rOpenSci HQ


Software 📦

CRAN: GitHub:

New packages

  • A new version (v1.0.1) of nasapower is on CRAN - NASA POWER API client. Checkout the docs to get started.

New versions

  • A new version (v0.8.0) of bold is on CRAN - interface to Bold Systems (http://www.boldsystems.org/) API. See the release notes for changes. Checkout the vignette to get started.

    bold_identify_parents() improvements, and bold_specimens() bug fix

  • A new version (v6.1.0) of drake is on CRAN - pipeline toolkit for reproducible computation at scale. See the release notes for changes. Checkout the docs to get started.

    new fxns map_plan()/plan_to_code()/drake_debug(); many improvements and bug fixes

  • A new version (v0.7.0) of rbison is on CRAN - interface to the USGS BISON API. See the release notes for changes. Checkout the vignette to get started.

    bison() now paginates internally and loses what parameter; bisonmap() fix

  • A new version (v0.4.0) of microdemic is on CRAN - Microsoft Academic API client. See the release notes for changes. Checkout the README to get started.

    tests now use vcr; ma_abstract() now a data.frame

  • A new version (v0.15.4) of DataPackageR is on CRAN - construct reproducible analytic data sets as R packages. Checkout the vignette to get started.
  • A new version (v2.0-3) of CoordinateCleaner is on CRAN - automated cleaning of occurrence records from biological collections. See the NEWS for changes. Checkout the docs to get started.
  • A new version (v0.3.0) of isdparser is on CRAN - parse NOAA Integrated Surface data files. See the release notes for changes. Checkout the vignette to get started.

    small bug fix; working on incorporating metadata

  • A new version (v1.1.0) of jqr is on CRAN - a client for JQ, the JSON processor. See the release notes for changes. Checkout the vignette to get started.

    jq() now supports connections (file paths, urls) and json objects; new build_ fxns

  • A new version (v0.0.8) of osmdata is on CRAN - import OpenStreetMap data as simple features or spatial objects. See the release notes for changes. Checkout the docs to get started.

    bug fixes in trim_osmdata and opq

  • A new version (v0.2.2) of bikedata is on CRAN - download and aggregate data from public hire bicycle systems. See the release notes for changes. Checkout the docs to get started.

    minor bug fixes

  • A new version (v0.5.0) of epubr is on CRAN - read EPUB file metadata and text. See the release notes for changes. Checkout the vignette to get started.

    new fxn epub_cat(); epub() gains encoding param

  • A new version (v0.2.6) of stplanr is on CRAN - sustainable transport planning. See the release notes for changes. Checkout the docs to get started.

    new fxn route_local(); line2route() gains time_sleep param

  • A new version (v1.1.0) 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.

    new fxns cache_file_info() & as.ft_data(); better error info in ft_get(); many, many, many bug fixes and improvements

  • A new version (v1.1.0) 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.

    now using vcr for tests; name issues metadata added; map_fetch() changes

  • A new version (v0.2.8) of webmockr is on CRAN - stubbing and setting expectations on HTTP requests. See the release notes for changes. Checkout the HTTP testing book to get started.

    gains support for httr!

  • A new version (v0.2.0) 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.

    gains support for httr!

  • A new version (v0.3.0) of wikitaxa is on CRAN - taxonomic information from Wikipedia. See the release notes for changes. Checkout the docs to get started.

    now using vcr for tests; wt_wikipedia() bug fix

  • A new version (v0.3.0) of charlatan is on CRAN - make fake data. See the release notes for changes. Checkout the vignette to get started.

    ch_job()/JobsProvider gain da_DK locale support; many fixes for JobsProvider/PersonProvider

  • A new version (v0.3.4) of jstor is on CRAN - read data from JSTOR/DfR. See the release notes for changes. Checkout the docs to get started.

    parse references if available



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 packages were recently submitted:



On the blog

Technotes

Scott Chamberlain wrote about a new package pubchunks: pubchunks: extract parts of scholarly XML articles. Check out the package at ropensci/pubchunks.


rOpenSci HQ

Stefanie Butland writes about our next upcoming community call. Community Call - Working with images in R. Please join us for our next community call!



Use cases

The following 12 works use/cite rOpenSci software:



In the news

Two people played with one of our newest packages (av) and shared their experience:


In a blog post Animated Prison someone used av to help visualize the rate of incarceration over time in the US.


In a recent presentation rnoaa was cited: Improving pollution source resolution for real time low cost sensors using widely available data resources






Keep up with rOpenSci


Footnotes

  1. Baquero, O. S., & Machado, G. (2018). Spatiotemporal dynamics and risk factors for human Leptospirosis in Brazil. Scientific Reports, 8(1). https://doi.org/10.1038/s41598-018-33381-3 

  2. Rahman, R., Ung, P. M.-U., & Schlessinger, A. (2018). KinaMetrix: a web resource to investigate kinase conformations and inhibitor space. Nucleic Acids Research. https://doi.org/10.1093/nar/gky916 

  3. Vieilledent, G., Fischer, F. J., Chave, J., Guibal, D., Langbour, P., & Gérard, J. (2018). New formula and conversion factor to compute basic wood density of tree species using a global wood technology database. American Journal of Botany. https://doi.org/10.1002/ajb2.1175 

  4. McAfee, S. A., McCabe, G. J., Gray, S. T., & Pederson, G. T. (2018). Changing station coverage impacts temperature trends in the Upper Colorado River Basin. International Journal of Climatology. https://doi.org/10.1002/joc.5898 

  5. Shema, H., Mazarakis, A., Hahn, O., & Peters, I. Retractions from altmetric and bibliometric perspectives. http://altmetrics.org/wp-content/uploads/2018/09/altmetrics18_paper_3_Shema_new.pdf 

  6. Borer, D. (2018). Creating a Water Quality Geodatabase for the West Hawai ‘i Island Region (Doctoral dissertation, University of Southern California). https://spatial.usc.edu/wp-content/uploads/2018/10/72893.pdf 

  7. Testo, W. L., Sessa, E., & Barrington, D. S. (2018). The rise of the Andes promoted rapid diversification in Neotropical Phlegmariurus (Lycopodiaceae). New Phytologist. https://doi.org/10.1111/nph.15544 

  8. Horvatić, A., Guillemin, N., Kaab, H., McKeegan, D., O’Reilly, E., Bain, M., … Eckersall, P. D. (2018). Integrated dataset on acute phase protein response in chicken challenged with Escherichia coli lipopolysaccharide endotoxin. Data in Brief. https://doi.org/10.1016/j.dib.2018.09.103 

  9. 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 

  10. Hagerman, A. D., South, D. D., Sondgerath, T. C., Patyk, K. A., Sanson, R. L., Schumacher, R. S., … Magzamen, S. (2018). Temporal and geographic distribution of weather conditions favorable to airborne spread of foot-and-mouth disease in the coterminous United States. Preventive Veterinary Medicine, 161, 41–49. https://doi.org/10.1016/j.prevetmed.2018.10.016 

  11. Yu, G., Tsan-Yuk Lam, T., Zhu, H., & Guan, Y. (2018). Two methods for mapping and visualizing associated data on phylogeny using ggtree. Molecular Biology and Evolution. https://doi.org/10.1093/molbev/msy194 

  12. Degen, R., & Faulwetter, S. (2018). The Arctic Traits Database – A repository of arctic benthic invertebrate traits. Earth System Science Data Discussions, 1–25. https://doi.org/10.5194/essd-2018-97