rOpenSci HQ

rOpenSci Announces a New $896k Award From The Gordon and Betty Moore Foundation to Improve the Scientific Package Ecosystem for R. Read the blog post by Karthik Ram


Software 📦

CRAN: GitHub:

New Versions

  • A new version (v2.3) of pdftools is on CRAN - Text extraction, rendering and converting of PDF documents. See the release notes for changes. Checkout the README to get started. pdftools pdftools

    pdf_text() improvements; new fxns pdf_ocr_text/pdf_ocr_data wrap tesseract

  • A new version (v0.5.3) of gender is on CRAN - Predict gender from names using historical data. See the release notes for changes. Checkout the vignette to get started. gender gender

    docs improvements, testing fixes

  • A new version (v2.4.0) of RNeXML is on CRAN - Semantically Rich I/O for the NeXML Format. See the release notes for changes. Checkout the vignettes to get started. RNeXML RNeXML

    use Additional_repositories for taxadb

  • A new version (v0.2.0) of citecorp is on CRAN - client for the Open Citations Corpus. See the release notes for changes. Checkout the docs to get started. citecorp citecorp

    oc_doi2ids/oc_pmid2ids/oc_pmcid2ids functions now vectorized; bug fixes

  • A new version (v0.9.4) of rnoaa is on CRAN - NOAA Weather Data from R. See the release notes for changes. Checkout the vignettes to get started. rnoaa rnoaa

    new gefs fxns gefs_dimensions/gefs_ensembles; gefs fxn fixes; argo family fxns no longer work as API is gone - but FTP fxns still work (argo_guoy_files()/argo())

  • A new version (v0.2.3) of tidync is on CRAN - a tidy approach to NetCDF data exploration and extraction. See the release notes for changes. Checkout the docs to get started. tidync tidync

    test fixes

  • A new version (v0.9.0) 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. crul crul

    HttpResponse object gains methods for checking response content type; head verb now uses auth correctly

  • A new version (v1.0.4) of essurvey is on CRAN - data from the European Social Survey. See the release notes for changes. Checkout the docs to get started. essurvey essurvey
  • A new version (v1.1.4) of solrium is on CRAN - general purpose R interface to Solr. See the release notes for changes. Checkout the vignettes to get started. solrium solrium

    fix delete_by_query()/$delete_by_query() method

  • A new version (v1.0.2) 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. spocc spocc

    fix failing tests on cran

  • A new version (v1.4.0) 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. rgbif rgbif

    new fxn mvt_fetch() for GBIF’s Map Vector Tiles; overhaul of occ_issues/name_issues fxns; many fixes

  • A new version (v0.8.0) 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. geojsonio geojsonio

    geojson_read() gains method for PostGIS; geojson_read() now uses sf instead of sp; geojson_list() gains precision param; bug fixes

  • A new version (v0.8.0) of ritis is on CRAN - an R client for ITIS (Integrated Taxonomic Information Service). See the release notes for changes. Checkout the docs to get started. ritis ritis

    improve itis_search() examples; bug fix for itis_group()



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 package was recently submitted:

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



On the blog

Michael Quinn and Elin Waring wrote about a new version (v2) of their package skimr - (Re)introducing skimr v2 - A year in the life of an open source R project


Michael Sumner wrote about his package tidync that was recently approved in rOpenSci software review - tidync: scientific array data from NetCDF in R



Use Cases

The following 15 works use/cite rOpenSci software:



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’ve got one package in need of a new maintainer:






Keep up with rOpenSci


Footnotes

  1. Palstrøm N.B., Matthiesen R., Beck H.C. (2020) Data Imputation in Merged Isobaric Labeling-Based Relative Quantification Datasets. In: Matthiesen R. (eds) Mass Spectrometry Data Analysis in Proteomics. Methods in Molecular Biology, vol 2051. Humana, New York, NY https://doi.org/10.1007/978-1-4939-9744-2_13 

