rOpenSci HQ

Maëlle Salmon and Scott Chamberlain introduced the new HTTP Testing in R book: Learn All About HTTP Testing: Book Update

Stefanie Butland and Steffi LaZerte wrote a post on Introducing the rOpenSci Community Contributing Guide



Software 📦

CRAN: GitHub:

New packages

  • The first version (v0.0.2) of tarchetypes is on CRAN - archetypes for targets. Checkout the docs to get started. tarchetypes tarchetypes
  • The first version (v0.0.2) of targets is on CRAN - dynamic function-oriented make-like declarative workflows. Checkout the docs to get started. targets targets
  • The first version (v0.13.5) of coder is on CRAN - deterministic categorization of items based on external code data. Checkout the docs to get started. coder coder

New Versions

  • A new version (v1.1.1) of webchem is on CRAN - Chemical information from the web. See the release notes for changes. Checkout the docs to get started. webchem webchem
  • A new version (v0.6.0) of ckanr is on CRAN - client for the CKAN API. See the release notes for changes. Checkout the docs to get started. ckanr ckanr
  • A new version (v7.13.1) 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. drake drake
  • A new version (v1.0.0) 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
  • A new version (v0.3.2) of grainchanger is on CRAN - Data aggregation methods for raster data. See the release notes for changes. Checkout the docs to get started. grainchanger grainchanger
  • A new version (v1.0.6) 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 (v1.2.0) of rebird is on CRAN - client for the eBird database of bird observations. See the release notes for changes. Checkout the vignette to get started. rebird rebird
  • A new version (v3.5.2) of rgbif is on CRAN - interface to the Global Biodiversity Information Facility API. See the release notes for changes. Checkout the docs to get started. rgbif rgbif
  • A new version (v1.1.0) of gert is on CRAN - simple git client for R. See the release notes for changes. Checkout the docs to get started. gert
  • A new version (v2.8) of assertr is on CRAN - Assertive Programming for R Analysis Pipelines. See the release notes for changes. Checkout the vignette to get started. assertr assertr
  • A new version (v0.2.0) of rgnparser is on CRAN - parse scientific names using the Go tool gnparser. See the release notes for changes. Checkout the docs to get started. rgnparser rgnparser
  • A new version (v3.0.0) of GSODR is on CRAN - Global Surface Summary of the Day (GSOD) Weather Data from R. See the release notes for changes. Checkout the docs to get started. GSODR GSODR
  • A new version (v0.4.4) of nomisr is on CRAN - access UK official statistics from the Nomis database. See the release notes for changes. Checkout the docs to get started. nomisr nomisr
  • A new version (v0.3.1) of git2rdata is on CRAN - store and retrieve data.frames in a Git repository. See the release notes for changes. Checkout the docs to get started. git2rdata git2rdata
  • A new version (v0.7) of roadoi is on CRAN - find free versions of scholarly publications via Unpaywall. See the release notes for changes. Checkout the vignette to get started. roadoi roadoi
  • A new version (v0.7.0) of rorcid is on CRAN - Interface to the Orcid.org API. See the release notes for changes. Checkout the vignette to get started. rorcid rorcid
  • A new version (v1.4.0) of UCSCXenaTools is on CRAN - download and explore datasets from UCSC Xena data hubs. See the release notes for changes. Checkout the docs to get started. UCSCXenaTools UCSCXenaTools
  • A new version (v3.1.5) of rfishbase is on CRAN - interface to Fishbase data. See the release notes for changes. Checkout the docs to get started. rfishbase rfishbase
  • A new version (v0.3.0) of taxizedb is on CRAN - tools for working with taxonomic databases. See the release notes for changes. Checkout the docs to get started. taxizedb taxizedb
  • A new version (v0.5.0) of weathercan is on CRAN - Download weather data from the Environment and Climate Change Canada website. See the release notes for changes. Checkout the docs to get started. weathercan weathercan
  • A new version (v0.9.3) of hddtools is on CRAN - Hydrological Data Discovery Tools. See the release notes for changes. Checkout the docs to get started. hddtools hddtools
  • A new version (v2.2.5) 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
  • A new version (v0.4.2) of nodbi is on CRAN - the NoSQL database connector. See the release notes for changes. Checkout the README to get started. nodbi nodbi
  • A new version (v3.1.4) of qualtRics is on CRAN - download Qualtrics survey data. See the release notes for changes. Checkout the docs to get started. qualtRics qualtRics
  • A new version (v0.9.4) 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
  • A new version (v2.6.0) of magick is on CRAN - Advanced graphics and Image-Processing in R. See the release notes for changes. Checkout the docs to get started. magick magick
  • A new version (v1.4.1) 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. cld3 cld3



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 packages were recently approved:

The following packages were recently submitted:



On the blog

Maëlle Salmon and Scott Chamberlain introduced the HTTP Testing in R book: Learn All About HTTP Testing: Book Update.


Stefanie Butland and Steffi LaZerte wrote a post on Introducing the rOpenSci Community Contributing Guide.


Stefanie Butland and Emily Lescak wrote about How rOpenSci Runs Community Calls - arising from a presentation Stefanie gave to a Code for Science & Society Event.


