rOpenSci HQ

We’ve just released the fifth version (v0.5) of the rOpenSci Developer Guide. Some noteable updates:


On Oct 22, our Community Manager Stefanie Butland, and Software Peer Review Editor Brooke Anderson, presented to R-Ladies East Lansing and Chicago about our Community Contributing Guide and software peer review process. Brooke’s slides



Software 📦

CRAN: GitHub:

New Versions

  • A new version (v0.3.2) of getCRUCLdata is on CRAN - use and explore CRU CL v. 2.0 climatology elements. See the release notes for changes. Checkout the docs to get started. getCRUCLdata getCRUCLdata
  • A new version (v0.0.9) 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 (v3.0.1) of nasapower is on CRAN - NASA POWER API Client. See the release notes for changes. Checkout the docs to get started. nasapower nasapower
  • A new version (v0.3.0) of opentripplanner is on CRAN - client for OpenTripPlanner for journey planning. See the release notes for changes. Checkout the docs to get started. opentripplanner opentripplanner
  • A new version (v0.0.8) of plotdap is on CRAN - easily visualize data from ERDDAP servers via the rerddap package. See the release notes for changes. Checkout the vignette to get started. plotdap plotdap
  • A new version (v3.0.11) of rotl is on CRAN - an interface to the Open Tree of Life API. See the release notes for changes. Checkout the vignettes to get started. rotl rotl
  • A new version (v0.1.15) of spatsoc is on CRAN - detecting spatial and temporal groups in GPS relocations. See the release notes for changes. Checkout the docs to get started. spatsoc spatsoc
  • A new version (v0.7.0) of wellknown is on CRAN - Convert between WKT and GeoJSON. See the release notes for changes. Checkout the vignette to get started. wellknown wellknown
  • A new version (v0.4.2) 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 (v1.6.0) 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
  • A new version (v2.2.2) 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 (v2.2) of spelling is on CRAN - tools for spell checking. See the release notes for changes. Checkout the README to get started. spelling spelling
  • A new version (v2.2) of beastier is on CRAN - Provides a way to call BEAST2 from R. See the release notes for changes. Checkout the docs to get started. beastier beastier
  • A new version (v2.4) of beautier is on CRAN - create BEAST2 input files programmatically. See the release notes for changes. Checkout the docs to get started. beautier beautier
  • A new version (v2.5.0) of magick is on CRAN - Advanced graphics and Image-Processing in R. See the release notes for changes. Checkout the vignette to get started. magick magick
  • A new version (v0.0.7) 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. arkdb arkdb
  • A new version (v0.3.0) of handlr is on CRAN - Convert among citation formats. See the release notes for changes. Checkout the docs to get started. handlr handlr
  • A new version (v1.0.1) 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 (v2.0-18) 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
  • A new version (v0.5.1) of iheatmapr is on CRAN - Interactive and complex heatmaps. See the release notes for changes. Checkout the docs to get started. iheatmapr iheatmapr
  • A new version (v0.1.6) of rinat is on CRAN - R client for iNaturalist APIs. See the release notes for changes. Checkout the docs to get started. rinat rinat
  • A new version (v2.0.4) 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. MODIStsp MODIStsp
  • A new version (v0.3.0) of parzer is on CRAN - parse messy geographic coordinates. See the release notes for changes. Checkout the docs to get started. parzer parzer
  • A new version (v0.2.2) of rbace is on CRAN - Bielefeld Academic Search Engine (BASE) client. See the release notes for changes. Checkout the docs to get started. rbace rbace
  • A new version (v2.0.2) of rmangal is on CRAN - interface to the Mangal database of ecological networks. See the release notes for changes. Checkout the docs to get started. rmangal rmangal
  • A new version (v0.5.2) of mapr is on CRAN - visualize species occurrence data. See the release notes for changes. Checkout the vignette to get started. mapr mapr



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 package was recently approved:

The following package was recently submitted:



On the blog

It’s time for another installment of … 2 Months in 2 Minutes - rOpenSci News, October 2020 - if you want a brief summary of the last 2 months of these newsletters, these blog posts are for you (written by Stefanie Butland)


Zhang-He Goh, Jonny Coates, and Hugo Gruson wrote a blog post that was cross-posted on the preLights blog: Covidpreprints.com: Automating Website Updates with the europepmc and rAltmetric Packages. In the post, they detail how they have used rOpenSci packages rAltmetric and europepmc (in addition to other R packages) to automate updating covidpreprints.com.


Software Review

Luke McGuinness wrote about his recently rOpenSci reviewed package medrxivr: Searching medRxiv and bioRxiv Preprint Data . He discusses the motivation behind the package, and highlights cases for medrxivr.



