rOpenSci HQ


Software 📦

CRAN: GitHub:

New packages

  • The first version (v1.0.0) of restez is on CRAN - create and query a local copy of GenBank. Checkout the docs to get started. You can find the software review at ropensci/onboarding#232
  • The first version (v1.0.0) of rcites is on CRAN - access the CITES Speciesplus database. See the release notes for changes. Checkout the docs to get started. You can find the software review at ropensci/onboarding#244

New versions

  • Two new versions (v0.2.0/v0.2.1) of rdflib are on CRAN - High level wrapper around the redland rdf package. See the release notes for changes. Checkout the docs to get started.

    rdf() now supports all major storage backends; new fxn length()

  • A new version (v0.3.5) of jstor is on CRAN - read data from JSTOR/DfR. See the release notes for changes. Checkout the docs to get started.

    readr compatibility fix; column names in jst_get_refernces have been renamed to avoid ambiguity when matching with output from jst_get_article

  • A new version (v1.3.0) of GSODR is on CRAN - Global Surface Summary of the Day (GSOD) Weather Data from R. See the release notes for changes. Checkout the docs to get started.

    use future_apply in processing files after downloading

  • A new version (v0.2.1) of tiler is on CRAN - Generate geographic and non-geographic map tiles from R. See the release notes for changes. Checkout the docs to get started.

    improved help for Windows users; added leaflet examples; bug fix for Windows users

  • A new version (v0.4) of NLMR is on CRAN - Simulating neutral landscape models. See the release notes for changes. Checkout the docs to get started.

    nlm_neigh, nlm_mpd, nlm_randomrectangularcluster now implemented in Rcpp

  • A new version (v0.9.0) 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.

    AntWeb data source removed; fixes to eBird internals; occ() now collects HTTP request error info & gains throw_warnings param to control warnings

  • A new version (v1.19.1) of rtika is on CRAN - R Interface to Apache Tika. See the release notes for changes. Checkout the docs to get started.

    updated Tika version

  • A new version (v0.2.0) of fingertipsR is on CRAN - Fingertips data for public health http://fingertips.phe.org.uk/. See the release notes for changes. Checkout the vignettes to get started.

    fix for select_indicators(); speed ups for indicators() fxn



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 recently went through our onboarding process and have been approved!

The following package was recently submitted:



On the blog

Ben Raymond and Michael Sumner wrote about The Antarctic/Southern Ocean rOpenSci community. Do check it out to see what’s going on in this flourishing community within rOpenSci of folks interested in Antarctic/Southern Ocean data and software.


Peter Desmet, Damiano Oldoni, and Lien Reyserhove wrote about Checklist Recipe - How we created a template to standardize species data. Their work won the recent GBIF Ebbe Nielsen Challenge. It’s a great example of leveraging R to create reproducible workflows!



Use cases

The following 16 works use/cite rOpenSci software:



In the news

Dean Marchiori used our package bomrang (from maintainer Adam Sparks) to create an automated surf conditions email Surf Check - Automating Weather Forecast Emails in R


Simon Coulombe used our package weathercan (from maintainer Steffi LaZerte) in his blog post about Buying a heat pump the data scientist way






Keep up with rOpenSci


Footnotes

  1. Tickler, D., Meeuwig, J. J., Bryant, K., David, F., Forrest, J. A. H., Gordon, E., … Zeller, D. (2018). Modern slavery and the race to fish. Nature Communications, 9(1). https://doi.org/10.1038/s41467-018-07118-9 

  2. Lynd, A., Oruni, A., van’t Hof, A. E., Morgan, J. C., Naego, L. B., Pipini, D., … Weetman, D. (2018). Insecticide resistance in Anopheles gambiae from the northern Democratic Republic of Congo, with extreme knockdown resistance (kdr) mutation frequencies revealed by a new diagnostic assay. Malaria Journal, 17(1). https://doi.org/10.1186/s12936-018-2561-5 

  3. Robitaille, A. L., Webber, Q. M. R., & Vander Wal, E. (2018). Conducting social network analysis with animal telemetry data: applications and methods using spatsoc. https://doi.org/10.1101/447284 

