rOpenSci HQ

Community Calls

Join us for our next Community Call - The Wild World of Data Repositories - on 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 Review

We’re thrilled to announce three new rOpenSci Software Review Editors: Laura DeCicco, Julia Gustavsen, Mauro Lepore



Software 📦

CRAN: GitHub:

New Packages

  • The first version (v1.12) of mcbette is on CRAN - model comparison using babette. Checkout the docs to get started. This package recently went through rOpenSci software review. mcbette mcbette
  • The firstversion (v0.0.14) of BaseSet is on CRAN - working with sets the tidy way. Checkout the docs to get started. This package recently went through rOpenSci software review. BaseSet BaseSet
  • The first version (v0.1.0) of rgnparser is on CRAN - parse scientific names using the Go tool gnparser. Checkout the docs to get started. rgnparser rgnparser
  • The first version (v1.0.0) of dataspice is on CRAN - create lightweight Schema.org descriptions of data. Checkout the docs to get started. dataspice dataspice
  • The first version (v0.2.0) of taxlist is on CRAN - handling taxonomic lists. Checkout the docs to get started. This package recently went through rOpenSci software review. taxlist taxlist

New Versions

  • 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 (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
  • A new version (v0.6.0) of microdemic is on CRAN - Microsoft Academic API client. See the release notes for changes. Checkout the README to get started. microdemic microdemic
  • A new version (v0.7.2) 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 (v0.4.2) of nlrx is on CRAN - setup, run and analyze NetLogo model simulations. See the release notes for changes. Checkout the docs to get started. nlrx nlrx
  • A new version (v0.5.2) of tidyhydat is on CRAN - Water Survey of Canada hydrometric data. See the release notes for changes. Checkout the docs to get started. tidyhydat tidyhydat
  • A new version (v1.2.0) of jqr is on CRAN - a client for JQ, the JSON processor. See the release notes for changes. Checkout the docs to get started. jqr jqr
  • A new version (v1.3.0) of RefManageR is on CRAN - tools for importing and working with bibliographic references. See the NEWS for changes. Checkout the vignettes to get started. RefManageR RefManageR
  • A new version (v1.0.2) of gert is on CRAN - simple git client for R. See the release notes for changes. Checkout the docs to get started. gert gert
  • A new version (v2.0.4) of EML is on CRAN - read and write ecological metadata language files. See the release notes for changes. Checkout the docs to get started. EML EML
  • A new version (v2.5.2) 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 (v1.2.3) of rentrez is on CRAN - ENTREZ in R. See the release notes for changes. Checkout the docs to get started. rentrez rentrez
  • A new version (v0.2.11) of ropenaq is on CRAN - air quality data from the open data platform OpenAQ. See the release notes for changes. Checkout the docs to get started. ropenaq ropenaq
  • A new version (v2.2.4) 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 (v0.3.1) 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 (v2.2) of babette is on CRAN - control BEAST2 from R. See the release notes for changes. Checkout the docs to get started. babette babette
  • A new version (v0.0.8) 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 (v1.4.0) of datapack is on CRAN - flexible container to transport and manipulate data. See the release notes for changes. Checkout the docs to get started. datapack datapack
  • A new version (v0.1.4) of gitignore is on CRAN - create useful .gitignore files for your project. See the release notes for changes. Checkout the docs to get started. gitignore gitignore
  • A new version (v0.1.4) of osmdata is on CRAN - import OpenStreetMap data as simple features or spatial objects. See the release notes for changes. Checkout the docs to get started. osmdata osmdata
  • A new version (v0.7.0) of rerddap is on CRAN - General Purpose Client for ERDDAP Servers. See the release notes for changes. Checkout the docs to get started. rerddap rerddap
  • A new version (v2.3) of mauricer is on CRAN - install BEAST2 packages. See the release notes for changes. Checkout the docs to get started. mauricer mauricer
  • A new version (v1.1-5) of suppdata is on CRAN - downloading supplementary data from published manuscripts. See the release notes for changes. Checkout the vignette to get started. suppdata suppdata
  • A new version (v2.2.1) 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 (v0.9.99) of taxize is on CRAN - taxonomic toolbelt for R. See the release notes for changes. Checkout the taxize book to get started. taxize taxize
  • A new version (v0.7.0) of rredlist is on CRAN - IUCN Red List client. See the release notes for changes. Checkout the README to get started. rredlist rredlist
  • A new version (v0.0.9) 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 (v0.8.0) of stplanr is on CRAN - sustainable transport planning. See the release notes for changes. Checkout the docs to get started. stplanr stplanr
  • A new version (v7.12.7) 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 (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



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 packages were recently submitted:



On the blog

Liam Brierley wrote a very nice post on our blog about using some rOpenSci tools to study Coronaviruses: Using Open-Access Tools (rentrez, taxize) to Find Coronaviruses, Their Genetic Sequences, and Their Hosts


Tech notes

Scott Chamberlain wrote a post titled fulltext: Behind the Scenes, going behind the scenes of the fulltext package. The post describes the wandering path the package has gone through to help R users obtain full text versions of scholarly articles for text-mining, including working with Crossref, to building custom web APIs and balancing performance against other considerations.


Jeroen Ooms wrote a post about the V8 package: Installing V8 is now even easier.

Jeroen Ooms wrote a post on: Moving away from Travis CI.