Software review

Will Landau introduces his new packages targets - a new pipeline toolkit for R: targets: Democratizing Reproducible Analysis Pipelines. targets is the successor of drake, which succeeded remake.


Lluís Revilla Sancho introduces the package BaseSet that recently went through rOpenSci Software Review: Introducing BaseSet for mathematical sets


Tech notes

Jeroen Ooms wrote about updates to the magick package: Behind the magick: updates to imagemagick and beyond



Citations

The following 15 works use/cite rOpenSci software:



From the Forum

We have a discussion forum (using Discourse) for the rOpenSci community. It’s a really nice way to have conversations on the internet. From time to time we’ll highlight recent discussions of interest.


Four new use cases were shared in the forum over the past month since our last newsletter:



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. Check out our guidance for taking over maintenance of a package.

We’ve had eight recent examples of maintainer transitions within rOpenSci:



Get involved with rOpenSci

We maintain a Contributing Guide that can help direct you to the right place, whether you want to make code contributions, non-code contributions, or other things like sharing use cases.






Keep up with rOpenSci


Footnotes

  1. Lucky, A., Atchison, R. A., Ohyama, L., Zhang, Y. M., Williams, J. L., Pinkney IV, J. L., … & Lippi, C. A. Myrmecology, Gender, and Geography: changing demographics of a research community over thirty years. Myrmecological News. https://bit.ly/3oVg7OU 

  2. Bonnet, E., Jean-Pierre, D., & Paul, L. (2020). Optimizing Literature Search: TEMAS, A New Text-Mining Algorithm-Assisted Search Tool. https://www.researchsquare.com/article/rs-71504/latest.pdf 

  3. Brightly, W. H., Hartley, S. E., Osborne, C. P., Simpson, K. J., & Strömberg, C. A. E. (2020). High silicon concentrations in grasses are linked to environmental conditions and not associated with C4 photosynthesis. Global Change Biology. https://doi.org/10.1111/gcb.15343 

  4. Germani, E., Lelouard, H., & Fallet, M. (2020). SAPHIR: a Shiny application to analyze tissue section images. F1000Research, 9, 1276. https://doi.org/10.12688/f1000research.27062.1 

  5. Fastovich, D., Russell, J. M., Jackson, S. T., Krause, T. R., Marcott, S. A., & Williams, J. W. (2020). Spatial Fingerprint of Younger Dryas Cooling and Warming in Eastern North America. Geophysical Research Letters. https://doi.org/10.1029/2020gl090031 

  6. Rycyk, A. M., Tyson Moore, R. B., Wells, R. S., McHugh, K. A., Berens McCabe, E. J., & Mann, D. A. (2020). Passive acoustic listening stations (PALS) show rapid onset of ecological effects of harmful algal blooms in real time. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-74647-z 

  7. Wenndt, A., Sudini, H. K., Pingali, P., & Nelson, R. (2020). Exploring aflatoxin contamination and household-level exposure risk in diverse Indian food systems. PLOS ONE, 15(10), e0240565. https://doi.org/10.1371/journal.pone.0240565 

  8. Abbas, H. K., Zablotowicz, R. M., Bruns, H. A., & Abel, C. A. (2006). Biocontrol of aflatoxin in corn by inoculation with non-aflatoxigenicAspergillus flavusisolates. Biocontrol Science and Technology, 16(5), 437–449. https://doi.org/10.1080/09583150500532477 

  9. Jacobs, E., Bittig, H. C., Gräwe, U., Graves, C. A., Glockzin, M., Müller, J. D., … Rehder, G. (2020). Upwelling-induced trace gas dynamics in the Baltic Sea inferred from 8 years of autonomous measurements on a ship of opportunity. https://doi.org/10.5194/bg-2020-365 

  10. Hotez, P., Bottazzi, M. E., Strub-Wourgaft, N., Sosa-Estani, S., Torrico, F., Pajín, L., … Sancho, J. (2020). A new patient registry for Chagas disease. PLOS Neglected Tropical Diseases, 14(10), e0008418. https://doi.org/10.1371/journal.pntd.0008418 

  11. Raut, S. (2020). A computer vision approach to assess wood variability from whole-disk images of longleaf pine (Order No. 28023614). https://search.proquest.com/docview/2446699035 

  12. Cramer, M. T., Fidler, R. Y., Penrod, L. M., Carroll, J., & Turingan, R. G. (2020). A spatiotemporal comparison of length-at-age in the coral reef fish Acanthurus nigrofuscus between marine reserves and fished reefs. PLOS ONE, 15(9), e0239842. https://doi.org/10.1371/journal.pone.0239842 

  13. Winter-Billington, A., Moore, R. D., & Dadic, R. (2020). Evaluating the transferability of empirical models of debris-covered glacier melt. Journal of Glaciology, 1–18. https://doi.org/10.1017/jog.2020.57 

  14. Meng, B., Loonen, R. C. G. M., & Hensen, J. L. M. (2020). Data-driven inference of unknown tilt and azimuth of distributed PV systems. Solar Energy, 211, 418–432. https://doi.org/10.1016/j.solener.2020.09.077 

  15. Perez, T. M., & Feeley, K. J. (2020). Weak phylogenetic and climatic signals in plant heat tolerance. Journal of Biogeography. https://doi.org/10.1111/jbi.13984