Software 📦

CRAN: GitHub:

New packages

  • The first version (v0.1.0) of chirps is on CRAN - client for the Climate Hazards Group InfraRed Precipitation with Station Data. Checkout the docs to get started. chirps went through rOpenSci software review. chirps chirps

New Versions

  • A new version (v2.1.2) of skimr is on CRAN - compact and flexible summaries of data. See the release notes for changes. Checkout the vignettes to get started. skimr skimr
  • Two new versions (v2.1.0/v2.1.1) of ijtiff are 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
  • A new version (v0.1.14) of spatsoc is on CRAN - detecting spatial and temporal groups in GPS relocations. See the release notes for changes. Checkout the docs to get started. spatsoc spatsoc
  • A new version (v1.5.0) 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
  • A new version (v1.1.0) of rcites is on CRAN - access the CITES Speciesplus database. See the release notes for changes. Checkout the docs to get started. rcites rcites
  • Two new versions (v1.2/v1.3) of lightr are on CRAN - read spectrometric data and metadata. See the release notes for changes. Checkout the docs to get started. lightr lightr
  • A new version (v7.12.4) of drake is on CRAN - a pipeline toolkit for reproducible computation at scale. See the release notes for changes. Checkout the docs to get started. drake drake
  • A new version (v0.4.0) of wikitaxa is on CRAN - taxonomic information from Wikipedia. See the release notes for changes. Checkout the docs to get started. wikitaxa wikitaxa
  • A new version (v0.2.2) of pubchunks is on CRAN - Fetch Sections of XML Scholarly Articles. See the release notes for changes. Checkout the README to get started. pubchunks pubchunks
  • A new version (v0.4.0) of crminer is on CRAN - Fetch scholarly full text from Crossref. See the release notes for changes. Checkout the README to get started. crminer crminer
  • A new version (v0.7.7) 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 (v0.4.0) of sofa is on CRAN - Connector to CouchDB. See the release notes for changes. Checkout the vignettes to get started. sofa sofa
  • Two new versions (v1.2.0/v1.2.1) of credentials are 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 (v1.0.0) of rdryad is on CRAN - R client for Dryad. See the release notes for changes. Checkout the README to get started. rdryad rdryad
  • A new version (v0.3.4) of geojson is on CRAN - Classes for GeoJSON. See the release notes for changes. Checkout the vignettes to get started. geojson geojson
  • A new version (v2.4.0) of magick is on CRAN - Advanced graphics and Image-Processing in R. See the release notes for changes. Checkout the vignette to get started. magick magick
  • Two new versions (v3.0.0/v3.1.0) of rgbif are 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 (v0.6.1) of stplanr is on CRAN - sustainable transport planning. See the release notes for changes. Checkout the docs to get started. stplanr stplanr



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.



Use Cases

The following 25 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:

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

  • rflybase: The current maintainer is looking for a new maintainer. Email Scott if you’re interested.



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. Rossi, M. (2020). Monitoring the vegetation dynamics and stress of mountainous grasslands using a multisensor approach. Dissertation. https://bit.ly/2Cf7BHF 

  2. Jost, L., & Jansen, P. (2020). A novel approach to analyzing all trials in chronometric mental rotation and description of a flexible extended library of stimuli. OSF Preprints https://osf.io/y92fw 

  3. Michaels, I. H., Pirani, S. J., & Carrascal, A. (2020). Visualizing 50 Years of Cancer Mortality Rates Across the US at Multiple Geographic Levels Using a Synchronized Map and Graph Animation. Preventing Chronic Disease, 17. https://doi.org/10.5888/pcd17.190286 

  4. Brick, C., McDowell, M., & Freeman, A. L. J. (2020). Risk communication in tables versus text: a registered report randomized trial on “fact boxes.” Royal Society Open Science, 7(3), 190876. https://doi.org/10.1098/rsos.190876 

  5. Yang, D. (2020). Choice of clear-sky model in solar forecasting. Journal of Renewable and Sustainable Energy, 12(2), 026101. https://doi.org/10.1063/5.0003495 

  6. Stropp, J., Umbelino, B., Correia, R. A., Campos-Silva, J. V., Ladle, R. J., & Malhado, A. C. M. (2020). The ghosts of forests past and future: deforestation and botanical sampling in the Brazilian Amazon. Ecography. https://doi.org/10.1111/ecog.05026 

  7. Claes, M., & Mäntylä, M. (2020). 20-MAD–20 Years of Issues and Commits of Mozilla and Apache Development. arXiv preprint arXiv:2003.14015. https://arxiv.org/pdf/2003.14015.pdf 

  8. Trugman, A. T., Anderegg, L. D. L., Shaw, J. D., & Anderegg, W. R. L. (2020). Trait velocities reveal that mortality has driven widespread coordinated shifts in forest hydraulic trait composition. Proceedings of the National Academy of Sciences, 117(15), 8532–8538. https://doi.org/10.1073/pnas.1917521117 

  9. Zushi, Y., Hanari, N., Nabi, D., & Lin, B.-L. (2020). Mixture Touch: A Web Platform for the Evaluation of Complex Chemical Mixtures. ACS Omega, 5(14), 8121–8126. https://doi.org/10.1021/acsomega.0c00340 

