Software 📦

CRAN: GitHub:

New Versions

  • A new version (v0.3.2) of auk is on CRAN - eBird data extraction and processing. See the release notes for changes. Checkout the docs to get started. auk
  • A new version (v1.0.7) of helminthR is on CRAN - Access London Natural History Museum Host-Helminth Record Database. See the release notes for changes. Checkout the vignette to get started. helminthR helminthR

    changes to listLocations() due to ggmap API key requirement; cleanData() changes

  • A new version (v1.0.5) of nasapower is on CRAN - NASA POWER API Client. See the release notes for changes. Checkout the docs to get started. nasapower nasapower

    fixes problem with WS2M not being available through nasapower

  • A new version (v0.5.0) of lawn is on CRAN - Client for Turf.js for geospatial analysis. See the release notes for changes. Checkout the vignette to get started. lawn lawn

    fix unit tests for upcoming V8 pkg changes

  • A new version (v0.5.0) of rerddap is on CRAN - General Purpose Client for ERDDAP Servers. See the release notes for changes. Checkout the vignettes to get started. rerddap rerddap

    replace httr with crul; many griddap() fixes; set default server URL

  • A new version (v0.3.2) of geojson is on CRAN - Classes for GeoJSON. See the release notes for changes. Checkout the vignettes to get started. geojson geojson

    ndgeo_read() bug fix

  • A new version (v0.2.7) of ropenaq is on CRAN - Air quality data from the open data platform OpenAQ. See the release notes for changes. Checkout the vignettes to get started. ropenaq ropenaq

    better error messages; remove not used ggmap dep

  • A new version (v0.9.5) of taxize is on CRAN - taxonomic toolbelt for R. See the release notes for changes. Checkout the taxize book to get started. taxize taxize

    iucn_summary_id defunct; downstream gains WORMS data source; col_downstream() gains extant_only param; new fxn id2name(); lots and lots of small changes and bug fixes

  • A new version (v0.4.1) of NLMR is on CRAN - Simulating neutral landscape models. See the release notes for changes. Checkout the docs to get started. NLMR NLMR

    nlm_neigh, nlm_mpd, nlm_randomrectangularcluster now implemented in Rcpp; doc improvements; bug fixes

  • A new version (v0.2.2) of patentsview is on CRAN - An R client to the PatentsView API. See the release notes for changes. Checkout the docs to get started. patentsview patentsview

    vignettes removed from package

  • A new version (v0.6.1) 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

    extraction(add_geo=TRUE) correction for Kenya 2014 surveys; Geospatial covariate data sets now supported correctly

  • A new version (v2.3.0) 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

    add_meta() now works w/ trees and characters; pkg handles nested meta elements properly now

  • A new version (v0.3.0) of natserv is on CRAN - NatureServe R Interface. See the release notes for changes. Checkout the vignette to get started. natserv natserv

    new vignette; improve failure behavior; bug fixes

  • A new version (v2.6) 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

    bug fix for rlang pkg changes

  • A new version (v2.0-7) 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

    add pkg citation; improved docs for cc_outl()

  • A new version (v1.2.0) of fulltext is on CRAN - full text of scholarly articles across many data sources. See the release notes for changes. Checkout the fulltext book to get started. fulltext fulltext

    ft_get() gains progress param; can now set cache path with full_path param in cache_options_set(); ft_chunks/ft_tabularize defunct (see pubchunks); ft_get_si defunct (see suppdata); replace httr with crul



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.


No new submissions or approved submissions.



On the blog

Software Review

OJ Watson wrote about his recently reviewed package rdhs Interacting with The Demographic and Health Surveys (DHS) Program data, including the motivation for the package, what the package does, and some lessons from the process.

The rOpenSci editors wrote changes in our software review: first, “rOpenSci onboarding” has been changed to “rOpenSci Software Review”; new editors; changes in standards; issue templates to better direct the different types of submissions; and the new bookdown book “rOpenSci Packages: Development, Maintenance, and Peer Review”. Read the the post: rOpenSci Software Peer Review: Still Improving.


rOpenSci is excited to welcome two new editors: Announcing new software peer review editors: Melina Vidoni and Brooke Anderson.



Use Cases

The following 20 works use/cite rOpenSci software:



In The News

We’re elated Halley Froehlich found rnoaa to be useful.


rcrossref is coming in handy for librarians 👌



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 three recent examples of maintainer transitions within rOpenSci:

We’ve got two packages in need of a new maintainer:

  • webchem: The current maintainer of webchem, Eduard Szöcs, is looking for a new maintainer. See issue #155. Do ping Eduard in that issue and/or email us at info@ropensci.org
  • rsnps: The current maintainer would like to hand it over to someone with more expertise in the domain. Please get in touch with Scott if you’re interested.








