rOpenSci HQ


Software 📦

CRAN: GitHub:

New Versions

  • A new version (v7.5.2) 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.

    remove accidental creation of a dot file

  • A new version (v0.6.4/v0.6.5) of rerddap is on CRAN - General Purpose Client for ERDDAP Servers. See the release notes for changes. Checkout the vignettes to get started.

    fix internal http request error handler; fix a test

  • A new version (v1.0.4) of available is on CRAN - check if the title of a package is available. See the release notes for changes. Checkout the README to get started.

    tests requiring network access are not skipped on CRAN

  • A new version (v1.2) of cld3 is on CRAN - Bindings to Google’s Compact Language Detector 3. See the release notes for changes. Checkout the docs to get started.

    update to protobuf 3.8 for windows; suppress warnings about pragmas in autogen protobuf headers

  • A new version (v0.2.7) 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.

    add option AreaTypeId="All in fingertips_data(); added param to area_types(); change to category_types(); add http request retry

  • A new version (v0.2.0) of vitae is on CRAN - R Markdown Resumes and CVs. See the release notes for changes. Checkout the docs to get started.

    theme support for moderncv; other template changes; breaking change to bibliography_entries

  • A new version (v2.0.2) of ijtiff is on CRAN - Comprehensive TIFF I/O with full support for ImageJ TIFF files. See the release notes for changes. Checkout the docs to get started.

    bug fixes

  • A new version (v0.6.0) of bomrang is on CRAN - Australian government Bureau of Meteorology (BOM) data. See the release notes for changes. Checkout the docs to get started.

    many bug fixes

  • A new version (v0.26.1) of git2r is on CRAN - an interface to the libgit2 library, a pure C implementation of the Git core methods. See the release notes for changes. Checkout the README to get started.

    fixed the broken build on Solaris on CRAN

  • A new version (v0.4.2) of traits is on CRAN - species trait data from around the web. See the release notes for changes. Checkout the README to get started.

    minor betydb change; taxa_search() breaking change (Traitbank service completely changed)

  • A new version (v0.8.0) of crul is on CRAN - an R6 based HTTP client for R made for developers. See the release notes for changes. Checkout the docs to get started.

    can now pass params through parse() to iconv(); use httpcode pkg instead of fauxpas inside ok()

  • A new version (v0.2.0) of grainchanger is on CRAN - Data aggregation methods for raster data. See the release notes for changes. Checkout the docs to get started.
  • A new version (v0.9.8) of taxize is on CRAN - taxonomic toolbelt for R. See the release notes for changes. Checkout the taxize book to get started.

    new fxn taxize_options; all get_* fxns gain ability to track progress and restart in case of interruption - & prettier progress and summary info; bug fixes

  • A new version (v0.4.0) of worrms is on CRAN - client for World Register of Marine Species. See the release notes for changes. Checkout the vignette to get started.

    new fxns wm_ranks_id()/wm_ranks_name() for getting taxonomic ranks by rank identifier or rank name; new fxn wm_records_rank() for getting AphiaRecords for a given rank id

  • A new version (v0.9.0) 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.

    allow curl options to be passed into bold_identify_parents(); bug fix in bold_identify()

  • A new version (v1.3.0) 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.

    ft_get() gains new data source: ScienceDirect; ft_get() performance improvements; curl options can now be passed through nearly all fxns

  • A new version (v3.0.4) of rfishbase is on CRAN - interface to Fishbase data. See the release notes for changes. Checkout the docs to get started.

    use latest data version

  • A new version (v1.1.0) of jsonvalidate is on CRAN - Validate JSON. See the release notes for changes. Checkout the docs to get started.



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.

The following two packages recently went through our software-review process and have been approved:



On the blog

Stefanie Butland wrote about folks talking about rOpenSci projects at useR in Toulouse, France. The conference already happened; slides are linked from the talk schedule page, and video of talks may be up later.


Laura Graham wrote about her R package that recently went through software review Aggregating spatial data with the grainchanger package. grainchanger facilitates spatial data aggregation.



Use Cases

The following 20 works use/cite rOpenSci software:



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. 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.





Keep up with rOpenSci


Footnotes

  1. Steidinger, B. S., Crowther, T. W., Liang, J., Van Nuland, M. E., Werner, G. D. A., … Peay, K. G. (2019). Climatic controls of decomposition drive the global biogeography of forest-tree symbioses. Nature, 569(7756), 404–408. https://doi.org/10.1038/s41586-019-1128-0 ↩

  2. Mitchell, J. M. (2019). Computational Tools for the Untargeted Assignment of FT-MS Metabolomics Datasets. Dissertation. https://uknowledge.uky.edu/cgi/viewcontent.cgi?article=1042&context=biochem_etds ↩

  3. Bagley, M., Pilgrim, E., Knapp, M., Yoder, C., Santo Domingo, J., & Banerji, A. (2019). High-throughput environmental DNA analysis informs a biological assessment of an urban stream. Ecological Indicators, 104, 378–389. https://doi.org/10.1016/j.ecolind.2019.04.088 ↩

