rOpenSci HQ

Community Calls

Join us for our next Community Call - The Wild World of Data Repositories - this Wednesday, December 16th, 2020 (10-11 AM PST). This call will be moderated by Kara Woo with speakers Daniella Lowenberg, Matt Jones, Carl Boettiger and Karthik Ram.



Software 📦

CRAN: GitHub:

New Packages

  • The first version (v0.1.1) of outsider is on CRAN - “Install and Run Programs, Outside of R, Inside of R”. Checkout the docs to get started. outsider outsider
  • The first version (v0.0.2) of allcontributors is on CRAN - Acknowledge all Contributors to a Project. Checkout the docs to get started. allcontributors allcontributors

New Versions

  • A new version (v0.6.0) of vcr is on CRAN - record HTTP calls to disk for test caching. See the release notes for changes. Checkout the HTTP testing book to get started. vcr vcr
  • A new version (v0.0.4) of medrxivr is on CRAN - access and search MedRxiv and BioRxiv preprint data. See the release notes for changes. Checkout the docs to get started. medrxivr medrxivr
  • A new version (v3.0.1) of hunspell is on CRAN - High-Performance stemmer, tokenizer, and spell checker. See the release notes for changes. Checkout the vignette to get started. hunspell hunspell
  • A new version (v0.3.1) of tacmagic is on CRAN - positron emission tomography time-activity curve analysis. See the release notes for changes. Checkout the vignette to get started. tacmagic tacmagic
  • A new version (v0.7.4) 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
  • A new version (v1.13) of mcbette is on CRAN - model comparison using babette. See the release notes for changes. Checkout the docs to get started. mcbette mcbette
  • A new version (v0.2.0) of prism is on CRAN - Data from the Oregon State Prism Climate Project. See the release notes for changes. Checkout the vignette to get started. prism prism
  • A new version (v3.4.0) of rgbif is on CRAN - interface to the Global Biodiversity Information Facility API. See the release notes for changes. Checkout the occurrence manual to get started. rgbif rgbif
  • A new version (v0.3.0) of jaod is on CRAN - Directory of Open Access Journals client. See the release notes for changes. Checkout the docs to get started. jaod jaod
  • A new version (v1.1.1) of rnpn is on CRAN - Interface to the National Phenology Network API. See the release notes for changes. Checkout the docs to get started. rnpn rnpn
  • A new version (v0.7.3) 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
  • A new version (v0.7.1) 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
  • A new version (v0.4.3) 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 (v0.0.10) of phonfieldwork is on CRAN - linguistic phonetic fieldwork tools. See the release notes for changes. Checkout the docs to get started. phonfieldwork phonfieldwork
  • A new version (v1.3.6) 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



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 submitted:



On the blog

Richèl Bilderbeek wrote about using his mcbette package for: Selecting the Best Phylogenetic Evolutionary Model


Dennis Irorere wrote a post about solving a problem using a GraphQL service using the rOpenSci package ghql: Accessing GrahpQL from R



Citations

The following 22 works use/cite rOpenSci software:



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. Reimuth, J., & Zotz, G. (2020). The biogeography of the megadiverse genus Anthurium (Araceae). Botanical Journal of the Linnean Society, 194(2), 164-176. https://doi.org/10.1093/botlinnean/boaa044 

  2. Yu, V., Wyatt, S., Woodall, M., Sultan, M., Klaire, V., Bailey, K., & Mohammed, M. A. (2020). Impact of Vertical Integration of General Practices with an Acute Hospital on Hospital Admissions: a Retrospective Synthetic Matched Controlled Database Study. https://bit.ly/3gN1omx 

  3. Koch, L. K., Cunze, S., Kochmann, J., & Klimpel, S. (2020). Bats as putative Zaire ebolavirus reservoir hosts and their habitat suitability in Africa. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-71226-0 

  4. Göbel, S. (2020). Voting and Social Media-Based Political Participation. SocArXiv https://doi.org/10.31235/osf.io/sjq4g 

  5. Larouche, O., Benton, B., Corn, K. A., Friedman, S. T., Gross, D., Iwan, M., … Price, S. A. (2020). Reef-associated fishes have more maneuverable body shapes at a macroevolutionary scale. Coral Reefs, 39(5), 1427–1439. https://doi.org/10.1007/s00338-020-01976-w 