Keep up with rOpenSci


Footnotes

  1. Farache, F. H. A., Pereira, C. B., Koschnitzke, C., Barros, L. O., Souza, E. M. de C., Felício, D. T., … Pereira, R. A. S. (2018). The unknown followers: Discovery of a new species of Sycobia Walker (Hymenoptera: Epichrysomallinae) associated with Ficus benjamina L. (Moraceae) in the Neotropical region. Journal of Hymenoptera Research, 67, 85–102. https://doi.org/10.3897/jhr.67.29733 

  2. Shen, Z., & Spruit, M. (2019). A Systematic Review of Open Source Clinical Software on GitHub for Improving Software Reuse in Smart Healthcare. Applied Sciences, 9(1), 150. https://www.mdpi.com/2076-3417/9/1/150/pdf 

  3. Łącki, M. K., Lermyte, F., Miasojedow, B., Startek, M. P., Sobott, F., Valkenborg, D., & Gambin, A. (2019). masstodon: A tool for assigning peaks and modeling electron transfer reactions in top-down mass spectrometry. Analytical Chemistry. https://doi.org/10.1021/acs.analchem.8b01479 

  4. Shang, d., & Ghriga, m. (2018). Exploring social media analytics on community development practices. Journal of Information Technology Management, 29(4), 39. http://jitm.ubalt.edu/XXIX-4/article3.pdf 

  5. Duft, S. (2018). Development of a generic concept to process questionnaire result data in different statistical applications (Doctoral dissertation, Ulm University). http://dbis.eprints.uni-ulm.de/1722/1/BA_Duft_2018.pdf 

  6. Pettersen, A. K., White, C. R., Bryson-Richardson, R. J., & Marshall, D. J. (2019). Linking life-history theory and metabolic theory explains the offspring size-temperature relationship. Ecology Letters. https://doi.org/10.1111/ele.13213 

  7. Waltz, F., Nguyen, T.-T., Arrivé, M., Bochler, A., Chicher, J., Hammann, P., … Giegé, P. (2019). Small is big in Arabidopsis mitochondrial ribosome. Nature Plants, 5(1), 106–117. https://doi.org/10.1038/s41477-018-0339-y 

  8. Dağ, O. (2018). Binary Classification via GMDH-Type Neural Network Algorithm. PhD Thesis. http://www.openaccess.hacettepe.edu.tr:8080/xmlui/handle/11655/5673 

  9. Hofmann, A., Cross, M., Karow, M. A., Straub, J. H., Clemen, C. S., & Eichinger, L. (2019). A convenient tool for bivariate data analysis and bar graph plotting with R. Biochemistry and Molecular Biology Education. https://doi.org/10.1002/bmb.21205 

  10. Lovelace, R., Morgan, M., Hama, L., & Padgham, M. (2019). stats19: A package for working with open road crash data. Journal of Open Source Software, 4(33), 1181. https://doi.org/10.21105/joss.01181 

  11. Zuquim, G., Costa, F. R. C., Tuomisto, H., Moulatlet, G. M., & Figueiredo, F. O. G. (2019). The importance of soils in predicting the future of plant habitat suitability in a tropical forest. Plant and Soil. https://doi.org/10.1007/s11104-018-03915-9 

  12. Kim, K. W., Allen, D. W., Briese, T., Couper, J. J., Barry, S. C., … Colman, P. G. (2019). Distinct gut virome profile of pregnant women with type 1 diabetes in the ENDIA study. Open Forum Infectious Diseases. https://doi.org/10.1093/ofid/ofz025 

  13. Lee, C. K. F., Keith, D. A., Nicholson, E., & Murray, N. J. (2019). REDLISTR: Tools for the IUCN Red Lists of Ecosystems and Threatened Species in R. Ecography. https://doi.org/10.1111/ecog.04143 

  14. Krah, F.-S., Bates, S., & Miller, A. (2019). rMyCoPortal - an R package to interface with the Mycology Collections Portal. Biodiversity Data Journal, 7. https://doi.org/10.3897/bdj.7.e31511 

  15. Mankevich, V., Holmström, J., & McCarthy, I. P. (2019, January). Why Zlatan Ibrahimović is Bigger Than Manchester United: Investigating Digital Traces in Co-branding Processes on Social Media Platforms. In Proceedings of the 52nd Hawaii International Conference on System Sciences. https://scholarspace.manoa.hawaii.edu/bitstream/10125/59710/0270.pdf 

  16. Muñoz, G., Kissling, W. D., & van Loon, E. E. (2019). Biodiversity Observations Miner: A web application to unlock primary biodiversity data from published literature. Biodiversity Data Journal, 7. https://doi.org/10.3897/bdj.7.e28737 

  17. Smith, T. P., Thomas, T. J., Garcia-Carreras, B., Sal, S., Yvon-Durocher, G., Bell, T., & Pawar, S. (2019). Metabolic rates of prokaryotic microbes may inevitably rise with global warming. bioRxiv, 524264. https://doi.org/10.1101/524264 

  18. Ladwig, L. M., Chandler, J. L., Guiden, P. W., & Henn, J. J. (2019). Extreme winter warm event causes exceptionally early bud break for many woody species. Ecosphere, 10(1), e02542. https://doi.org/10.1002/ecs2.2542 

  19. Pimiento, C., Cantalapiedra, J. L., Shimada, K., Field, D. J., & Smaers, J. B. (2019). Evolutionary pathways toward gigantism in sharks and rays. Evolution. https://doi.org/10.1111/evo.13680 

  20. Halsey, L. G., & White, C. R. (2019). Terrestrial locomotion energy costs vary considerably between species: no evidence that this is explained by rate of leg force production or ecology. Scientific Reports, 9(1). https://doi.org/10.1038/s41598-018-36565-z