez, D., & Rymer, P. D. (2019). Assessing the vulnerability of Australia’s urban forests to climate extremes. Plants, People, Planet. https://doi.org/10.1002/ppp3.10064 

  6. Lacy, S. N., Corcoran, D., Alò, D., Lessmann, J., Meza, F., & Marquet, P. A. (2019). Main drivers of freshwater fish diversity across extra-tropical Southern Hemisphere rivers. Hydrobiologia. https://doi.org/10.1007/s10750-019-04044-9 

  7. Gonçalves, B., Coutinho, D., Exel, J., Travassos, B., Lago, C., & Sampaio, J. (2019). Extracting spatial-temporal features that describe a team match demands when considering the effects of the quality of opposition in elite football. PLOS ONE, 14(8), e0221368. https://doi.org/10.1371/journal.pone.0221368 

  8. Urquhart-Cronish, M., & Otto, S. P. (2019). Gender and language use in scientific grant writing. FACETS, 4(1), 442–458. https://doi.org/10.1139/facets-2018-0039 

  9. Wegrzyn, J. L., Falk, T., Grau, E., Buehler, S., Ramnath, R., & Herndon, N. (2019). Cyberinfrastructure and resources to enable an integrative approach to studying forest trees. Evolutionary Applications. https://doi.org/10.1111/eva.12860 

  10. Redmond, M. D., Morris, T. L., & Cramer, M. C. (2019). The cost of standing tall: wood nutrients associated with tree invasions in nutrient‐poor fynbos soils of South Africa. Ecosphere, 10(9). https://doi.org/10.1002/ecs2.2831 

  11. Hanna, A., & Hanna, L.-A. (2019). Topic Analysis of UK Fitness to Practise Cases: What Lessons Can Be Learnt? Pharmacy, 7(3), 130. https://doi.org/10.3390/pharmacy7030130 

  12. Ramagopalan, S. V., Malcolm, B., Merinopoulou, E., McDonald, L., & Cox, A. (2019). Automated extraction of treatment patterns from social media posts: an exploratory analysis in renal cell carcinoma. Future Oncology. https://doi.org/10.2217/fon-2019-0406 

  13. Bayley, D. T. I., Mogg, A. O. M., Purvis, A., & Koldewey, H. J. (2019). Evaluating the efficacy of small‐scale marine protected areas for preserving reef health: A case study applying emerging monitoring technology. Aquatic Conservation: Marine and Freshwater Ecosystems. https://doi.org/10.1002/aqc.3215 

  14. Mihalitsis, M., & Bellwood, D. (2019). Functional implications of dentition-based morphotypes in piscivorous fishes. Royal Society Open Science, 6(9), 190040. https://doi.org/10.1098/rsos.190040 

  15. Greco, M., Jonkers, L., Kretschmer, K., Bijma, J., & Kucera, M. (2019). Depth habitat of the planktonic foraminifera Neogloboquadrina pachyderma in the northern high latitudes explained by sea-ice and chlorophyll concentrations. Biogeosciences, 16(17), 3425–3437. https://doi.org/10.5194/bg-16-3425-2019 

  16. Flower, C. (2019). Food Plant Biogeography of the Sonoran Desert (Doctoral dissertation, Arizona State University). https://search.proquest.com/docview/2275500833 

  17. Rebolj, M., Parmar, D., Maroni, R., Blyuss, O., & Duffy, S. W. (In press). Concurrent participation in screening for cervical, breast, and bowel cancer in England. Journal of Medical Screening. 

  18. Sun, Z., Cang, J., Ruan, Y., & Zhu, D. (2019). Reporting gaps between news media and scientific papers on outdoor air pollution–related health outcomes: A content analysis. The International Journal of Health Planning and Management. https://doi.org/10.1002/hpm.2894