Software 📦

CRAN: GitHub:

New Versions

  • A new version (v0.9.0) of rplos is on CRAN - Interface to the Search API for Public Library of Science journals. See the release notes for changes. Checkout the vignettes to get started.
  • A new version (v0.3.2) of crminer is on CRAN - Fetch scholarly full text from Crossref. See the release notes for changes. Checkout the README to get started.
  • A new version (v0.9.2) of geojsonio is on CRAN - Convert Data from and to GeoJSON or TopoJSON. See the release notes for changes. Checkout the vignettes to get started.
  • A new version (v0.9.6) of rnoaa is on CRAN - NOAA Weather Data from R. See the release notes for changes. Checkout the vignettes to get started.
  • A new version (v0.3.2) of scrubr is on CRAN - clean biological occurrence records. See the release notes for changes. Checkout the docs to get started.
  • A new version (v2.0.5) 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.
  • A new version (v0.3.8) of rdefra is on CRAN - get data from DEFRA’s UK-AIR website https://uk-air.defra.gov.uk/. See the release notes for changes. Checkout the rdefra vignette to get started.
  • A new version (v0.5.2) of stplanr is on CRAN - sustainable transport planning. See the release notes for changes. Checkout the docs to get started.
  • A new version (v4.9.2.1) of plotly is on CRAN - Create Interactive Web Graphics via plotly.js. See the release notes for changes. Checkout the plotly book to get started.
  • A new version (v0.4.1) of auk is on CRAN - eBird data extraction and processing. See the release notes for changes. Checkout the docs to get started.
  • A new version (v0.3.8) of jstor is on CRAN - read data from JSTOR/DfR. See the release notes for changes. Checkout the docs to get started.
  • A new version (v1.0) of tradestatistics is on CRAN - open trade statistics api wrapper and utility program. See the release notes for changes. Checkout the docs to get started.
  • A new version (v1.4) of xslt is on CRAN - extensible style-sheet language transformations. See the release notes for changes. Checkout the README to get started.
  • A new version (v1.1) of lightr is on CRAN - read spectrometric data and metadata. See the release notes for changes. Checkout the docs to get started.
  • A new version (v0.9.94) of taxize is on CRAN - taxonomic toolbelt for R. See the release notes for changes. Checkout the taxize book to get started.
  • A new version (v0.5.4) of vcr is on CRAN - record HTTP calls to disk for test caching. See the release notes for changes. Checkout the HTTP testing book to get started.



Software Review ✔

In the interest of reducing load on reviewers and editors as we manage the COVID-19 crisis, rOpenSci is temporarily pausing new submissions for software peer review. Please check back at our software review repository after 17 April for updates. In this period new submissions will not be handled, nor new reviewers assigned. Reviews and responses to reviews will be handled on a ‘best effort’ basis, but no follow-up reminders will be sent. Other rOpenSci community activities continue. We express our continued great appreciation for the work of our authors and reviewers.



On the blog

Stefanie Butland and Maëlle Salmon wrote a post on lessons learned from creating the new blog guide: 10 Things We Learned in Creating the Blog Guide with bookdown



Use Cases

The following 21 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 new use case was reported in the forum recently:



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 eight 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.



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. Cirtwill, A. R., Dalla Riva, G. V., Baker, N. J., Ohlsson, M., Norström, I., Wohlfarth, I., … Stouffer, D. B. (2020). Related plants tend to share pollinators and herbivores, but strength of phylogenetic signal varies among plant families. New Phytologist. https://doi.org/10.1111/nph.16420 

  2. Léveillé-Bourret, É., Chen, B.-H., Garon-Labrecque, M.-È., Ford, B. A., & Starr, J. R. (2020). RAD sequencing resolves the phylogeny, taxonomy and biogeography of Trichophoreae despite a recent rapid radiation (Cyperaceae). Molecular Phylogenetics and Evolution, 145, 106727. https://doi.org/10.1016/j.ympev.2019.106727 

  3. Moudrý, V., & Devillers, R. (2020). Quality and usability challenges of global marine biodiversity databases: An example for marine mammal data. Ecological Informatics, 56, 101051. https://doi.org/10.1016/j.ecoinf.2020.101051 

  4. Deng, H., Wang, Q., Turner, D. P., Sexton, K. E., Burns, S. M., Eikermann, M., … Houle, T. T. (2020). Sentiment analysis of real-world migraine tweets for population research. Cephalalgia Reports, 3, 251581631989886. https://doi.org/10.1177/2515816319898867 

