rOpenSci HQ

Do you Want to Intern with rOpenSci’s Community Manager?: Stefanie Butland. Details are in the blog post.

We want to thank everyone in the rOpenSci community who contributed code, issues, and otherwise over the last year: Thank You, 2019.


Software 📦

CRAN: GitHub:

New Versions

  • A new version (v0.3.2) of phylocomr is on CRAN - Interface to Phylocom for analysis of phylogenetic community structure and character evolution. See the release notes for changes. Checkout the vignette to get started. phylocomr phylocomr

    bug fix for gcc -fno-common

  • A new version (v0.1.2) of osmdata is on CRAN - import OpenStreetMap data as simple features or spatial objects. See the release notes for changes. Checkout the docs to get started. osmdata osmdata

    new fxn unname_osmdata_sf() to remove row names from sf objects; minor changes; bug fixes

  • A new version (v1.4.0) of fulltext is on CRAN - full text of scholarly articles across many data sources. See the release notes for changes. Checkout the fulltext book to get started. fulltext fulltext

    ft_get() gains new publisher plugin (Cambridge); Wiley now has xml

  • A new version (v1.2.10) 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

    updated newest dataset list of UCSC Xena hubs

  • A new version (v1.23) of rtika is on CRAN - R Interface to Apache Tika. See the release notes for changes. Checkout the docs to get started. rtika rtika

    updated Tika to 1.23

  • A new version (v1.0.5) of essurvey is on CRAN - data from the European Social Survey. See the release notes for changes. Checkout the docs to get started. essurvey essurvey

    dont run examples on cran

  • A new version (v0.2.2) of citecorp is on CRAN - client for the Open Citations Corpus. See the release notes for changes. Checkout the docs to get started. citecorp citecorp

    better check if Citecorp is up before running examples



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.



On the blog

It’s time for another installment of … 2 Months in 2 Minutes - rOpenSci News, December 2019 - if you want a brief summary of the last 2 months of these newsletters, these blog posts are for you (written by Stefanie Butland)

Technotes

Scott Chamberlain wrote about HTTP testing in R: overview of tools and new features


Through time URLs can lead to nowhere, to sites that don’t exist anymore. We’ve accumulated many of these bad links in our website (https://ropensci.org/). Maëlle Salmon, Stefanie Butland, and Scott Chamberlain wrote about cleaning the bad links: We cleaned our website URLs with R!



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 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. 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. Gryseels, S., Watts, T. D., Kabongo, J.-M. M., Larsen, B. B., Lemey, P., Muyembe-Tamfum, J.-J., … Worobey, M. (2019). A near-full-length HIV-1 genome from 1966 recovered from formalin-fixed paraffin-embedded tissue. https://doi.org/10.1101/687863 

  2. Wittouck, S., Wuyts, S., Meehan, C. J., van Noort, V., & Lebeer, S. (2019). A Genome-Based Species Taxonomy of the Lactobacillus Genus Complex. mSystems, 4(5). https://doi.org/10.1128/msystems.00264-19 

  3. O’Rourke, D. R. (2019). Molecular Diet Analyses of North American Bats (Doctoral dissertation, University of New Hampshire). https://search.proquest.com/openview/b4e35aa33ed9212841cf9cdb83b3448f/1 

  4. Hamdi, T., Slimi, H., Bounhas, I., & Slimani, Y. (2020, January). A Hybrid Approach for Fake News Detection in Twitter Based on User Features and Graph Embedding. In International Conference on Distributed Computing and Internet Technology (pp. 266-280). Springer, Cham. https://link.springer.com/chapter/10.1007/978-3-030-36987-3_17 

  5. Roh, T., Jeong, Y., Jang, H., & Yoon, B. (2019). Technology opportunity discovery by structuring user needs based on natural language processing and machine learning. PLOS ONE, 14(10), e0223404. https://doi.org/10.1371/journal.pone.0223404 

