Software 📦

CRAN: GitHub:

New Packages

  • The first version (v0.1.0) of dittodb is on CRAN - a test environment for database requests. It went through rOpenSci software review recently - check out the reviews. Checkout the docs to get started. dittodb dittodb

New Versions

  • rdpla is now archived on cran. You can still install it from GitHub but it is no longer maintained.
  • A new version (v1.1-3) of suppdata is on CRAN - downloading supplementary data from published manuscripts. See the release notes for changes. Checkout the vignette to get started. suppdata suppdata
  • A new version (v1.1.0) of spocc is on CRAN - an interface to many species occurrence data sources. See the release notes for changes. Checkout the docs to get started. spocc spocc
  • A new version (v0.5.0) of ckanr is on CRAN - client for the CKAN API. See the release notes for changes. Checkout the docs to get started. ckanr ckanr
  • A new version (v1.0.0) of crul is on CRAN - an R6 based HTTP client for R made for developers. See the release notes for changes. Checkout the docs to get started. crul crul
  • A new version (v0.5.0) of mapr is on CRAN - visualize species occurrence data. See the release notes for changes. Checkout the vignette to get started. mapr mapr
  • A new version (v0.9.0) of gistr is on CRAN - work with GitHub Gists. See the release notes for changes. Checkout the docs to get started. gistr gistr
  • A new version (v0.2.10) of ropenaq is on CRAN - air quality data from the open data platform OpenAQ. See the release notes for changes. Checkout the docs to get started. ropenaq ropenaq
  • A new version (v0.7.0) of paleobioDB is on CRAN - download and process data from the Paleobiology database. See the release notes for changes. Checkout the docs to get started. paleobioDB paleobioDB
  • A new version (v0.7.8) of robotstxt is on CRAN - robots.txt parser and Webbot/Spider/Crawler permissions checker. See the release notes for changes. Checkout the docs to get started. robotstxt robotstxt
  • A new version (v2.1.2) of ijtiff is on CRAN - comprehensive TIFF I/O with full support for ImageJ TIFF files. See the release notes for changes. Checkout the docs to get started. ijtiff ijtiff
  • Two new versions (v2.0.2/v2.0.3) of EML are on CRAN - read and write ecological metadata language files. See the release notes for changes. Checkout the docs to get started. EML EML
  • A new version (v3.2.0) of rgbif is on CRAN - interface to the Global Biodiversity Information Facility API. See the release notes for changes. Checkout the occurrence manual to get started. rgbif rgbif
  • A new version (v1.3.0) of credentials is on CRAN - tools for managing ssh and git credentials. See the release notes for changes. Checkout the docs to get started. credentials credentials
  • A new version (v0.7.0) of ssh is on CRAN - secure shell (SSH) client for R. See the release notes for changes. Checkout the vignette to get started. ssh ssh



Software Review ✔


Software review is now accepting submissions again.

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.



Citations

The following 20 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.


A few new use cases were shared in the forum over the past two weeks since our last newsletter:



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. Check out our guidance for taking over maintenance of a package.

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



Get involved with rOpenSci

We maintain a Contributing Guide that can help direct you to the right place, whether you want to make code contributions, non-code contributions, or other things like sharing use cases.






Keep up with rOpenSci


Footnotes

  1. Scharmüller, A., Schreiner, V. C., & Schäfer, R. B. (2020). Standartox: Standardizing Toxicity Data. Data, 5(2), 46. https://doi.org/10.3390/data5020046 

  2. Nguyen, C. T., Nguyen, D. T. H., & Phan, D. K. (2020). Factors affecting urban electricity consumption: a case study in the Bangkok Metropolitan Area using an integrated approach of earth observation data and data analysis. Environmental Science and Pollution Research. https://doi.org/10.1007/s11356-020-09157-6 

  3. Upadhya, A., Agrawal, P., Vakacherla, S., & Kushwaha, M. (2020). mmaqshiny v1.0: R-Shiny package to explore Air-Quality Mobile-Monitoring data. Journal of Open Source Software, 5(50), 2250. https://doi.org/10.21105/joss.02250 

  4. Rahman, M. M., Ali, G. G., Li, X. J., Paul, K. C., & Chong, P. H. (2020). Twitter and Census Data Analytics to Explore Socioeconomic Factors for Post-COVID-19 Reopening Sentiment. Nawaz and Li, Xue Jun and Paul, Kamal Chandra and Chong, Peter HJ, Twitter and Census Data Analytics to Explore Socioeconomic Factors for Post-COVID-19 Reopening Sentiment (June 30, 2020). https://arxiv.org/pdf/2007.00054.pdf 

  5. Colling LJ, Szűcs D, De Marco D, et.al., A multilab registered replication of the attentional SNARC effect, Advances in Methods and Practices in Psychological Science (Forthcoming) https://dspace.stir.ac.uk/retrieve/cb22b749-5134-44ec-ae5b-7f66efbad76f/Colling%20et%20al_AMPPS_SNARC.pdf 

