rOpenSci HQ


Software 📦

CRAN: GitHub:

New packages

  • The first version (v0.1.0) of zbank is on CRAN - an interface to the ZooBank API (http://zoobank.org/Api); ZooBank (http://zoobank.org/) is the official registry of zoological nomenclature. Checkout the README to get started. zbank zbank

New versions

  • A new version (v0.2.0) 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. fingertipsR fingertipsR

    fixes to select_indicators, deprivation_decile, fingertips_data and indicators fxns

  • A new version (v3.0.0) of rfishbase is on CRAN - interface to Fishbase data. See the release notes for changes. Checkout the docs to get started. rfishbase rfishbase

    Major change: now uses static data; requests return all data in one go now

  • A new version (v1.3) of antiword is on CRAN - Extract text from Microsoft Word documents. See the release notes for changes. Checkout the README to get started. antiword antiword

    fix for sys 2.0

  • A new version (v1.3) of unrtf is on CRAN - Extract text from Rich Text Format (RTF) documents. See the release notes for changes. Checkout the README to get started. unrtf unrtf

    fix for sys 2.0; fix for Solaris

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

    add dialog when run interactively; now use BiocManager

  • A new version (v0.3.0) of worrms is on CRAN - client for World Register of Marine Species. See the release notes for changes. Checkout the vignette to get started. worrms worrms

    plural versions of fxns now only warn where they used to stop on error

  • A new version (v0.2.9) of webmockr is on CRAN - stubbing and setting expectations on HTTP requests. See the release notes for changes. Checkout the HTTP testing book to get started. webmockr webmockr

    fix for use case of using only webmockr without vcr; update docs

  • A new version (v4.0) of tesseract is on CRAN - bindings to Tesseract, an OCR engine https://opensource.google.com/projects/tesseract. See the release notes for changes. Checkout the vignette to get started. tesseract tesseract

    upgrade to Tesseract 4.0 for windows/macos users; drop hard dep on tibble

  • A new version (v2.2.0) 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

    various fixes; drops phylobase dep.

  • A new version (v1.5.0) 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

    allow ZIP compression; fix to write_txt_img

  • A new version (v0.0.5) of arkdb is on CRAN - archive and unarchive databases as flat text files. See the release notes for changes. Checkout the docs to get started. arkdb arkdb

    fix to ark() fxn when accessing Postgres connections



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.



On the blog

Technotes

Jeroen Ooms wrote about a new version of his package tesseract: Tesseract 4 is here! State of the art OCR in R!. Check out the package at ropensci/tesseract.


rOpenSci HQ

Stefanie Butland wrote up detailed notes on how to do a good unconference ice breaker: Sharing the Recipe for rOpenSci’s Unconf Ice Breaker.



Use cases

The following 13 works use/cite rOpenSci software:



In the news

Dominic Royé wrote a blog post on how to access OpenStreetMap data with R, that used our osmdata package from Mark Padgham and company:






Keep up with rOpenSci


Footnotes

  1. Milà, C., Salmon, M., Sanchez, M., Ambrós, A., Bhogadi, S., Sreekanth, V., … Tonne, C. (2018). When, Where, and What? Characterizing Personal PM2.5 Exposure in Periurban India by Integrating GPS, Wearable Camera, and Ambient and Personal Monitoring Data. Environmental Science & Technology. https://doi.org/10.1021/acs.est.8b03075 

  2. Barra, M., Labberton, A. S., Faiz, K. W., Lindstrøm, J. C., Rønning, O. M., Viana, J., … Rand, K. (2018). Stroke incidence in the young: evidence from a Norwegian register study. Journal of Neurology. https://doi.org/10.1007/s00415-018-9102-6 

  3. Ornstein, J. (2018). The Political Economy of Urban Growth. Dissertation. https://deepblue.lib.umich.edu/bitstream/handle/2027.42/145832/ornstein_1.pdf?sequence=1&isAllowed=y 

  4. Clegg, T., Ali, M., & Beckerman, A. P. (2018). The impact of intraspecific variation on food web structure. Ecology. https://doi.org./10.1002/ecy.2523 

  5. Guerra-Grenier Jr, E. (2018). Resisting the Pied Piper: Colorful Defense Mechanisms in Insect Eggs, with a Focus on Stink Bugs (Heteroptera: Pentatomidae) (Doctoral dissertation, Carleton University). https://curve.carleton.ca/system/files/etd/6c45742b-6f0e-4fb7-a131-4e7bddc3fb69/etd_pdf/cb0a257b1921794188a309b53d0d614a/guerra-grenier-resistingthepiedpipercolorfuldefensemechanisms.pdf 

  6. Orwoll, E. S., Fino, N. F., Gill, T. M., Cauley, J. A., Strotmeyer, E. S., … Ensrud, K. E. (2018). The relationships between physical performance, activity levels and falls in older men. The Journals of Gerontology: Series A. https://doi.org/10.1093/gerona/gly248 

  7. Kandlikar, G. S., Gold, Z. J., Cowen, M. C., Meyer, R. S., Freise, A. C., Kraft, N. J. B., … Curd, E. E. (2018). ranacapa: An R package and Shiny web app to explore environmental DNA data with exploratory statistics and interactive visualizations. F1000Research, 7, 1734. https://doi.org/10.12688/f1000research.16680.1 

  8. Smith, J. R., Letten, A. D., Ke, P.-J., Anderson, C. B., Hendershot, J. N., Dhami, M. K., … Daily, G. C. (2018). A global test of ecoregions. Nature Ecology & Evolution. https://doi.org/10.1038/s41559-018-0709-x 

  9. Collins, R. A., Wangensteen, O. S., O’Gorman, E. J., Mariani, S., Sims, D. W., & Genner, M. J. (2018). Persistence of environmental DNA in marine systems. Communications Biology, 1(1). https://doi.org/10.1038/s42003-018-0192-6 

  10. Mendez, P. K., Lee, S., & Venter, C. E. (2018). Imaging natural history museum collections from the bottom up: 3D print technology facilitates imaging of fluid-stored arthropods with flatbed scanners. ZooKeys, 795, 49–65. https://doi.org/10.3897/zookeys.795.28416 

  11. Bentz, C., Dediu, D., Verkerk, A., & Jäger, G. (2018). The evolution of language families is shaped by the environment beyond neutral drift. Nature Human Behaviour, 2(11), 816–821. https://doi.org/10.1038/s41562-018-0457-6 

  12. Chatzos, D. (2018). Project for the development of a higher education management dashboard in R (Master’s thesis, Universitat Politècnica de Catalunya). https://upcommons.upc.edu/bitstream/handle/2117/123443/memoria.pdf 

  13. Menegotto, A., & Rangel, T. F. (2018). Mapping knowledge gaps in marine diversity reveals a latitudinal gradient of missing species richness. Nature Communications, 9(1). https://doi.org/10.1038/s41467-018-07217-7