Software 📦

CRAN: GitHub:

New Packages

  • The first version (v0.0.3) of medrxivr is on CRAN - access and search MedRxiv and BioRxiv preprint data. Checkout the docs to get started. This package recently went through rOpenSci software review.

New Versions

  • A new version (v0.7.1) of bomrang is on CRAN - Australian government Bureau of Meteorology (BOM) data. See the release notes for changes. Checkout the docs to get started.
  • A new version (v0.5.1) of emld is on CRAN - ecological metadata as linked data. See the release notes for changes. Checkout the docs to get started.
  • A new version (v0.2.0) of opencv is on CRAN - bindings to the OpenCV computer vision library. See the release notes for changes. Checkout the docs to get started.
  • A new version (v2.0.0) of nasapower is on CRAN - NASA POWER API Client. See the release notes for changes. Checkout the docs to get started.
  • A new version (v0.2.0) of gutenbergr is on CRAN - Download and process public domain works from Project Gutenberg. See the release notes for changes. Checkout the vignette to get started.
  • A new version (v2.1.2) 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.
  • A new version (v2.0.3) of MODIStsp is on CRAN - Automate Download and Preprocessing of MODIS Land Products Data. See the release notes for changes. Checkout the docs to get started.
  • A new version (v0.0.6) 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.
  • A new version (v1.0.1) of rppo is on CRAN - access the Global Plant Phenology Data portal. See the release notes for changes. Checkout the docs to get started.
  • A new version (v0.9.98) of taxize is on CRAN - taxonomic toolbelt for R. See the release notes for changes. Checkout the taxize book to get started.
  • A new version (v1.1) of tradestatistics is on CRAN - open trade statistics api wrapper and utility program. See the release notes for changes. Checkout the docs to get started.
  • A new version (v3.0.0) of rdataretriever is on CRAN - R interface to the Data Retriever. See the release notes for changes. Checkout the docs to get started.



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 two packages were recently approved:



On the blog

Software Review:

April Wright, Christian Román-Palacios, and Josef Uyeda wrote about their recently rOpenSci reviewed package treedata.table: The treedata.table Package. They discuss how the package came about, why you should use the packag and a bit of high level talk on what can be done with the package.



Citations

The following 18 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 two weeks 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:

We’ve got one package in need of a new maintainer:



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. Ehlers, M., Nold, J., Kuhn, M., Klingelhöfer-Jens, M., & Lonsdorf, T. (2020). Natural variations in brain morphology do not account for inter-individual differences in defensive responding during fear acquisition training and extinction. https://psyarxiv.com/q2kyf/download?format=pdf 

  2. Jerabek M., Kubat J., Fabera V. (2020) Method to Comparison of Cities. In: Knapcikova L., Balog M., Peraković D., Periša M. (eds) New Approaches in Management of Smart Manufacturing Systems. EAI/Springer Innovations in Communication and Computing. Springer, Cham. https://doi.org/10.1007/978-3-030-40176-4_7 

  3. Westfall J. (2020) R Anywhere. In: Practical R 4. Apress, Berkeley, CA. https://doi.org/10.1007/978-1-4842-5946-7_8 

  4. Arranz, V., Pearman, W. S., Aguirre, J. D., & Liggins, L. (2020). MARES, a replicable pipeline and curated reference database for marine eukaryote metabarcoding. Scientific Data, 7(1). https://doi.org/10.1038/s41597-020-0549-9 

  5. Leonard, S. P. (2020). Engineering the gut microbiome of honey bees (Doctoral dissertation). https://bit.ly/3cFfZhT 

  6. LeBeau, B. C., & Aloe, A. M. (2020). Evolution of Statistical Software and Quantitative Methods. https://doi.org/10.17077/pp.005273 

  7. van Wieringen, W. N., & Binder, H. (2020). Transfer learning of regression models from a sequence of datasets by penalized estimation. arXiv preprint arXiv:2007.02117. https://arxiv.org/pdf/2007.02117 

  8. Hock, M., Hofmann, R., Essl, F., Pyšek, P., Bruelheide, H., & Erfmeier, A. (2020). Native distribution characteristics rather than functional traits explain preadaptation of invasive species to high‐UV‐B environments. Diversity and Distributions. https://doi.org/10.1111/ddi.13113 

  9. Cagua, F. (2020). Plant–pollinator communities: environmental gradients, trade-offs, and controllability. PhD Thesis. https://bit.ly/3kZDHrZ 

  10. Álvarez-Noriega, M., Burgess, S. C., Byers, J. E., Pringle, J. M., Wares, J. P., & Marshall, D. J. (2020). Global biogeography of marine dispersal potential. Nature Ecology & Evolution, 4(9), 1196–1203. https://doi.org/10.1038/s41559-020-1238-y 

  11. Anton, C. (2020). The Demography and Comparative Ethology of Top Predators in a Multi-Carnivore System (Doctoral dissertation, UC Santa Cruz). https://escholarship.org/content/qt3xd9379b/qt3xd9379b.pdf 

  12. Berkel, C., & Cacan, E. (2020). GAB2 and GAB3 are expressed in a tumor stage-, grade- and histotype-dependent manner and are associated with shorter progression-free survival in ovarian cancer. Journal of Cell Communication and Signaling. https://doi.org/10.1007/s12079-020-00582-3 

  13. Mallet, M. D. (2020). Meteorological normalisation of PM10 using machine learning reveals distinct increases of nearby source emissions in the Australian mining town of Moranbah. Atmospheric Pollution Research. https://doi.org/10.1016/j.apr.2020.08.001 

  14. Presa-Reyes, M., Bogosian, B., Schonhoff, B., Jerauld, C., Moreyra, C., Gardinali, P., & Chen, S. C. A Water Quality Research Platform for the Near-real-time Buoy Sensor Data. https://users.cs.fiu.edu/~chens/PDF/IRI20_Buoy.pdf 

  15. Dogucu, M., & Çetinkaya-Rundel, M. (2020). Web Scraping in the Statistics and Data Science Curriculum: Challenges and Opportunities. Journal of Statistics Education, 1–11. https://doi.org/10.1080/10691898.2020.1787116 

  16. Scott, T. A., Ulibarri, N., & Perez Figueroa, O. (2020). NEPA and National Trends in Federal Infrastructure Siting in the United States. Review of Policy Research. https://doi.org/10.1111/ropr.12399 

  17. Waldock, C. A., De Palma, A., Borges, P. A. V., & Purvis, A. (2020). Insect occurrence in agricultural land‐uses depends on realized niche and geographic range properties. Ecography. https://doi.org/10.1111/ecog.05162 

  18. Saleh, S. N., Lehmann, C. U., McDonald, S. A., Basit, M. A., & Medford, R. J. (2020). Understanding public perception of coronavirus disease 2019 (COVID-19) social distancing on Twitter. Infection Control & Hospital Epidemiology, 1–8. https://doi.org/10.1017/ice.2020.406