  6. Lam, K.-L., Cheng, W.-Y., Su, Y., Li, X., Wu, X., Wong, K.-H., … Cheung, P. C.-K. (2020). Use of random forest analysis to quantify the importance of the structural characteristics of beta-glucans for prebiotic development. Food Hydrocolloids, 108, 106001. https://doi.org/10.1016/j.foodhyd.2020.106001 

  7. Deconinck, D., Volckaert, F. A. M., Hostens, K., Panicz, R., Eljasik, P., Faria, M., … Derycke, S. (2020). A high-quality genetic reference database for European commercial fishes reveals substitution fraud of processed Atlantic cod (Gadus morhua) and common sole (Solea solea) at different steps in the Belgian supply chain. Food and Chemical Toxicology, 141, 111417. https://doi.org/10.1016/j.fct.2020.111417 

  8. Bohora Schlickmann, M., da Silva, A. C., de Oliveira, L. M., Oliveira Matteucci, D., Domingos Machado, F., Cuchi, T., … Higuchi, P. (2020). Specific leaf area is a potential indicator of tree species sensitive to future climate change in the mixed Subtropical Forests of southern Brazil. Ecological Indicators, 116, 106477. https://doi.org/10.1016/j.ecolind.2020.106477 

  9. Shrestha, R. K., & Shrestha, R. (2020). Group segmentation and heterogeneity in the choice of cooking fuels in post-earthquake Nepal. arXiv preprint arXiv:2005.09616. https://arxiv.org/pdf/2005.09616.pdf 

  10. Crowley, D., Becker, D., Washburne, A., & Plowright, R. (2020). Identifying Suspect Bat Reservoirs of Emerging Infections. Vaccines, 8(2), 228. https://doi.org/10.3390/vaccines8020228 

  11. Joyce, E., Thiele, K., Slik, F., & Crayn, D. (2020). Checklist of the vascular flora of the Sunda-Sahul Convergence Zone. Biodiversity Data Journal, 8. https://doi.org/10.3897/bdj.8.e51094 

  12. Camacho, K. (2020). Sentiment mapping: Point pattern analysis of sentiment classified twitter data (Order No. 27962629). Available from ProQuest Dissertations & Theses A&I; ProQuest Dissertations & Theses Global. (2404054000). Retrieved from https://search.proquest.com/docview/2404054000?accountid=14496 

  13. Haußner, S., & Klika, C. (2020). Who Is Connected to Whom? A Twitter-Based Network Analysis of Members of the European Parliament Elected in 2019. In Die Europawahl 2019 (pp. 423-435). Springer VS, Wiesbaden. https://doi.org/10.1007/978-3-658-29277-5_34 

  14. Petersen, T. K., Speed, J. D. M., Grøtan, V., & Austrheim, G. (2020). Urban aliens and threatened near-naturals: Land-cover affects the species richness of alien- and threatened species in an urban-rural setting. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-65459-2 

  15. Lindberg, C. L., Hanslin, H. M., Schubert, M., Marcussen, T., Trevaskis, B., Preston, J. C., & Fjellheim, S. (2020). Increased above‐ground resource allocation is a likely precursor for independent evolutionary origins of annuality in the Pooideae grass subfamily. New Phytologist. https://doi.org/10.1111/nph.16666 

  16. Donnellan, E., Aslan, S., Fastrich, G. M., & Murayama, K. (2020, May 20). How are Curiosity and Interest Different? Naïve Bayes Classification of People’s Naïve Belief. https://doi.org/10.31234/osf.io/697gk 

  17. Gold, Z. J. (2020). Design and Implementation of Environmental DNA Metabarcoding Methods for Monitoring the Southern California Marine Protected Area Network (Doctoral dissertation, UCLA) https://escholarship.org/content/qt7zf5g0cb/qt7zf5g0cb.pdf 

  18. Lenoir, J., Bertrand, R., Comte, L., Bourgeaud, L., Hattab, T., Murienne, J., & Grenouillet, G. (2020). Species better track climate warming in the oceans than on land. Nature Ecology & Evolution. https://doi.org/10.1038/s41559-020-1198-2 

  19. De Almeida Monteiro Melo Ferraz, M., Fujihara, M., Nagashima, J. B., Noonan, M. J., Inoue-Murayama, M., & Songsasen, N. (2020). Follicular extracellular vesicles enhance meiotic resumption of domestic cat vitrified oocytes. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-65497-w 

  20. Joo, R., Picardi, S., Boone, M. E., Clay, T. A., Patrick, S. C., Romero-Romero, V. S., & Basille, M. (2020). A decade of movement ecology. arXiv preprint arXiv:2006.00110 https://arxiv.org/pdf/2006.00110.pdf