  10. Martins, P. T., & Boeckx, C. (2020). Vocal learning: Beyond the continuum. PLOS Biology, 18(3), e3000672. https://doi.org/10.1371/journal.pbio.3000672 

  11. Hantgan-Sonko, A. (2020). Synchronic and diachronic strategies of mora preservation in Gújjolaay Eegimaa. Journal of African Languages and Literatures, (1), 1-25. http://www.politics.unina.it/index.php/jalalit/article/download/6732/7790 

  12. Fraser, N., Momeni, F., Mayr, P., & Peters, I. (2020). The relationship between bioRxiv preprints, citations and altmetrics. Quantitative Science Studies, 1–21. https://doi.org/10.1162/qss_a_00043 

  13. Staude, I. R., Waller, D. M., Bernhardt-Römermann, M., Bjorkman, A. D., Brunet, J., De Frenne, P., … Baeten, L. (2020). Replacements of small- by large-ranged species scale up to diversity loss in Europe’s temperate forest biome. Nature Ecology & Evolution, 4(6), 802–808. https://doi.org/10.1038/s41559-020-1176-8 

  14. Hernández‐Rojas, A. C., Kluge, J., Krömer, T., Carvajal‐Hernández, C., Silva‐Mijangos, L., Miehe, G., … Kessler, M. (2020). Latitudinal patterns of species richness and range size of ferns along elevational gradients at the transition from tropics to subtropics. Journal of Biogeography, 47(6), 1383–1397. https://doi.org/10.1111/jbi.13841 

  15. Cui, X., Paterson, A. M., Wyse, S. V., Alam, M. A., Maurin, K. J. L., Pieper, R., … Curran, T. J. (2020). Shoot flammability of vascular plants is phylogenetically conserved and related to habitat fire-proneness and growth form. Nature Plants, 6(4), 355–359. https://doi.org/10.1038/s41477-020-0635-1 

  16. Timpano, E. K., Scheible, M. K. R., & Meiklejohn, K. A. (2020). Optimization of the second internal transcribed spacer (ITS2) for characterizing land plants from soil. PLOS ONE, 15(4), e0231436. https://doi.org/10.1371/journal.pone.0231436 

  17. Bärenstrauch, M., Mann, S., Jacquemin, C., Bibi, S., Sylla, O.-K., Baudouin, E., … Kunz, C. (2020). Molecular crosstalk between the endophyte Paraconiothyrium variabile and the phytopathogen Fusarium oxysporum – Modulation of lipoxygenase activity and beauvericin production during the interaction. Fungal Genetics and Biology, 139, 103383. https://doi.org/10.1016/j.fgb.2020.103383 

  18. Zhao, P., & Cao, Y. (2020). Commuting inequity and its determinants in Shanghai: New findings from big-data analytics. Transport Policy, 92, 20–37. https://doi.org/10.1016/j.tranpol.2020.03.006 

  19. Mishler, B. D., Guralnick, R., Soltis, P. S., Smith, S. A., Soltis, D. E., Barve, N., … Laffan, S. W. (2020). Spatial phylogenetics of the North American flora. Journal of Systematics and Evolution. https://doi.org/10.1111/jse.12590 

  20. Sinval, J., & Marôco, J. (2020). Short Index of Job Satisfaction: Validity evidence from Portugal and Brazil. PLOS ONE, 15(4), e0231474. https://doi.org/10.1371/journal.pone.0231474 

  21. Barela, I., Burger, L. M., Taylor, J., Evans, K. O., Ogawa, R., McClintic, L., & Wang, G. (2020). Relationships between survival and habitat suitability of semi‐aquatic mammals. Ecology and Evolution, 10(11), 4867–4875. https://doi.org/10.1002/ece3.6239 

  22. Menounos, B., Pelto, B. M., Fleming, S. W., Moore, R. D., Weber, F., Hutchinson, D., & Brahney, J. (2020). Glaciers in the Canadian Columbia Basin, Technical Report. https://digitalcommons.usu.edu/cgi/viewcontent.cgi?article=2134&context=wats_facpub 

  23. Bernardi, A. P., Lauterjung, M. B., Mantovani, A., & dos Reis, M. S. (2020). Phylogeography and species distribution modeling reveal a historic disjunction for the conifer Podocarpus lambertii. Tree Genetics & Genomes, 16(3). https://doi.org/10.1007/s11295-020-01434-2 

  24. Martínez, A., Eckert, E. M., Artois, T., Careddu, G., Casu, M., Curini-Galletti, M., … Fontaneto, D. (2020). Human access impacts biodiversity of microscopic animals in sandy beaches. Communications Biology, 3(1). https://doi.org/10.1038/s42003-020-0912-6 

  25. Hagan, A. K., Pollet, R. M., & Libertucci, J. (2020). Suggestions for Improving Invited Speaker Diversity To Reflect Trainee Diversity. Journal of Microbiology & Biology Education, 21(1). https://doi.org/10.1128/jmbe.v21i1.2105