rOpenSci HQ


Software 📦

CRAN: GitHub:

New versions

  • A new version (v0.2.0) of crminer is on CRAN - Fetch scholarly full text from Crossref. See the release notes for changes. Checkout the README to get started. crminer crminer

    can now set full cache path more easily

  • A new version (v0.5.0) of hoardr is on CRAN - Manage cached files. See the release notes for changes. Checkout the vignette to get started. hoardr hoardr

    can now set full cache path more easily

  • A new version (v1.2.3) of GSODR is on CRAN - Global surface summary of the day (GSOD) weather data client. See the release notes for changes. Checkout the docs to get started. GSODR GSODR

    bug fixes and many minor changes

  • A new version (v0.2.8) of weathercan is on CRAN - Download weather data from the Environment and Climate Change Canada website. See the NEWS for changes. Checkout the docs to get started. weathercan weathercan

    minor fixes

  • A new version (v1.2) of antiword is on CRAN - Extract text from Microsoft Word documents. See the release notes for changes. Checkout the README is get started. antiword antiword

    fix gcc8 warning

  • A new version (v0.3) of ssh is on CRAN - Secure shell (SSH) client for R. See the release notes for changes. Checkout the vignette is get started. ssh ssh

    fix gcc8 warnings; update libssh to v0.8.3

  • A new version (v1.4.2) 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. ijtiff ijtiff

    Solaris fixes

  • A new version (v0.0.8) of piggyback is on CRAN - Managing larger data on a GitHub repository. See the NEWS for changes. Checkout the docs to get started. piggyback piggyback

    update docs; remove dependency on utils::askYesNo

  • A new version (v2.0) of magick is on CRAN - Advanced graphics and Image-Processing in R. See the release notes for changes. Checkout the vignette is get started. magick magick

    split manual page because examples take too long

  • A new version (v0.2.2) of comtradr is on CRAN - Interface with the United Nations Comtrade API. See the release notes for changes. Checkout the vignette to get started. comtradr comtradr

    remove unused dependency methods from Imports

  • A new version (v1.1.19) of rtika is on CRAN - R Interface to Apache Tika. See the NEWS for changes. Checkout the docs to get started. rtika rtika

    new java() function to help usability

  • A new version (v0.3.0) of auk is on CRAN - eBird data extraction and processing. See the NEWS for changes. Checkout the docs to get started. auk

    new functions and many fixes and improvements

  • A new version (v0.3.2) of NLMR is on CRAN - Simulating neutral landscape models. See the NEWS for changes. Checkout the docs to get started. NLMR NLMR



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 packages were recently submitted:



On the blog

Software Review / Onboarding

Rafael Pilliard Hellwig wrote about his recently rOpenSci reviewed package outcomerate: outcomerate: Transparent Communication of Quality in Social Surveys. The review: ropensci/onboarding#213


Thomas Klebel wrote about his recently rOpenSci reviewed package jstor: Parsing Metadata with R - A Package Story. It includes some great lessons learned about package development. The review: ropensci/onboarding#189


Technotes

Our own Jeroen Ooms wrote about a new package av: The av Package: Production Quality Video in R. Check out the package at ropensci/av


Our own Maëlle Salmon wrote about how to Distinguish yourself in CRAN person() with ORCID.


rOpenSci HQ

Stefanie Butland writes about our upcoming community call (tomorrow!). Community Call - Code Review in the Lab, or … How do you review code that accompanies a research project?. Please join us for our next community call; this is going to be a good one.



Use cases

The following 15 works use/cite rOpenSci software:



In the news

Ryo Nakagawara used riem, by our own Maëlle Salmon, in a blog post about weather in Japan


Angela Li gave a workshop at the Center for Spatial Data Science (CSDS) at Univrersity of Chicago for State of the Map 2018 event. In the materials for her GitHub repository https://github.com/angela-li/sotmus-r she uses our package osmdata


In a package from the company dreamRs (Victor Perrier and Fanny Meyer) they use our package geojsonio






Keep up with rOpenSci


Footnotes

  1. Gye-Soo, K. 2018. Text Mining and Big Data Analysis in the Relational Database with R. International Journal of Trend in Research and Development. 4(5): 384-386. http://www.ijtrd.com/papers/IJTRD12170.pdf 