  4. Moura, M. M., dos Santos, A. R., Pezzopane, J. E. M., Alexandre, R. S., da Silva, S. F., Pimentel, S. M., … de Carvalho, J. R. (2019). Relation of El Niño and La Niña phenomena to precipitation, evapotranspiration and temperature in the Amazon basin. Science of The Total Environment, 651, 1639–1651. https://doi.org/10.1016/j.scitotenv.2018.09.242 

  5. Bartomeus, I., Stavert, J. R., Ward, D., & Aguado, O. (2018). Historical collections as a tool for assessing the global pollination crisis. Philosophical Transactions of the Royal Society B: Biological Sciences, 374(1763), 20170389. https://doi.org/10.1098/rstb.2017.0389 

  6. Jarić, I., Lennox, R. J., Kalinkat, G., Cvijanović, G., & Radinger, J. (2018). Susceptibility of European freshwater fish to climate change: species profiling based on life-history and environmental characteristics. Global Change Biology. https://doi.org/10.1111/gcb.14518 

  7. Weishäupl, D., Schneider, J., Peixoto Pinheiro, B., Ruess, C., Dold, S. M., von Zweydorf, F., … Schmidt, T. (2018). Physiological and pathophysiological characteristics of ataxin-3 isoforms. Journal of Biological Chemistry, jbc.RA118.005801. https://doi.org/10.1074/jbc.ra118.005801 

  8. Perez, T. M., Valverde-Barrantes, O., Bravo, C., Taylor, T. C., Fadrique, B., Hogan, J. A., … Feeley, K. J. (2018). Botanic gardens are an untapped resource for studying the functional ecology of tropical plants. Philosophical Transactions of the Royal Society B: Biological Sciences, 374(1763), 20170390. https://doi.org/10.1098/rstb.2017.0390 

  9. Albrecht, U.-V., Hasenfuß, G., & von Jan, U. (2018). Description of Cardiological Apps From the German App Store: Semiautomated Retrospective App Store Analysis. JMIR mHealth and uHealth, 6(11), e11753. https://doi.org/10.2196/11753 

  10. Patel, D. 2018. Sentiment Analysis of Harry Potter Book Series using R. http://www.j-asc.com/gallery/66-november-1233.pdf 

  11. Varela, S. (2018). Applications of remote sensing in agriculture via unmanned aerial systems and satellites (Doctoral dissertation). http://krex.k-state.edu/dspace/bitstream/handle/2097/39333/SebastianVarela2018.pdf 

  12. Garmendia, A., Beltrán, R., Zornoza, C., Breijo, F., Reig, J., Bayona, I., & Merle, H. (2019). Insect repellent and chemical agronomic treatments to reduce seed number in “Afourer” mandarin. Effect on yield and fruit diameter. Scientia Horticulturae, 246, 437–447. https://doi.org/10.1016/j.scienta.2018.11.025 

  13. Watts, A. W., & Miksis-Olds, J. 2018. The Ocean as a Living Sensor: Environmental DNA and Acoustics for Detecting Marine Life. https://phe.rockefeller.edu/eDNAmarine2018/papers/Watts-Miksis-Olds_paper_Ocean_as_a_Living_Sensor.pdf 

  14. Hurtado, L., Rigg, C., Calzada, J., Dutary, S., Bernal, D., Koo, S., & Chaves, L. (2018). Population Dynamics of Anopheles albimanus (Diptera: Culicidae) at Ipetí-Guna, a Village in a Region Targeted for Malaria Elimination in Panamá. Insects, 9(4), 164. https://doi.org/10.3390/insects9040164 

  15. Pietrosemoli, N., & Dobay, M. P. (2018). Optimized Protein–Protein Interaction Network Usage with Context Filtering. In Computational Cell Biology (pp. 33-50). Humana Press, New York, NY. https://link.springer.com/protocol/10.1007/978-1-4939-8618-7_2 

  16. Boettiger, C. (2018). Managing Larger Data on a GitHub Repository. Journal of Open Source Software, 3(29), 971. https://doi.org/10.21105/joss.00971