rOpenSci News is four years old! 🎉 Our first newsletter came out on December 15th, 2014. Check it out at https://news.ropensci.org/update-2014-12-15/. As you can see the newsletter has changed a lot since then. Thanks for reading!


rOpenSci HQ


Software 📦

CRAN: GitHub:

New versions

  • A new version (v0.5.2) of visdat is on CRAN - create preliminary exploratory data visualisations of an entire dataset to identify problems or unexpected features using ggplot2. See the release notes for changes. Checkout the docs to get started.

    fix for readr

  • A new version (v0.3.1) of auk is on CRAN - eBird data extraction and processing. See the release notes for changes. Checkout the docs to get started.

    rlang fixes and change to auk_unique()

  • A new version (v0.4.0) of brranching is on CRAN - Fetch Phylogenies from Many Sources. See the release notes for changes. Checkout the vignette to get started.

    now using phylocomr for phylomatic_local and rbladj fxns

  • A new version (v1.3.7) 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.

    bug fix for computation of custom spectral indices containing additive parameters

  • A new version (v0.8.0) of rnoaa is on CRAN - NOAA Weather Data from R. See the release notes for changes. Checkout the vignettes to get started.

    3 new data sources (& fxns); new fxn ghcnd_read(); optionally get units for ncdc() output

  • A new version (v0.5.2) of hoardr is on CRAN - Manage cached files. See the release notes for changes. Checkout the vignette to get started.

    important bug fix: now multiple hoardr() objects in same R session don’t collide

  • A new version (v1.1) of writexl is on CRAN - a portable, light-weight data frame to xlsx exporter. See the release notes for changes. Checkout the README to get started.

    update bundled libxlswriter; don’t write blank xlsx strings for NA and ""

  • A new version (v1.5) of graphql is on CRAN - Bindings to libgraphqlparser for R. See the release notes for changes. Checkout the README to get started.

    update bundled libgraphqlpaser

  • A new version (v0.1.2) of phylocomr is on CRAN - Interface to Phylocom for analysis of phylogenetic community structure and character evolution. See the release notes for changes. Checkout the vignette to get started.

    bug fix - ph_phylomatic() wasn’t working with some phylogenies



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.

The following packages recently went through our onboarding process and have been approved!

The following packages were recently submitted:



On the blog

Community

Hoa Ye, Melanie Frazier, Julia Stewart-Lowndes, Carl Beottiger and Noam Ross wrote up a summary of our recent community call on code review in the lab, with links to notes and a recording of the call. Community Call Summary - Code Review in the Lab


Dan Sholler and Stefanie Butland wrote about an upcoming community call: Community Call - Governance strategies for open source research software projects

Software Review

Mahmoud Ahmed wrote about his recently rOpenSci reviewed package colocr, for conducting co-localization analysis of fluorescence microscopy images. Co-localization analysis of fluorescence microscopy images

Alec Robitaille, Quinn Webber, and Eric Vander Wal wrote about their recently rOpenSci reviewed package spatsoc for detecting spatial and temporal groups in GPS relocations. Detecting spatiotemporal groups in relocation data with spatsoc

tech notes

Dom Bennett wrote about his package just gone through rOpenSci review for working with a local copy of GenBank data in R. restez: Query GenBank locally


Scott Chamberlain wrote about a new release of our rnoaa package for working with many NOAA datasets, including a number of new data sets and the addition of units to rnoaa::ncdc() data. rnoaa: new data sources and NCDC units



Use cases

The following 17 works use/cite rOpenSci software:



In the news

William Chase wrote a blog post using our package rgbif: Animated Species Invasions with rgbif and gganimate. A static map is below - check out the post for the animated maps.


Hiroaki Yutani used our package magick in a nice post about How To Convert A Human To Waves By Magick Package. A static image is below - check out the post for the animated image.