  6. De Sousa, K., & Solberg, S. Ø. (2020). Conservation Gaps in Traditional Vegetables Native to Europe and Fennoscandia. Agriculture, 10(8), 340. https://doi.org/10.3390/agriculture10080340 

  7. Polaina, E., Pärt, T., & Recio, M. R. (2020). Identifying hotspots of invasive alien terrestrial vertebrates in Europe to assist transboundary prevention and control. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-68387-3 

  8. Ihaka, R., & Gentleman, R. (1996). R: A Language for Data Analysis and Graphics. Journal of Computational and Graphical Statistics, 5(3), 299–314. https://doi.org/10.1080/10618600.1996.10474713 

  9. Mothes, C. C., Howell, H. J., & Searcy, C. A. (2020). Habitat suitability models for the imperiled wood turtle (Glyptemys insculpta) raise concerns for the species’ persistence under future climate change. Global Ecology and Conservation, 24, e01247. https://doi.org/10.1016/j.gecco.2020.e01247 

  10. Scott, A. 2020. Spatial variation in PM2. 5 concentrations across Timaru. Report, Environment Canterbury Regional Council https://bit.ly/3icvorg 

  11. Tonnis, B., Wang, M. L., Li, X., Wang, J., Puppala, N., Tallury, S., & Yu, J. (2020). Peanut FAD2 Genotype and Growing Location Interactions Significantly Affect the Level of Oleic Acid in Seeds. Journal of the American Oil Chemists’ Society, 97(9), 1001–1010. https://doi.org/10.1002/aocs.12401 

  12. Da Silva Abel, E. L., Delgado, R. C., Vilanova, R. S., Teodoro, P. E., da Silva Junior, C. A., Abreu, M. C., & Silva, G. F. C. (2020). Environmental dynamics of the Juruá watershed in the Amazon. Environment, Development and Sustainability. https://doi.org/10.1007/s10668-020-00890-z 

  13. Vantas, K., Sidiropoulos, E., & Evangelides, C. (2020). Estimating Rainfall Erosivity from Daily Precipitation Using Generalized Additive Models. Environmental Sciences Proceedings, 2(1), 21. https://doi.org/10.3390/environsciproc2020002021 

  14. Weber, A. (2020). Digital elevation models of German waterway and navigation. Report. http://doi.bafg.de/BfG/2020/BfG-2011.pdf 

  15. Nania, D., Flecks, M., & Rödder, D. (2020). Continuous expansion of the geographic range linked to realized niche expansion in the invasive Mourning gecko Lepidodactylus lugubris (Duméril & Bibron, 1836). PLOS ONE, 15(7), e0235060. https://doi.org/10.1371/journal.pone.0235060 

  16. Keppeler, F. W., Montaña, C. G., & Winemiller, K. O. (2020). The relationship between trophic level and body size in fishes depends on functional traits. Ecological Monographs. https://doi.org/10.1002/ecm.1415 

  17. Doyle, M. A., Schurer, S., & Silburn, S. (2020). Unintended Consequences of Welfare Reform: Evidence from Birth Outcomes of Aboriginal Australians. SSRN. http://ftp.iza.org/dp13543.pdf 

  18. Sass, C. A. B., Pimentel, T. C., Aleixo, M. G. B., Dantas, T. M., Cyrino Oliveira, F. L., Freitas, M. Q., … Esmerino, E. A. (2020). Exploring social media data to understand consumers’ perception of eggs: A multilingual study using Twitter. Journal of Sensory Studies. https://doi.org/10.1111/joss.12607 

  19. Allerton, T. A. P. (2020). Functional Attributes of Post-Disturbance Regeneration in Puerto Rican Tropical Dry Forest. Dissertation Thesis. https://bit.ly/2R9upwT 

  20. Davies, A. D., Lewis, Z., & Dougherty, L. R. (2020). A meta-analysis of factors influencing the strength of mate-choice copying in animals. Behavioral Ecology. https://doi.org/10.1093/beheco/araa064 

  21. Becker, D. J., & Han, B. A. (2020). The macroecology and evolution of avian competence for Borrelia burgdorferi. bioRxiv https://doi.org/10.1101/2020.04.15.040352 

  22. Greenville, A. C., Newsome, T. M., Wardle, G. M., Dickman, C. R., Ripple, W. J., & Murray, B. R. (2020). Simultaneously operating threats cannot predict extinction risk. Conservation Letters. https://doi.org/10.1111/conl.12758