  2. Cinelli, M., Ficcadenti, V., & Riccioni, J. (2019). The interconnectedness of the economic content in the speeches of the US Presidents. Annals of Operations Research. https://doi.org/10.1007/s10479-019-03372-2 

  3. Umlauf, N., Klein, N., Simon, T., & Zeileis, A. (2019). bamlss: A Lego Toolbox for Flexible Bayesian Regression (and Beyond). arXiv preprint arXiv:1909.11784. https://arxiv.org/abs/1909.11784 

  4. Bager Olsen, M. T., Geldmann, J., Harfoot, M., Tittensor, D. P., Price, B., Sinovas, P., … Burgess, N. D. (2019). Thirty-six years of legal and illegal wildlife trade entering the USA. Oryx, 1–10. https://doi.org/10.1017/s0030605319000541 

  5. Vidal, M. C., Quinn, T. W., Stireman, J. O., Tinghitella, R. M., & Murphy, S. M. (2019). Geography is more important than host plant use for the population genetic structure of a generalist insect herbivore. Molecular Ecology. https://doi.org/10.1111/mec.15218 

  6. De Luca, D., Kooistra, W. H. C. F., Sarno, D., Gaonkar, C. C., & Piredda, R. (2019). Global distribution and diversity of Chaetoceros (Bacillariophyta, Mediophyceae): integration of classical and novel strategies. PeerJ, 7, e7410. https://doi.org/10.7717/peerj.7410 

  7. Ondra, M. 2019. Reliability based design approach to stochastic supply planning. https://iaee2019ljubljana.oyco.eu/download/contribution/fullpaper/345/345_fullpaper_20190608_130510.pdf 

  8. Wang, Y., Goring, S. J., & McGuire, J. L. (2019). Bayesian ages for pollen records since the last glaciation in North America. Scientific Data, 6(1). https://doi.org/10.1038/s41597-019-0182-7 

  9. Nalborczyk, L., Grandchamp, R., Koster, E. H. W., Perrone-Bertolotti, M., & Loevenbruck, H. (2019). Can we decode phonetic features in inner speech using surface electromyography? https://doi.org/10.31234/osf.io/8v5yd 

  10. Stanstrup, J., Broeckling, C., Helmus, R., Hoffmann, N., Mathé, E., Naake, T., … Neumann, S. (2019). The metaRbolomics Toolbox in Bioconductor and beyond. Metabolites, 9(10), 200. https://doi.org/10.3390/metabo9100200 

  11. Feng, X., Park, D. S., Walker, C., Peterson, A. T., Merow, C., & Papeş, M. (2019). A checklist for maximizing reproducibility of ecological niche models. Nature Ecology & Evolution. https://doi.org/10.1038/s41559-019-0972-5 

  12. Duffany, J. (2019). Developing CyberSecurity Skills with Intermediate Programming Courses. Proceedings of the 17th LACCEI International Multi-Conference for Engineering, Education, and Technology: “Industry, Innovation, and Infrastructure for Sustainable Cities and Communities.” https://doi.org/10.18687/laccei2019.1.1.414 

  13. Maherali, H. (2019). Mutualism as a plant functional trait: linking variation in the mycorrhizal symbiosis to climatic tolerance, geographic range and population dynamics. International Journal of Plant Sciences. https://doi.org/10.1086/706187 

  14. Havinga, I., Hein, L., Vega-Araya, M., & Languillaume, A. (2020). Spatial quantification to examine the effectiveness of payments for ecosystem services: A case study of Costa Rica’s Pago de Servicios Ambientales. Ecological Indicators, 108, 105766. https://doi.org/10.1016/j.ecolind.2019.105766 

  15. Jin, L., Tefft, B. C., & Horrey, W. J. (2019). Mining consumer complaints to identify unsuccessful interactions with advanced driver assistance systems. Proceedings of the 11th International Conference on Automotive User Interfaces and Interactive Vehicular Applications Adjunct Proceedings - AutomotiveUI ’19. https://doi.org/10.1145/3349263.3351313