Keep up with rOpenSci


Footnotes

  1. Anderson, B., Eyers, D., Ford, R., Giraldo Ocampo, D., Peniamina, R., Stephenson, J., … & Jack, M. NZ GREEN Grid Household Electricity Demand Study. http://reshare.ukdataservice.ac.uk/853334/14/NZ_GREEN_GridHouseholdElectricityDemandStudy_HouseholdAttributeData_v1.0.pdf 

  2. Sabatini, F. M., de Andrade, R. B., Paillet, Y., Ódor, P., Bouget, C., Campagnaro, T., … & Sitzia, T. Trade‐offs between carbon stocks and biodiversity in European temperate forests. Global Change Biology. https://onlinelibrary.wiley.com/doi/full/10.1111/gcb.14503 

  3. Walsh, E. I., & Cherbuin, N. (preprint). Mapping the Literature on Nutritional Interventions in Cognitive Health: A Data-Driven Approach. https://www.preprints.org/manuscript/201811.0527/download/final_file 

  4. António, N., de Almeida, A., & Nunes, L. (2018). Hotel booking demand datasets. Data in Brief. https://doi.org/10.1016/j.dib.2018.11.126 

  5. Aprosio, A. P., & Moretti, G. (2018). Tint 2.0: An all-inclusive Suite for NLP in Italian. Proceedings of CLIC-it. http://ceur-ws.org/Vol-2253/paper58.pdf 

  6. Borstein, S. R., Fordyce, J. A., O’Meara, B. C., Wainwright, P. C., & McGee, M. D. (2018). Reef fish functional traits evolve fastest at trophic extremes. Nature Ecology & Evolution. https://doi.org/10.1038/s41559-018-0725-x 

  7. Ott, C. J., Federation, A. J., Schwartz, L. S., Kasar, S., Klitgaard, J. L., Lenci, R., … Bradner, J. E. (2018). Enhancer Architecture and Essential Core Regulatory Circuitry of Chronic Lymphocytic Leukemia. Cancer Cell. https://doi.org/10.1016/j.ccell.2018.11.001 

  8. White, L., & Santy, S. (2018). DataDepsGenerators.jl: making reusing data easy by automatically generating DataDeps.jl registration code. Journal of Open Source Software, 3(31), 921. https://doi.org/10.21105/joss.00921 

  9. Soul, J., Hardingham, T., Boot-Handford, R., & Schwartz, J. M. (2018). SkeletalVis: An exploration and meta-analysis data portal of cross-species skeletal transcriptomics data. Bioinformatics. https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/bty947/26770069/bty947.pdf 

  10. Hanson, J. O., Fuller, R. A., & Rhodes, J. R. (2018). Conventional methods for enhancing connectivity in conservation planning do not always maintain gene flow. Journal of Applied Ecology. https://doi.org/10.1111/1365-2664.13315 

  11. Evans, L. K., & Nishioka, J. (2018). Accumulation processes of trace metals into Arctic sea ice: distribution of Fe, Mn and Cd associated with ice structure. Marine Chemistry. https://doi.org/10.1016/j.marchem.2018.11.011 

  12. Sinval, J., Casanova, J. R., Marôco, J., & Almeida, L. S. (2018). University student engagement inventory (USEI): Psychometric properties. Current Psychology. https://doi.org/10.1007/s12144-018-0082-6 

  13. Pelletier, T. A., Carstens, B. C., Tank, D. C., Sullivan, J., & Espíndola, A. (2018). Predicting plant conservation priorities on a global scale. Proceedings of the National Academy of Sciences, 201804098. https://doi.org/10.1073/pnas.1804098115 

  14. Da Silva, R., Pearce Kelly, P., Zimmerman, B., Knott, M., Foden, W., & Conde, D. A. (2018). Assessing the Conservation Potential of Fish and Corals in Aquariums Globally. Journal for Nature Conservation. https://doi.org/10.1016/j.jnc.2018.12.001 

  15. Vidal, J. de D., de Souza, A. P., & Koch, I. (2018). Impacts of landscape composition, marginality of distribution, soil fertility, and climatic stability on the patterns of woody plant endemism in the Cerrado. https://doi.org/10.1101/362475 

  16. Kline, B. P., Schieffer, K. M., Choi, C. S., Connelly, T., Chen, J., Harris, L., … Koltun, W. A. (2018). Multifocal Versus Conventional Unifocal Diverticulitis: A Comparison of Clinical and Transcriptomic Characteristics. Digestive Diseases and Sciences. https://doi.org/10.1007/s10620-018-5403-y 

  17. Zill, B. (2018). Enriching the feature space of transfer learning in user analysis in online social networks. Thesis. Universität Koblenz-Landau. https://kola.opus.hbz-nrw.de/opus45-kola/frontdoor/index/index/docId/1763