  6. Benun Sutton, F., & Wilson, A. B. (2019). Where are all the moms? External fertilization predicts the rise of male parental care in bony fishes. Evolution. https://doi.org/10.1111/evo.13846 

  7. Yang, D. (2019). Making reference solar forecasts with climatology, persistence, and their optimal convex combination. Solar Energy, 193, 981–985. https://doi.org/10.1016/j.solener.2019.10.006 

  8. Zheleznova, G., Shubina, T., Degteva, S., Chadin, I., & Rubtsov, M. (2019). Moss occurrences in Yugyd Va National Park, Subpolar and Northern Urals, European North-East Russia. Biodiversity Data Journal, 7. https://doi.org/10.3897/bdj.7.e32307 

  9. Kearney, M. R., Gillingham, P. K., Bramer, I., Duffy, J. P., & Maclean, I. M. D. (2019). A method for computing hourly, historical, terrain‐corrected microclimate anywhere on earth. Methods in Ecology and Evolution. https://doi.org/10.1111/2041-210x.13330 

  10. Alex Dornburg, Dustin J. Wcisel, J. Thomas Howard et al. Transcriptome Ortholog Alignment Sequence Tools (TOAST) for Phylogenomic Dataset Assembly, 21 October 2019, PREPRINT (Version 1) available at Research Square https://doi.org/10.21203/rs.2.16269/v1 

  11. Elmslie, B. G., Gushulak, C. A., Boreux, M. P., Lamoureux, S. F., Leavitt, P. R., & Cumming, B. F. (2019). Complex responses of phototrophic communities to climate warming during the Holocene of northeastern Ontario, Canada. The Holocene, 095968361988301. https://doi.org/10.1177/0959683619883014 

  12. Rodewald, A. D., Strimas-Mackey, M., Schuster, R., & Arcese, P. (2019). Tradeoffs in the value of biodiversity feature and cost data in conservation prioritization. Scientific Reports, 9(1). https://doi.org/10.1038/s41598-019-52241-2 

  13. Outhwaite, C. L., Powney, G. D., August, T. A., Chandler, R. E., Rorke, S., Pescott, O. L., … Isaac, N. J. B. (2019). Annual estimates of occupancy for bryophytes, lichens and invertebrates in the UK, 1970–2015. Scientific Data, 6(1). https://doi.org/10.1038/s41597-019-0269-1 

  14. Schwarz, M. 2019 Protecting the predators? Assessing the overlap between marine protected areas and endangered shark species on a global scale. http://bit.ly/2QDNbgS 

  15. Smith, T. P., Thomas, T. J. H., García-Carreras, B., Sal, S., Yvon-Durocher, G., Bell, T., & Pawar, S. (2019). Community-level respiration of prokaryotic microbes may rise with global warming. Nature Communications, 10(1). https://doi.org/10.1038/s41467-019-13109-1 

  16. Özyıldırım, E. (2019). Subjective Value Assessment Based on Emojis for Applications in Landscape and Urban Planning (Doctoral dissertation, Department of Geo-information Processing, University of Twente). https://cartographymaster.eu/wp-content/theses/2019_Ozyildirim_Thesis.pdf 

  17. Mpandeli, S., Nhamo, L., Moeletsi, M., Masupha, T., Magidi, J., Tshikolomo, K., … Mabhaudhi, T. (2019). Assessing climate change and adaptive capacity at local scale using observed and remotely sensed data. Weather and Climate Extremes, 26, 100240. https://doi.org/10.1016/j.wace.2019.100240 

  18. Ahmad, S., Yang, L., Khan, T. U., Wanghe, K., Li, M., & Luan, X. (2020). Using an ensemble modelling approach to predict the potential distribution of Himalayan gray goral (Naemorhedus goral bedfordi) in Pakistan. Global Ecology and Conservation, 21, e00845. https://doi.org/10.1016/j.gecco.2019.e00845