We want to thank everyone in the rOpenSci community who contributed code, issues, and otherwise over the last year: Thank You, 2019.
- A new version (
phylocomris 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 (
osmdatais 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
unname_osmdata_sf()to remove row names from sf objects; minor changes; bug fixes
- A new version (
fulltextis 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 (
UCSCXenaToolsis 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 (
rtikais 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 (
essurveyis 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 (
citecorpis 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)
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!
The following 18 works use/cite rOpenSci software:
- Gryseels et al. used taxize in their paper A near-full-length HIV-1 genome from 1
- Wittouck et al. used rentrez in their paper A Genome-Based Species Taxonomy of the Lactobacillus Genus Complex 2
- O’Rourke used taxize in their paper Molecular Diet Analyses of North American Bats 3
- Hamdi et al. used rtweet in their paper Hybrid Approach Based on Graph Embedding and Users Features to Detect Source of Fake News in Twitter Social Network Using Machine Learning 4
- Roh et al. used RSelenium in their paper Technology opportunity discovery by structuring user needs based on natural language processing and machine learning 5
- Benun Sutton & Wilson used rfishbase in their paper Where are all the moms? External fertilization predicts the rise of male parental care in bony fishes 6
- Yang used camsRad in their paper Making reference solar forecasts with climatology, persistence, and their optimal convex combination 7
- Zheleznova et al. used taxize in their paper Moss occurrences in Yugyd Va National Park, Subpolar and Northern Urals, European North-East Russia 8
- Kearney et al. used rnoaa in their paper A method for computing hourly, historical, terrain‐corrected microclimate anywhere on earth 9
- Dornburg et al. used rentrez in their paper Transcriptome Ortholog Alignment Sequence Tools (TOAST) for Phylogenomic Dataset Assembly 10
- Elmslie et al. used neotoma in their paper Complex responses of phototrophic communities to climate warming during the Holocene of northeastern Ontario, Canada 11
- Rodewald et al. used rnaturalearth in their paper Tradeoffs in the value of biodiversity feature and cost data in conservation prioritization 12
- Outhwaite et al. used taxize in their paper Annual estimates of occupancy for bryophytes, lichens and invertebrates in the UK, 1970–2015 13
- Schwarz used rgbif in their paper Protecting the predators? Assessing the overlap between marine protected areas and endangered shark species on a global scale 14
- Smith et al. used taxize in their paper Community-level respiration of prokaryotic microbes may rise with global warming 15
- Özyıldırım used geojsonio in their paper Subjective Value Assessment Based on Emojis for Applications in Landscape and Urban Planning 16
- Mpandeli et al. used MODIStsp in their paper Assessing climate change and adaptive capacity at local scale using observed and remotely sensed data 17
- Ahmad et al. used rgbif in their paper Using an ensemble modelling approach to predict the potential distribution of Himalayan gray goral (Naemorhedus goral bedfordi) in Pakistan 18
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.
- Rob Lanfear asked a question about the magick package having to do with handling gifs. magick is maintained by Jeroen Ooms.
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:
- RSelenium: now maintained by Ju Kim
- chromer: now maintained by Paula Andrea
- qualtRics: now maintained by Julia Silge
- rsnps: now maintained by Julia Gustavsen and Sina Rüeger
- rdpla: now maintained by Alyssa Columbus
- webchem: now maintained by Erik Sapper
- mregions: in process of moving to maintenance by VLIZ
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
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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 ↩
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 ↩
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 ↩
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 ↩
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 ↩
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 ↩
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 ↩
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 ↩
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 ↩
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 ↩
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 ↩
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 ↩
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 ↩
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 ↩
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 ↩