Citations

The following 21 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:

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. Bauder, J. M., Stodola, K. W., Benson, T. J., Miller, C. A., & Allen, M. L. (2020). Raccoon Pelt Price and Trapper Harvest Relationships Are Temporally Inconsistent. The Journal of Wildlife Management. https://doi.org/10.1002/jwmg.21928 

  2. Nalley, E. (2020). Picky eater or generalist feeder? Diet diversity and functional homogenization in herbivorous reef fishes (Doctoral dissertation, University of Hawai’i at Manoa). https://bit.ly/34wYk9y 

  3. Kleinschroth, F., Winton, R. S., Calamita, E., Niggemann, F., Botter, M., Wehrli, B., & Ghazoul, J. (2020). Living with floating vegetation invasions. Ambio. https://doi.org/10.1007/s13280-020-01360-6 

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

  5. Calero Valdez A. (2020) Making Reproducible Research Simple Using RMarkdown and the OSF. In: Meiselwitz G. (eds) Social Computing and Social Media. Design, Ethics, User Behavior, and Social Network Analysis. HCII 2020. Lecture Notes in Computer Science, vol 12194. Springer, Cham. https://link.springer.com/chapter/10.1007/978-3-030-49570-1_3 

  6. Roa-Ureta, R. H., Henríquez, J., & Molinet, C. (2020). Achieving sustainable exploitation through co-management in three Chilean small-scale fisheries. Fisheries Research, 230, 105674. https://doi.org/10.1016/j.fishres.2020.105674 

  7. Ramiller, A. J. (2020). Don’t Destroy Our Neighborhood: Neighborhood Imaginaries and the Politics of Upzoning/Displacement through Development: Spatial and Temporal Dynamics of Residential Eviction and Capital Investment (Doctoral dissertation). https://bit.ly/2TtRE5P 

  8. Lawlor, J. A., & Arellano, S. M. (2020). Temperature and salinity, not acidification, predict near-future larval growth and larval habitat suitability of Olympia oysters in the Salish Sea. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-69568-w 

  9. Puschmann, C., & Pentzold, C. (2020). A field comes of age: tracking research on the internet within communication studies, 1994 to 2018. Internet Histories, 1–19. https://doi.org/10.1080/24701475.2020.1749805 

  10. Cahill, C. L., Anderson, S. C., Paul, A. J., MacPherson, L., Sullivan, M. G., van Poorten, B. T., … & Post, J. R. (2020). A spatial-temporal approach to modeling somatic growth across inland recreational fisheries landscapes. Canadian Journal of Fisheries and Aquatic Sciences, (ja). https://cdnsciencepub.com/doi/abs/10.1139/cjfas-2019-0434 

  11. Colli‐Silva, M., Reginato, M., Cabral, A., Forzza, R. C., Pirani, J. R., & Vasconcelos, T. N. da C. (2020). Evaluating shortfalls and spatial accuracy of biodiversity documentation in the Atlantic Forest, the most diverse and threatened Brazilian phytogeographic domain. TAXON, 69(3), 567–577. https://doi.org/10.1002/tax.12239 

  12. Madritsch, S., Bomers, S., Posekany, A., Burg, A., Birke, R., Emerstorfer, F., … Sehr, E. M. (2020). Integrative transcriptomics reveals genotypic impact on sugar beet storability. Plant Molecular Biology. https://doi.org/10.1007/s11103-020-01041-8 

  13. Kamiński, M., Muth, A., & Bogdański, P. (2020). Smoking, Vaping, and Tobacco Industry During COVID-19 Pandemic: Twitter Data Analysis. Cyberpsychology, Behavior, and Social Networking. https://doi.org/10.1089/cyber.2020.0384 

  14. Torregroza Espinosa, A. C. (2020). Spatio-temporal distribution of temperature, salinity and suspended sediment on the deltaic front of the Magdalena River: Influence on nutrient concentration and primary productivity. PhD Thesis. https://bit.ly/3jCPUCc 

  15. Mancosu, M., & Vegetti, F. (2020). What You Can Scrape and What Is Right to Scrape: A Proposal for a Tool to Collect Public Facebook Data. Social Media + Society, 6(3), 205630512094070. https://doi.org/10.1177/2056305120940703 

  16. Li, Z. R., Martin, B. D., Dong, T. Q., Fuglstad, G. A., Paige, J., Riebler, A., … & Wakefield, J. (2020). Space-Time Smoothing of Demographic and Health Indicators using the R Package SUMMER. arXiv preprint arXiv:2007.05117 https://arxiv.org/pdf/2007.05117

  17. Foster, Z. S. L. (2020). Development of Computational, Visualization, and Molecular Tools for Fungal and Oomycete Community Ecology. PhD Dissertation. Oregon State University. https://ir.library.oregonstate.edu/downloads/qr46r6685 

  18. Portik, D. M., & Wiens, J. J. (2020). Do Alignment and Trimming Methods Matter for Phylogenomic (UCE) Analyses? Systematic Biology. https://doi.org/10.1093/sysbio/syaa064 

  19. Brandão, L. A. C., Agrelli, A., Bernardo, L., Paparella, F., Moura, R., & Crovella, S. (2020). PlatCOVID: A Novel Web Tool to Analyze, Curate and Share COVID-19 Literature. https://doi.org/10.21203/rs.3.rs-42169/v1 

  20. Larouche, O., Hodge, J. R., Alencar, L. R. V., Camper, B., Adams, D. S., Zapfe, K., … Price, S. A. (2020). Do key innovations unlock diversification? A case-study on the morphological and ecological impact of pharyngognathy in acanthomorph fishes. Current Zoology. https://doi.org/10.1093/cz/zoaa048 

  21. Lakoba, V. T., Brooks, R. K., Haak, D. C., & Barney, J. N. (2020). An Analysis of US State Regulated Weed Lists: A Discordance between Biology and Policy. BioScience, 70(9), 804–813. https://doi.org/10.1093/biosci/biaa081