rOpenSci HQ


Software 📦

CRAN: GitHub:

New versions

  • A new version (v0.2.1) of bikedata is on CRAN - extract data from public hire bicycle systems. See the NEWS for changes. Checkout the bikedata docs to get started.

    new fxn bike_cities()

  • A new version (v0.2.0) of cRegulome is on CRAN - access, manage and visualize regulome (microRNA/transcription factors)-gene correlations in cancer. See the NEWS for changes. Checkout the cRegulome vignettes to get started.
  • A new version (v0.2.5) of getCRUCLdata is on CRAN - use and explore CRU CL v. 2.0 climatology elements. See the release notes for changes. Checkout the getCRUCLdata docs to get started.

    remove startup message, reorg internal fxns

  • A new version (v0.4.0) of bomrang is on CRAN - Australian government Bureau of Meteorology (BOM) data. See the NEWS for changes. Checkout the bomrang docs to get started.

    bug fixes; many small changes

  • A new version (v0.0.3) of arkdb is on CRAN - archive and unarchive databases as flat text files. See the NEWS for changes. Checkout the arkdb docs to get started.

    remove dependency on utils::askYesNo

  • A new version (v1.4.0) of ijtiff is on CRAN - TIFF file I/O which plays nice with ImageJ. See the release notes for changes. Checkout the ijtiff docs to get started.

    better docs; better error messages

  • A new version (v0.1.9) of fingertipsR is on CRAN - Public Health England’s Fingertips data tool. See the NEWS for changes. Checkout the fingertipsR vignettes to get started.

    new fields in fingertips_data()

  • A new version (v1.1.1) of hydroscoper is on CRAN - Greek National Data Bank for Hydrometeorological Information. See the release notes for changes. Checkout the hydroscoper docs to get started.
  • A new version (v1.0.2) of essurvey is on CRAN - data from the European Social Survey. See the release notes for changes. Checkout the essurvey docs to get started.
  • A new version (v0.15.3) of DataPackageR is on CRAN - construct reproducible analytic data sets as R packages. See the NEWS for changes. Checkout the DataPackageR vignettes to get started.
  • A new version (v0.3.5) of tidyhydat is on CRAN - Water Survey of Canada hydrometric data. See the release notes for changes. Checkout the tidyhydat vignettes to get started.

    two new fxns; some output column names changed case; bug fixes



Software Review ✔

We accept community contributed packages via our onboarding 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.

The following package recently went through our onboarding process and has been approved!

The following package was recently submitted:



On the blog

Animal Movement series

We’re doing a series of posts corresponding to the material for a talk Maëlle gave at the Animal Movement Analysis summer school in Radolfzell, Germany on September 12th, at the Max Planck Institute of Ornithology. All five posts are out now:


Technotes

Scott Chamberlain wrote about one of our oldest packages: rgbif: seven years of GBIF in R


Maëlle Salmon had two technotes in the past month:



Use cases

The following 19 works use/cite rOpenSci software:



In the news

In a blog post Leaving the house - where preprints go Karthik Ram and Jennifer Lin sort out where preprints are published, using our rcrossref package.


At the recent R in Pharma conference Sebastian Wolfe of Roche talked about bioWARP, a large Shiny application for their employees - which uses RSelenium. He goes into detail in a recent blog post: https://zappingseb.github.io/biowarptruck/.


In a blog post Francesco Bailo showed how to enrich a map with details, leveraging our package osmdata: How to (quickly) enrich a map with natural and anthropic details


Megan Winton made a nice plot using our rerddap package:


Michele Tobias used rgbif:


Bob Rudis visualized hurricanes with our rrricanes package






Keep up with rOpenSci


Footnotes

  1. Sánchez-Hernández, J., & Amundsen, P.-A. (2018). Ecosystem type shapes trophic position and omnivory in fishes. Fish and Fisheries. https://doi.org/10.1111/faf.12308 

  2. Bharanidharan, R., Arokiyaraj, S., Kim, E. B., Lee, C. H., Woo, Y. W., Na, Y., … Kim, K. H. (2018). Ruminal methane emissions, metabolic, and microbial profile of Holstein steers fed forage and concentrate, separately or as a total mixed ration. PLOS ONE, 13(8), e0202446. https://doi.org/10.1371/journal.pone.0202446 

  3. Martín-Martín, A., Orduna-Malea, E., Thelwall, M., & López-Cózar, E. D. (2018). Google Scholar, Web of Science, and Scopus: a systematic comparison of citations in 252 subject categories. arXiv preprint arXiv:1808.05053 https://arxiv.org/abs/1808.05053 

  4. Grenié, M., Mouillot, D., Villéger, S., Denelle, P., Tucker, C. M., Munoz, F., & Violle, C. (2018). Functional rarity of coral reef fishes at the global scale: Hotspots and challenges for conservation. Biological Conservation, 226, 288–299. https://doi.org/10.1016/j.biocon.2018.08.011 

