rOpenSci HQ

  • More than 50 people attended our Community Call on Research Applications of rOpenSci Taxonomy and Biodiversity Tools. Video, slides, and code are available: https://ropensci.org/commcalls/2019-03-27/. Thank you to our speakers: Kathryn Turner, Zachary Foster, Kari Norman, Margaret Siple, Scott Chamberlain and Ciera Martinez.
  • We’re planning a Community Call on Security for R with Ildi Czeller & Bob Rudis. Create Your Own Security Adventure by telling us what you want to know about the topic.


Software 📦

CRAN: GitHub:

New packages

  • The first version (v1.0.1) of cyphr is on CRAN - high level encryption wrappers. See the release notes for changes. Checkout the vignettes to get started. cyphr cyphr
  • The first version (v0.1.0) of nlrx is on CRAN - setup, run and analyze NetLogo model simulations. See the release notes for changes. Checkout the vignettes to get started. nlrx nlrx

New Versions

  • A new version (v0.15.7) of DataPackageR is on CRAN - construct reproducible analytic data sets as R packages. See the release notes for changes. Checkout the vignettes to get started. DataPackageR DataPackageR

    fix test/vignette bugs related to upcoming version of usethis

  • A new version (v0.7.4) 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

    request/response hooks now supported; improve $parse behavior; Paginator gains progress bar option

  • A new version (v0.2.18) of rglobi is on CRAN - R Interface to Global Biotic Interactions. See the release notes for changes. Checkout the vignette to get started. rglobi rglobi

    update cypher query endpoint after server upgrade to neo4j

  • A new version (v0.5) of ssh is on CRAN - Secure shell (SSH) client for R. See the release notes for changes. Checkout the vignette to get started. ssh ssh

    use key management fxns from credentials pkg; refactor password callback; rename ssh_info() to ssh_session_info()

  • A new version (v0.4.0) of tidyhydat is on CRAN - Water Survey of Canada hydrometric data. See the release notes for changes. Checkout the vignettes to get started. tidyhydat tidyhydat

    all fxns now return either “hy” or “realtime” class with associated print and plot methods; fxns now fail with an informative error message

  • A new version (v0.4.2) of Rpolyhedra is on CRAN - polyhedra database from various sources as R6 objects and visualizing capabilities. See the release notes for changes. Checkout the vignette to get started. Rpolyhedra Rpolyhedra

    calculates & normalizes polyhedra size using geometry::convhulln instead of bounding box; a polyhedron now applies internal transformation matrix

  • A new version (v0.2.8) of stplanr is on CRAN - sustainable transport planning. See the release notes for changes. Checkout the docs to get started. stplanr stplanr

    STATS19 fxns such as dl_stats19() split-out into the new package stats19; new fxns route_dodgr(), overline2() … a substantial refactoring operation has begun

  • A new version (v0.5.0) of bomrang is on CRAN - Australian government Bureau of Meteorology (BOM) data. See the release notes for changes. Checkout the docs to get started. bomrang bomrang

    some new print methods; new aliases for some fxns; new default image when image failed to download

  • A new version (v2.0-8) 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. CoordinateCleaner CoordinateCleaner

    moved vignettes to online documentation; added an area column to the countryref dataset

  • A new version (v0.0.10) 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. osmdata osmdata

    bug fix for vectorized lists of values in add_osm_feature; bug fix to ensure all sf data.frame objects have stringsAsFactors = FALSE

  • A new version (v3.2-2) of clifro is on CRAN - easily download and visualise climate data from CliFlo. See the release notes for changes. Checkout the vignettes to get started. clifro clifro

    fixed error in cf_find_station() fxn when searching for CliFlo stations based on geog. proximity & when using a datatype

  • A new version (v0.25.2) 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. git2r git2r

    improved build configuration script

  • A new version (v0.6.3) of rdhs is on CRAN - Client for Demographic and Health Survey (DHS) Data. See the release notes for changes. Checkout the docs to get started. rdhs rdhs

    new delabel_df() fxn for converting labelled data frames to characters

Un-Archived

  • rdefra was archived on CRAN for a bit - Now it’s back up.



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:



Use Cases

The following 12 works use/cite rOpenSci software:



In The News

Erik Gahner Larsen and Zoltán Fazekas have a bookdown book titled Quantitative Politics with R in which they include Chapter 4: Get existing data with a section on the European Social Survey using the rOpenSci package esssurvey, maintained by Jorge Cimentada.



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 five recent examples of maintainer transitions within rOpenSci:

We’ve got only one package in need of new maintainers:






Keep up with rOpenSci


Footnotes

  1. Phelps, K., Hamel, L., Alhmoud, N., Ali, S., Bilgin, R., Sidamonidze, K., … Olival, K. (2019). Bat Research Networks and Viral Surveillance: Gaps and Opportunities in Western Asia. Viruses, 11(3), 240. https://doi.org/10.3390/v11030240 

  2. Angel, J., & Markus, M. (2019). Frequency Distributions of Heavy Precipitation in Illinois: Updated Bulletin 70. ISWS CR 2019-05. https://www.ideals.illinois.edu/handle/2142/103172 

  3. Mitchell, J. M., & Moseley, H. N. B. (2019). Deriving Accurate Lipid Classification based on Molecular Formula. https://doi.org/10.1101/572883 

  4. Solt, F. Measuring Income Inequality Across Countries and Over Time: The Standardized World Income Inequality Database [DRAFT]. http://www.globalfactcheck.org/documents/2019-03-08%20Standardized%20World%20Income%20Inequality%20Database.%20updating_swiid%20Solt.pdf 

  5. Michalak, W., Tsiamis, V., Schwämmle, V., & Rogowska-Wrzesińska, A. (2019). ComplexBrowser: a tool for identification and quantification of protein complexes in large scale proteomics datasets. https://doi.org/10.1101/573774 

  6. Su, W., Sun, J., Shimizu, K., & Kadota, K. (2019). TCC-GUI: a Shiny-based application for differential expression analysis of RNA-Seq count data. BMC Research Notes, 12(1). https://doi.org/10.1186/s13104-019-4179-2 

  7. König, C., Weigelt, P., Schrader, J., Taylor, A., Kattge, J., & Kreft, H. (2019). Biodiversity data integration–The significance of data resolution and domain. PLOS Biology, 17(3), e3000183. https://doi.org/10.1371/journal.pbio.3000183 

  8. Ravenhall, M., Campino, S., & Clark, T. G. (2019). SV-Pop: population-based structural variant analysis and visualization. BMC Bioinformatics, 20(1). https://doi.org/10.1186/s12859-019-2718-4 

  9. Higino, G., & Vital, M. V. C. (2019). Mapping and understanding the digital biodiversity knowledge about vertebrates in the Atlantic Rainforest. https://doi.org/10.32942/osf.io/c63vj 

  10. Ahmed, M., Lai, T. H., & Kim, D. R. (2019). colocr: An R package for conducting co-localization analysis on fluorescence microscopy images. https://doi.org/10.7287/peerj.preprints.27613v1 

  11. Jo, J., Lee, H.-G., Kim, K. Y., & Park, C. (2019). SoEM: a novel PCR-free biodiversity assessment method based on small-organelles enriched metagenomics. ALGAE, 34(1), 57–70. https://doi.org/10.4490/algae.2019.34.2.26 

  12. Shefferson, R. P., Bunch, W., Cowden, C. C., Lee, Y., Kartzinel, T. R., Yukawa, T., … Jiang, H. (2019). Does evolutionary history determine specificity in broad ecological interactions? Journal of Ecology. https://doi.org/10.1111/1365-2745.13170