Citations

The following 20 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. Bayley, D. T. I., Purvis, A., Nellas, A. C., Arias, M., & Koldewey, H. J. (2020). Measuring the long-term success of small-scale marine protected areas in a Philippine reef fishery. Coral Reefs. https://doi.org/10.1007/s00338-020-01987-7 

  2. Carraro, L., Mächler, E., Wüthrich, R., & Altermatt, F. (2020). Environmental DNA allows upscaling spatial patterns of biodiversity in freshwater ecosystems. Nature Communications, 11(1). https://doi.org/10.1038/s41467-020-17337-8 

  3. Weyna, A., & Romiguier, J. (2020). Relaxation of purifying selection suggests low effective population size in eusocial Hymenoptera and solitary pollinating bees. https://doi.org/10.1101/2020.04.14.038893 

  4. Sanchez‐Martinez, P., Martínez‐Vilalta, J., Dexter, K. G., Segovia, R. A., & Mencuccini, M. (2020). Adaptation and coordinated evolution of plant hydraulic traits. Ecology Letters. https://doi.org/10.1111/ele.13584 

  5. Feenstra, B. (2020). Development of Methodologies for the Use and Application of Air Quality Sensors to Enable Community Air Monitoring (Doctoral dissertation, UC Riverside) https://escholarship.org/content/qt0659j8sn/qt0659j8sn.pdf 

  6. Westgate, M. J., Barton, P. S., Lindenmayer, D. B., & Andrew, N. R. (2020). Quantifying shifts in topic popularity over 44 years of Austral Ecology. Austral Ecology, 45(6), 663–671. https://doi.org/10.1111/aec.12938 

  7. Behrendt, I., Fasshauer, M., & Eichner, G. (2020). Gluten intake and metabolic health: conflicting findings from the UK Biobank. European Journal of Nutrition. https://doi.org/10.1007/s00394-020-02351-9 

  8. Chugunkova, A. V., & Pyzhev, A. I. (2020). Impacts of Global Climate Change on Duration of Logging Season in Siberian Boreal Forests. Forests, 11(7), 756. https://doi.org/10.3390/f11070756 

  9. Kakioka, R., Mori, S., Kokita, T., Hosoki, T. K., Nagano, A. J., Ishikawa, A., … Kitano, J. (2020). Multiple waves of freshwater colonization of the three-spined stickleback in the Japanese Archipelago. https://doi.org/10.21203/rs.3.rs-59443/v1 

  10. Hovorka, A. (2020). Predictive Modeling in Fugitive Emissions Testing. Thesis. https://shareok.org/bitstream/handle/11244/325365/2020_Hovorka_Abigail_Faye_Thesis.pdf?sequence=2 

  11. Montero-Manso, P., & Hyndman, R. J. (2020). Principles and Algorithms for Forecasting Groups of Time Series: Locality and Globality. arXiv preprint arXiv:2008.00444 https://arxiv.org/pdf/2008.00444.pdf 

  12. Feenstra, B., Collier-Oxandale, A., Papapostolou, V., Cocker, D., & Polidori, A. (2020). The AirSensor open-source R-package and DataViewer web application for interpreting community data collected by low-cost sensor networks. Environmental Modelling & Software, 134, 104832. https://doi.org/10.1016/j.envsoft.2020.104832 

  13. Li, M. Application of automatic sentiment analysis: The role of emotions in an experimental learning intervention. https://psyarxiv.com/upfs9/download?format=pdf 

  14. Kuempel, C. D., Frazier, M., Nash, K. L., Jacobsen, N. S., Williams, D. R., Blanchard, J. L., … Halpern, B. S. (2020). Integrating Life Cycle and Impact Assessments to Map Food’s Cumulative Environmental Footprint. One Earth, 3(1), 65–78. https://doi.org/10.1016/j.oneear.2020.06.014 

  15. Laguna, L., Fiszman, S., Puerta, P., Chaya, C., & Tárrega, A. (2020). The impact of COVID-19 lockdown on food priorities. Results from a preliminary study using social media and an online survey with Spanish consumers. Food Quality and Preference, 86, 104028. https://doi.org/10.1016/j.foodqual.2020.104028 

  16. Sodhi, K., Wang, X., Chaudhry, M. A., Lakhani, H. V., Zehra, M., Pratt, R., … Shapiro, J. I. (2020). Central Role for Adipocyte Na,K-ATPase Oxidant Amplification Loop in the Pathogenesis of Experimental Uremic Cardiomyopathy. Journal of the American Society of Nephrology, 31(8), 1746–1760. https://doi.org/10.1681/asn.2019101070 

  17. Minoli I., Pérez C.H.F., Morando M., Avila L.J. (2020) Biogeography, Ecology, and Spatial Patterns of Patagonian Lizards. In: Morando M., Avila L. (eds) Lizards of Patagonia. Natural and Social Sciences of Patagonia. Springer, Cham. https://doi.org/10.1007/978-3-030-42752-8_8 

  18. Yeşilkanat, C. M. (2020). Spatio-temporal estimation of the daily cases of COVID-19 in worldwide using random forest machine learning algorithm. Chaos, Solitons & Fractals, 140, 110210. https://doi.org/10.1016/j.chaos.2020.110210 

  19. Kopp, T., & Salecker, J. (2020). How traders influence their neighbours: Modelling social evolutionary processes and peer effects in agricultural trade networks. Journal of Economic Dynamics and Control, 117, 103944. https://doi.org/10.1016/j.jedc.2020.103944 

  20. Aragão e Pina, J., Passos, A. M., Maynard, M. T., & Sinval, J. (2021). Self-efficacy, mental models and team adaptation: A first approach on football and futsal refereeing. Psychology of Sport and Exercise, 52, 101787. https://doi.org/10.1016/j.psychsport.2020.101787