  5. Shan, S., Soltis, P. S., Soltis, D. E., & Yang, B. (2020). Considerations in adapting CRISPR/Cas9 in nongenetic model plant systems. Applications in Plant Sciences, 8(1). https://doi.org/10.1002/aps3.11314 

  6. Horne, C. R., Hirst, A. G., & Atkinson, D. (2020). Selection for increased male size predicts variation in sexual size dimorphism among fish species. Proceedings of the Royal Society B: Biological Sciences, 287(1918), 20192640. https://doi.org/10.1098/rspb.2019.2640 

  7. Akpınar, B. A., Carlson, P. O., Paavilainen, V. O., & Dunn, C. D. (2020). Pathogenicity of human mtDNA variants is revealed by combining a novel phylogenetic analysis with machine learning. https://doi.org/10.1101/2020.01.10.902239 

  8. Milla, R., Bastida, J. M., Turcotte, M. M., Jones, G., Violle, C., Osborne, C. P., … Byun, C. (2018). Phylogenetic patterns and phenotypic profiles of the species of plants and mammals farmed for food. Nature Ecology & Evolution, 2(11), 1808–1817. https://doi.org/10.1038/s41559-018-0690-4 

  9. Scherer, C., Radchuk, V., Franz, M., Thulke, H., Lange, M., Grimm, V., & Kramer‐Schadt, S. (2020). Moving infections: individual movement decisions drive disease persistence in spatially structured landscapes. Oikos. https://doi.org/10.1111/oik.07002 

  10. Burns, M. D., & Bloom, D. D. (2020). Migratory lineages rapidly evolve larger body sizes than non-migratory relatives in ray-finned fishes. Proceedings of the Royal Society B: Biological Sciences, 287(1918), 20192615. https://doi.org/10.1098/rspb.2019.2615 

  11. Santos, J. C. (2020). Phylogenetic Analyses of Chemokine Receptors from Sequence Retrieval to Phylogenetic Trees. In Immune Mediators in Cancer (pp. 313-343). Humana, New York, NY. https://link.springer.com/protocol/10.1007/978-1-0716-0247-8_27 

  12. Walczyńska, A., Gudowska, A., & Sobczyk, Ł. (2020). Should I shrink or should I flow? – body size adjustment to thermo-oxygenic niche. https://doi.org/10.1101/2020.01.14.905901 

  13. Mathes, S. (2019). The Dynamics of Residential Sorting and Health: Implications of Climate Change in the US. https://sophiemathescom.files.wordpress.com/2019/11/job_market_paper_sophie_mathes-1.pdf 

  14. Théroux-Rancourt, G., Roddy, A. B., Earles, J. M., Gilbert, M. E., Zwieniecki, M. A., Boyce, C. K., … Brodersen, C. R. (2020). Maximum CO2 diffusion inside leaves is limited by the scaling of cell size and genome size. https://doi.org/10.1101/2020.01.16.904458 

  15. Lakicevic M., Povak N., Reynolds K.M. (2020) Creating Maps. In: Introduction to R for Terrestrial Ecology. Springer, Cham https://link.springer.com/chapter/10.1007/978-3-030-27603-4_3 

  16. Wraith, J., Norman, P., & Pickering, C. (2020). Orchid conservation and research: An analysis of gaps and priorities for globally Red Listed species. Ambio. https://doi.org/10.1007/s13280-019-01306-7 

  17. Vincent, F., & Bowler, C. (2020). Diatoms Are Selective Segregators in Global Ocean Planktonic Communities. mSystems, 5(1). https://doi.org/10.1128/msystems.00444-19 

  18. Sawa, T., Momiyama, K., Mihara, T., Kainuma, A., Kinoshita, M., & Moriyama, K. (2020). Molecular epidemiology of clinically high‐risk Pseudomonas aeruginosa strains: Practical overview. Microbiology and Immunology. https://doi.org/10.1111/1348-0421.12776 

  19. Yuan, M. L., Jung, C., Wake, M. H., & Wang, I. J. (2020). Habitat use, interspecific competition and phylogenetic history shape the evolution of claw and toepad morphology in Lesser Antillean anoles. Biological Journal of the Linnean Society, 129(3), 630–643. https://doi.org/10.1093/biolinnean/blz203 

  20. Gilbertson, M. L. J., White, L. A., & Craft, M. E. (2020). Trade‐offs with telemetry‐derived contact networks for infectious disease studies in wildlife. Methods in Ecology and Evolution. https://doi.org/10.1111/2041-210x.13355 

  21. Bachman, S., Walker, B., Barrios, S., Copeland, A., & Moat, J. (2020). Rapid Least Concern: towards automating Red List assessments. Biodiversity Data Journal, 8. https://doi.org/10.3897/bdj.8.e47018