  5. Magoga, G., Sahin, D. C., Fontaneto, D., & Montagna, M. (2018). Barcoding of Chrysomelidae of Euro-Mediterranean area: efficiency and problematic species. Scientific Reports, 8(1). https://doi.org/10.1038/s41598-018-31545-9 

  6. Catalano, J. (2018). Digitally Analyzing the Uneven Ground: Language Borrowing Among Indian Treaties. Current Research in Digital History, 1. https://doi.org/10.31835/crdh.2018.02 

  7. Rakitko, A. COITR​—​ novel algorithm for predicting child’s externally visible traits. https://www.researchgate.net/profile/Alexander_Rakitko/publication/327136498_Title_COITR_-_novel_algorithm_for_predicting_child%27s_externally_visible_traits/links/5b7bcd70a6fdcc5f8b585910/Title-COITR-novel-algorithm-for-predicting-childs-externally-visible-traits.pdf 

  8. Cano, J., Rodríguez, A., Simpson, H., Tabah, E. N., Gómez, J. F., & Pullan, R. L. (2018). Modelling the spatial distribution of aquatic insects (Order Hemiptera) potentially involved in the transmission of Mycobacterium ulcerans in Africa. Parasites & Vectors, 11(1). http://doi.org/10.1186/s13071-018-3066-3 

  9. Otten, C., Knox, J., Boulday, G., Eymery, M., Haniszewski, M., Neuenschwander, M., … Abdelilah‐Seyfried, S. (2018). Systematic pharmacological screens uncover novel pathways involved in cerebral cavernous malformations. EMBO Molecular Medicine, e9155. https://doi.org/10.15252/emmm.201809155 

  10. Liu, C. H., Nowak, A. D., & Smith, P. S. (2018). Asymmetric or Incomplete Information about Asset Values?. http://fmaconferences.org/SanDiego/Papers/LNS_Some_Remarks_Info_Asymmetry_FMA.pdf 

  11. Boria, R. A., & Blois, J. L. (2018). The effect of large sample sizes on ecological niche models: Analysis using a North American rodent, Peromyscus maniculatus. Ecological Modelling, 386, 83–88. https://doi.org/10.1016/j.ecolmodel.2018.08.013 

  12. Albert, S., Flores, O., Rouget, M., Wilding, N., & Strasberg, D. (2018). Why are woody plants fleshy-fruited at low elevations? Evidence from a high-elevation oceanic island. Journal of Vegetation Science. https://doi.org/10.1111/jvs.12676 

  13. Lusseau, D., & Mancini, F. (2018). A global assessment of tourism and recreation conservation threats to prioritise interventions. arXiv preprint https://arxiv.org/abs/1808.08399 

  14. Lusseau, D., & Mancini, F. (2018). A global assessment of tourism and recreation conservation threats to prioritise interventions. arXiv preprint https://arxiv.org/abs/1808.08399 

  15. Abdala-Roberts, L., Galmán, A., Petry, W. K., Covelo, F., de la Fuente, M., Glauser, G., & Moreira, X. (2018). Interspecific variation in leaf functional and defensive traits in oak species and its underlying climatic drivers. PLOS ONE, 13(8), e0202548. https://doi.org/10.1371/journal.pone.0202548 

  16. Barneche, D. R., Burgess, S. C., & Marshall, D. J. (2018). Global environmental drivers of marine fish egg size. Global Ecology and Biogeography, 27(8), 890–898. https://doi.org/10.1111/geb.12748 

  17. Tierney, N. J., & Cook, D. H. (2018). Expanding tidy data principles to facilitate missing data exploration, visualization and assessment of imputations. arXiv preprint arXiv:1809.02264. https://arxiv.org/abs/1809.02264 

  18. Dezordi, M. L., Hölbig, C. A., Pavan, W., & Fernandes, J. M. C. An R package to access climate change data for South America regionalized by the Eta Model of CPTEC/INPE. https://www.researchgate.net/profile/Carlos_Holbig/publication/327078798_An_R_package_to_access_climate_change_data_for_South_America_regionalized_by_the_Eta_Model_of_CPTECINPE/links/5b770844299bf1d5a70e95ba/An-R-package-to-access-climate-change-data-for-South-America-regionalized-by-the-Eta-Model-of-CPTEC-INPE.pdf 

  19. Yángüez, E., Hunziker, A., Dobay, M. P., Yildiz, S., Schading, S., Elshina, E., … Stertz, S. (2018). Phosphoproteomic-based kinase profiling early in influenza virus infection identifies GRK2 as antiviral drug target. Nature Communications, 9(1). https://doi.org/10.1038/s41467-018-06119-y