  4. Foisy, M. R., Albert, L. P., Hughes, D. W. W., & Weber, M. G. (2019). Do latex and resin canals spur plant diversification? Re‐examining a classic example of escape and radiate coevolution. Journal of Ecology. https://doi.org/10.1111/1365-2745.13203 ↩

  5. Ogłuszka, M., Orzechowska, M., Jędroszka, D., Witas, P., & Bednarek, A. K. (2019). Evaluate Cutpoints: Adaptable continuous data distribution system for determining survival in Kaplan-Meier estimator. Computer Methods and Programs in Biomedicine, 177, 133–139. https://doi.org/10.1016/j.cmpb.2019.05.023 ↩

  6. Westmeijer, G., Everaert, G., Pirlet, H., De Clerck, O., & Vandegehuchte, M. B. (2019). Mechanistic niche modelling to identify favorable growth sites of temperate macroalgae. Algal Research, 41, 101529. https://doi.org/10.1016/j.algal.2019.101529 ↩

  7. Kortz, A. R., & Magurran, A. E. (2019). Increases in local richness (α-diversity) following invasion are offset by biotic homogenization in a biodiversity hotspot. Biology Letters, 15(5), 20190133. https://doi.org/10.1098/rsbl.2019.0133 ↩

  8. Pérez-Palma, E., Gramm, M., Nürnberg, P., May, P., & Lal, D. (2019). Simple ClinVar: an interactive web server to explore and retrieve gene and disease variants aggregated in ClinVar database. Nucleic Acids Research. https://doi.org/10.1093/nar/gkz411 ↩

  9. Green, E. P., Whitcomb, A., Kahumbura, C., Rosen, J. G., Goyal, S., Achieng, D., & Bellows, B. (2019). What is the best method of family planning for me?: a text mining analysis of messages between users and agents of a digital health service in Kenya. Gates Open Research, 3, 1475. https://doi.org/10.12688/gatesopenres.12999.1 ↩

  10. Mihalitsis, M., & Bellwood, D. R. (2019). Morphological and functional diversity of piscivorous fishes on coral reefs. Coral Reefs. https://doi.org/10.1007/s00338-019-01820-w ↩

  11. Kannenberg, S. A., Novick, K. A., Alexander, M. R., Maxwell, J. T., Moore, D. J. P., Phillips, R. P., & Anderegg, W. R. L. (2019). Linking drought legacy effects across scales: From leaves to tree rings to ecosystems. Global Change Biology. https://doi.org/10.1111/gcb.14710 ↩

  12. Aspillaga, E., Safi, K., Hereu, B., & Bartumeus, F. (2019). Modelling the three‐dimensional space use of aquatic animals combining topography and Eulerian telemetry data. Methods in Ecology and Evolution. https://doi.org/10.1111/2041-210x.13232 ↩

  13. Gibson, K. M., Nguyen, B. N., Neumann, L. M., Miller, M., Buss, P., Daniels, S., … Pukazhenthi, B. (2019). Gut microbiome differences between wild and captive black rhinoceros – implications for rhino health. Scientific Reports, 9(1). https://doi.org/10.1038/s41598-019-43875-3 ↩

  14. Sinval, J., Sirgy, M. J., Lee, D.-J., & Marôco, J. (2019). The Quality of Work Life Scale: Validity Evidence from Brazil and Portugal. Applied Research in Quality of Life. https://doi.org/10.1007/s11482-019-09730-3 ↩

  15. Iserman, M., Nalabandian, T., & Ireland, M. (2019, June). Dictionaries and Decision Trees for the 2019 CLPsych Shared Task. In Proceedings of the Sixth Workshop on Computational Linguistics and Clinical Psychology (pp. 188-194). https://www.aclweb.org/anthology/W19-3025 ↩

  16. Goodman, M. C., Hannah, S. M., & Ruttenberg, B. I. (2019). The relationship between geographic range extent, sea surface temperature and adult traits in coastal temperate fishes. Journal of Biogeography. https://doi.org/10.1111/jbi.13595 ↩

  17. Fioravanti, G., Piervitali, E., & Desiato, F. (2019). A new homogenized daily data set for temperature variability assessment in Italy. International Journal of Climatology. https://doi.org/10.1002/joc.6177 ↩

  18. Logemann, A., Schafberg, M., & Brockmeyer, B. (2019). Using the HPTLC-bioluminescence bacteria assay for the determination of acute toxicities in marine sediments and its eligibility as a monitoring assessment tool. Chemosphere. https://doi.org/10.1016/j.chemosphere.2019.05.246 ↩

  19. Al-Mustanjid, A. (2019). Design of a common pathway drug for all types of cardiovascular diseases: A network biology approach. Network Biology, 9(2), 28. http://www.iaees.org/publications/journals/nb/articles/2019-9(2)/design-of-a-common-pathway-drug-for-cardiovascular-diseases.pdf ↩

  20. Wambui, K. M., & Musenge, E. (2019). A space-time analysis of recurrent malnutrition-related hospitalisations in Kilifi, Kenya for children under-5 years. BMC Nutrition, 5(1). https://doi.org/10.1186/s40795-019-0296-5 ↩