Software 📦

CRAN: GitHub:

New Versions

  • A new version (v0.9.0) 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.

    geojson_sf()/geojson_sp() now accept strings; replace httr with crul & rgdal replaced with sf

  • A new version (v0.4.0) of geojsonlint is on CRAN - Tools for Validating GeoJSON. See the release notes for changes. Checkout the docs to get started.

    geojson_lint() defunct - the geojsonlint.com API is down

  • A new version (v2.1.0) 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.

    occ_download() bug fix for within predicates for geometry queries; occ_spellcheck() now defunct

  • A new version (v4.9.2) 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.

    upgrade plotly.js to v1.52.2

  • A new version (v0.9.92) of taxize is on CRAN - taxonomic toolbelt for R. See the release notes for changes. Checkout the taxize book to get started.

    all Catalogue of Life functions removed (get in touch if you need help); new fxn gn_parse() for Global Names name parser

  • A new version (v1.0.8) 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.
  • A new version (v1.1.1) of lingtypology is on CRAN - linguistic typology and mapping. See the release notes for changes. Checkout the docs to get started.

    update glottolog from v2.7 to v4.1; some fxns removed

  • A new version (v0.3.0) of scrubr is on CRAN - clean biological occurrence records. See the release notes for changes. Checkout the docs to get started.

    new fxn fix_names(); new fxn eco_region to filter data by ecoregions; new fxns coord_imprecise()/coord_uncertain() to clean coordinates

  • A new version (v1.0.2) 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.

    bug fix for fingertips_data()

  • A new version (v0.1.3) 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.

    osmdata_pbf() function removed; remove deprecated add_feature() - replaced by add_osm_feature()

  • A new version (v2.0.2) of EML is on CRAN - read and write ecological metadata language files. See the release notes for changes. Checkout the docs to get started.
  • A new version (v0.4.1) of nlrx is on CRAN - setup, run and analyze NetLogo model simulations. See the release notes for changes. Checkout the vignettes to get started.
  • A new version (v0.2.0.8) of opentripplanner is on CRAN - client for OpenTripPlanner for journey planning. See the release notes for changes. Checkout the docs to get started.
  • A new version (v0.6.4) of rorcid is on CRAN - Interface to the Orcid.org API. See the release notes for changes. Checkout the vignette to get started.

    recursive parameter removed from orcid(); orcid_search() loses some parameters; orcid() gains additional fields to query, e.g., peer-review-type

  • A new version (v2.7) of assertr is on CRAN - Assertive Programming for R Analysis Pipelines. See the release notes for changes. Checkout the vignette to get started.

    added “inverse” option to predicates

  • A new version (v0.4.0) of emld is on CRAN - ecological metadata as linked data. See the release notes for changes. Checkout the vignette to get started.

    fixed serialization bug in references attribute; fixed validation bugs

  • A new version (v0.3.3) of weathercan is on CRAN - Download weather data from the Environment and Climate Change Canada website. See the release notes for changes. Checkout the docs to get started.

    update internal datasets

  • A new version (v1.7.7) of RSelenium is on CRAN - R client for Selenium Remote WebDriver. See the release notes for changes. Checkout the docs to get started.

    re-submission to CRAN after archiving



Software Review ✔

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.

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Use Cases

The following 13 works use/cite rOpenSci software:



From the Forum

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Two use cases have been 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 six 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.






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Footnotes

  1. Næss, M. W. (2019). From hunter-gatherers to nomadic pastoralists: forager bands do not tell the whole story of the evolution of human cooperation. https://doi.org/10.31235/osf.io/9c8bm 

  2. Wang, S., He, Z., Wang, X., Li, H., & Liu, X.-S. (2019). Antigen presentation and tumor immunogenicity in cancer immunotherapy response prediction. eLife, 8. https://doi.org/10.7554/elife.49020 

  3. Thorson, J. T. (2019). Predicting recruitment density dependence and intrinsic growth rate for all fishes worldwide using a data‐integrated life‐history model. Fish and Fisheries. <https://doi.org/10.1111/faf.12427 

  4. Geary, W. L., Doherty, T. S., Nimmo, D. G., Tulloch, A. I. T., & Ritchie, E. G. (2020). Predator responses to fire: A global systematic review and meta‐analysis. Journal of Animal Ecology. https://doi.org/10.1111/1365-2656.13153 

  5. Hong, T., Xu, Y., Sun, K., Zhang, W., & Luo, X. (2019). Visualizing Urban Microclimate and Quantifying its Impact on Building Energy Use in San Francisco. Proceedings of the 1st ACM International Workshop on Urban Building Energy Sensing, Controls, Big Data Analysis, and Visualization - UrbSys’19. https://doi.org/10.1145/3363459.3363536 

  6. Lange, H., Ndecky, S. Y. A., Gomez-Diaz, C., Pflieger, D., Butel, N., Zumsteg, J., … Gagliardi, D. (2019). RST1 and RIPR connect the cytosolic RNA exosome to the Ski complex in Arabidopsis. Nature Communications, 10(1). https://doi.org/10.1038/s41467-019-11807-4 

  7. Báez, J. C., Barbosa, A. M., Pascual, P., Ramos, M. L., & Abascal, F. (2019). Ensemble modeling of the potential distribution of the whale shark in the Atlantic Ocean. Ecology and Evolution, 10(1), 175–184. https://doi.org/10.1002/ece3.5884 

  8. Estrada-Peña, A., Nava, S., Tarragona, E., Bermúdez, S., de la Fuente, J., Domingos, A., … Guglielmone, A. A. (2019). Species occurrence of ticks in South America, and interactions with biotic and abiotic traits. Scientific Data, 6(1). https://doi.org/10.1038/s41597-019-0314-0 

  9. Lecocq, T., Benard, A., Pasquet, A., Nahon, S., Ducret, A., Dupont-Marin, K., … Thomas, M. (2019). TOFF, a database of traits of fish to promote advances in fish aquaculture. Scientific Data, 6(1). https://doi.org/10.1038/s41597-019-0307-z 

  10. Reis, V. S. (2019). Uma perspectiva macroecológica sobre o risco de extinção em mamíferos. Thesis. http://bit.ly/38mfmHG 

  11. Yagli, G. M., Yang, D., Gandhi, O., & Srinivasan, D. (2019). Can we justify producing univariate machine-learning forecasts with satellite-derived solar irradiance? Applied Energy, 114122. https://doi.org/10.1016/j.apenergy.2019.114122 

  12. Li, Y., Ge, D., & Lu, C. (2019). The SMART App: an interactive web application for comprehensive DNA methylation analysis and visualization. Epigenetics & Chromatin, 12(1). https://doi.org/10.1186/s13072-019-0316-3 

  13. Fu, D. Y., & Hughey, J. J. (2019). Releasing a preprint is associated with more attention and citations for the peer-reviewed article. eLife, 8. https://doi.org/10.7554/elife.52646