rOpenSci HQ


Software 📦

CRAN: GitHub:

New packages

  • The first version (v1.1-1) of suppdata is on CRAN - downloading supplementary data from published manuscripts. Checkout the vignette to get started.
  • The first version (v0.1.0) of conditionz is on CRAN - control how many times conditions are thrown. Checkout the README to get started.

New Versions

  • A new version (v0.2.19) of rglobi is on CRAN - R Interface to Global Biotic Interactions. See the release notes for changes. Checkout the vignette to get started.

    show informative messages when internet not up

  • A new version (v0.3.0) of finch is on CRAN - parse Darwin Core files. See the release notes for changes. Checkout the README to get started.

    fix to unit tests for new EML version

  • A new version (v0.7.0) 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.

    geo2topo/topojson_write fxns gain new parameter quantization; fixes related to sf package

  • A new version (v0.1.0) 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.

    new fxn osm_elevation; new vignette

  • A new version (v2.0-11) of CoordinateCleaner is on CRAN - automated cleaning of occurrence records from biological collections. See the release notes for changes. Checkout the docs to get started.

    changes to the description file

  • A new version (v2.0.0) 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 ground-up rewrite of EML; primary difference is it’s now built on S3 instead of S4; most high level functions are preserved

  • A new version (v0.1.8) of codemetar is on CRAN - Generate codemeta metadata for R packages. See the release notes for changes. Checkout the docs to get started.

    address internet timeout issue

  • A new version (v2.5.7) of FedData is on CRAN - get geospatial data from several federated government data sources. See the release notes for changes. Checkout the README to get started.

    skip tests on CRAN that require internet

  • A new version (v0.2.1) of smapr is on CRAN - acquisition and processing of NASA Soil Moisture Active-Passive (SMAP) data. See the release notes for changes. Checkout the docs to get started.

    skip tests on CRAN that require internet; updated SMAP data versions

  • A new version (v0.2) 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 (v7.2.0) of drake is on CRAN - a pipeline toolkit for reproducible computation at scale. See the release notes for changes. Checkout the docs to get started.

    many changes, see release notes

  • A new version (v1.1.1) of nasapower is on CRAN - NASA POWER API Client. See the release notes for changes. Checkout the docs to get started.

    fixes for tests; fixes for NA’s and a documentation fix



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 was recently submitted:



On the blog

Main blog

Stefanie Butland, Nick Golding, Chris Grieves, Hugo Gruson, Thomas White and Hao Ye wrote a post jointly published on our blog as well as the Methods in Ecology and Evolution blog: When Standards Go Wild - Software Review for a Manuscript.

Tech notes

Jeroen Ooms wrote about an update to the pdftools package: Join, split, and compress PDF files with pdftools.

Scott Chamberlain wrote about a new package called conditionz: conditionz: control how many times conditions are thrown.



Use Cases

The following 11 works use/cite rOpenSci software:



In The News

Tuija Sonkkila wrote about working with altmetrics data in her post Everyday altmetrics, and used our package crevents to get Crossref Event data for a Shiny app. Source code: https://github.com/tts/aaltoced/blob/master/getdata.R



Call For Contributors

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. 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.








Keep up with rOpenSci


Footnotes

  1. Chakroborty, D., Kurppa, K. J., Paatero, I., Ojala, V. K., Koivu, M., Tamirat, M. Z., … & Elenius, K. (2019). An unbiased in vitro screen for activating epidermal growth factor receptor mutations. Journal of Biological Chemistry, jbc-RA118. http://www.jbc.org/content/early/2019/04/05/jbc.RA118.006336 

  2. van Zonneveld, Mohamed Rakha, Shin-yee Tan, Yu-yu Chou, Ching-huan Chang, Joyce Yen, Roland Schafleitner, Ramakrishnan Nair, Ken Naito, Svein Ø. Solberg. Understanding patterns of abiotic and biotic stress resilience to unleash the potential of crop wild relatives for climate-smart legume breeding. bioRxiv 596072; doi: https://doi.org/10.1101/596072 

  3. Axtner, J., Crampton-Platt, A., Hörig, L. A., Mohamed, A., Xu, C. C. Y., Yu, D. W., & Wilting, A. (2019). An efficient and robust laboratory workflow and tetrapod database for larger scale environmental DNA studies. GigaScience, 8(4). https://doi.org/10.1093/gigascience/giz029 

  4. Blakey, R. V., Webb, E. B., Kesler, D. C., Siegel, R. B., Corcoran, D., & Johnson, M. (2019). Bats in a changing landscape: Linking occupancy and traits of a diverse montane bat community to fire regime. Ecology and Evolution. https://doi.org/10.1002/ece3.5121 

  5. Miranda, L. S., Imperatriz-Fonseca, V. L., & Giannini, T. C. (2019). Climate change impact on ecosystem functions provided by birds in southeastern Amazonia. PLOS ONE, 14(4), e0215229. https://doi.org/10.1371/journal.pone.0215229 

  6. Rodrigues, S., Sinval, J., Queirós, C., Marôco, J., & Kaiseler, M. (2019). Transitioning from recruit to officer: An investigation of how stress appraisal and coping influence work engagement. International Journal of Selection and Assessment. https://doi.org/10.1111/ijsa.12238 

  7. Sanger, W., & Warin, T. (2019). Dataset of Jaccard similarity indices from 1,597 European political manifestos across 27 countries (1945–2017). Data in Brief, 103907. https://doi.org/10.1016/j.dib.2019.103907 

  8. Van de Perre, F., Leirs, H., & Verheyen, E. (2019). Paleoclimate, ecoregion size, and degree of isolation explain regional biodiversity differences among terrestrial vertebrates within the Congo Basin. Belgian Journal of Zoology, 149(1). https://doi.org/10.26496/bjz.2019.28 

  9. Chileen, B. (2019). Vegetation response to wildfire and climate forcing in a Rocky Mountain lodgepole pine forest over the past 2,500 years. Thesis. https://krex.k-state.edu/dspace/bitstream/handle/2097/39566/BarrieChileen2019.pdf?sequence=1 

  10. Medury, A., Griswold, J. B., Huang, L., & Grembek, O. (2019). Pedestrian Count Expansion Methods: Bridging the Gap between Land Use Groups and Empirical Clusters. Transportation Research Record: Journal of the Transportation Research Board, 036119811983826. https://doi.org/10.1177/0361198119838266 

  11. Conde, D. A., Staerk, J., Colchero, F., da Silva, R., Schöley, J., Baden, H. M., … Vaupel, J. W. (2019). Data gaps and opportunities for comparative and conservation biology. Proceedings of the National Academy of Sciences, 201816367. https://doi.org/10.1073/pnas.1816367116