  2. Merkling, T., Nakagawa, S., Lagisz, M., & Schwanz, L. E. (2017). Maternal Testosterone and Offspring Sex-Ratio in Birds and Mammals: A Meta-Analysis. Evolutionary Biology, 45(1), 96–104. https://doi.org/10.1007/s11692-017-9432-9 

  3. Pfeffer, D. A., Lucas, T. C. D., May, D., Harris, J., Rozier, J., Twohig, K. A., … Gething, P. W. (2018). malariaAtlas: an R interface to global malariometric data hosted by the Malaria Atlas Project. Malaria Journal, 17(1). https://doi.org/10.1186/s12936-018-2500-5 

  4. Gadelha Jr, L. M., de Siracusa, P. C., Ziviani, A., Dalcin, E. C., Affe, H. M., de Siqueira, M. F., … & Costa, R. L. (2018). A Survey of e-Biodiversity: Concepts, Practices, and Challenges. arXiv preprint arXiv:1810.00224 https://arxiv.org/abs/1810.00224 

  5. Kimmelman, V., Klezovich, A., & Moroz, G. (2018). IPSL: A Database of Iconicity Patterns in Sign Languages. Creation and Use. In LREC. http://vadimkimmelman.com/papers/Kimmelman%20Klezovich%20Moroz%202018%20IPSL.pdf 

  6. Sánchez, C. A., Becker, D. J., Teitelbaum, C. S., Barriga, P., Brown, L. M., Majewska, A. A., … & Altizer, S. 2018. On the relationship between body condition and parasite infection in wildlife: a review and meta‐analysis. Ecology Letters. https://onlinelibrary.wiley.com/doi/abs/10.1111/ele.13160 

  7. Denecker, T., & Lelandais, G. (2018). Empowering the detection of ChIP-seq “basic peaks” (bPeaks) in small eukaryotic genomes with a web user-interactive interface. BMC Research Notes, 11(1). https://doi.org/10.1186/s13104-018-3802-y 

  8. Wylie, K. M., Blankenship, S. A., Tuuli, M. G., Macones, G. A., & Stout, M. J. (2018). Evaluation of patient- versus provider-collected vaginal swabs for microbiome analysis during pregnancy. BMC Research Notes, 11(1). https://doi.org/10.1186/s13104-018-3809-4 

  9. Davydov, Y. Forecasting Retirements: The Case of the New York City Government Workforce. https://data.bloomberglp.com/company/sites/2/2018/09/retirement-forecasting.pdf 

  10. Johnson, E. C. B., Dammer, E. B., Duong, D. M., Yin, L., Thambisetty, M., Troncoso, J. C., … Seyfried, N. T. (2018). Deep proteomic network analysis of Alzheimer’s disease brain reveals alterations in RNA binding proteins and RNA splicing associated with disease. Molecular Neurodegeneration, 13(1). https://doi.org/10.1186/s13024-018-0282-4 

  11. Haddaway, N. R., & Westgate, M. J. (2018). Predicting the time needed for environmental systematic reviews and systematic maps. Conservation Biology. https://doi.org/10.1111/cobi.1323 

  12. Schmidt, B. (2018). Stable random projection: lightweight, general-purpose dimensionality reduction for digitized libraries. Journal of Cultural Analytics. https://doi.org/10.22148/16.025 

  13. Becker, D., Czirják, G., Rynda-Apple, A., & Plowright, R. (2018). Handling stress and sample storage are associated with weaker complement-mediated bactericidal ability in birds but not bats. Physiological and Biochemical Zoology. https://doi.org/10.1086/701069 

  14. Roettger, T., & Gordon, M. (2017). Methodological issues in the study of word stress correlates. Linguistics Vanguard, 3(1). http://www.linguistics.ucsb.edu/faculty/gordon/Roettger&Gordon_AcousticMethodologoy.pdf 

  15. Kollar, B., Shubin, A., Borges, T. J., Tasigiorgos, S., Win, T. S., Lian, C. G., … Riella, L. V. (2018). Increased levels of circulating MMP3 correlate with severe rejection in face transplantation. Scientific Reports, 8(1). https://doi.org/10.1038/s41598-018-33272-7