rOpenSci HQ

  • Join us for our next Community Call - Maintaining an R package - on March 18, 2020, with Julia Silge, Leonardo Collado Torres, Erin Grand, Elin Waring, and Scott Chamberlain.

Software 📦

CRAN: GitHub:

New Packages

  • The first version (v0.2.8) of osfr is on CRAN - interface to the Open Science Framework (OSF). See the release notes for changes. Checkout the docs to get started.
  • The first version (v0.1.0) of taxadb is on CRAN - a local taxonomic database interface. Checkout the docs to get started.
  • The first version (v0.1.0) of outsider.base is on CRAN - base package for outsider. Checkout the docs to get started.

New Versions

  • A new version (v1.0.3) of cyphr is on CRAN - high level encryption wrappers. See the release notes for changes. Checkout the docs to get started.

    fix test for stringsAsFactors change for R v4

  • A new version (v0.2.1) of git2rdata is on CRAN - store and retrieve data.frames in a Git repository. See the release notes for changes. Checkout the docs to get started.

    fix examples and tests for stringsAsFactors change for R v4

  • A new version (v0.5.0) of webchem is on CRAN - Chemical information from the web. See the release notes for changes. Checkout the docs to get started.

    new data sources; many bug fixes

  • A new version (v0.6.0) 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.

    improved function reference in docs site; fixes for JSON encoded body requests; many other fixes

  • A new version (v7.11.0) 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.

    allow dynamic files; many improvements and bug fixes

  • A new version (v1.1.2) of lingtypology is on CRAN - linguistic typology and mapping. See the release notes for changes. Checkout the docs to get started.

    many parameter name changes across functions; fixes for stringsAsFactors change for R v4

  • A new version (v2.4.3) of RNeXML is on CRAN - Semantically Rich I/O for the NeXML Format. See the release notes for changes. Checkout the docs to get started.

    fix tests for stringsAsFactors change for R v4

  • A new version (v0.5.1) of stplanr is on CRAN - sustainable transport planning. See the release notes for changes. Checkout the docs to get started.

    fixes for stringsAsFactors change for R v4

  • A new version (v1.3.0) 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.

    added two new data hubs; improved a function

  • A new version (v2.3.5) of beautier is on CRAN - create BEAST2 input files programmatically. See the release notes for changes. Checkout the docs to get started.

    gains 4 new functions, renames a few functions

  • A new version (v0.0.11) of piggyback is on CRAN - Managing larger data on a GitHub repository. See the release notes for changes. Checkout the docs to get started.

    guess_repo() now infers a remote when there are multiple remotes; fixes to release_info() and pb_info()

  • A new version (v0.3.3) of taxa is on CRAN - taxonomic classes for groupings of taxonomic names without data, and those with data. See the release notes for changes. Checkout the docs to get started.

    numeric column names in tables in taxmap are now supported; bug fixes

  • A new version (v3.1.2) of qualtRics is on CRAN - download Qualtrics survey data. See the release notes for changes. Checkout the docs to get started.

    5 functions deprecated; now using updated version of Qualtrics API

  • A new version (v1.1.0) of dbparser is on CRAN - DrugBank database XML parser. See the release notes for changes. Checkout the docs to get started.

    complete overhaul of exported function names

  • A new version (v0.4.0) of isdparser is on CRAN - parse NOAA Integrated Surface data files. See the release notes for changes. Checkout the docs to get started.

    new function isd_parse_csv() to work with ISD csv files

  • A new version (v0.0.6) 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.

    fixed problem when no time coordinate in dataset; add_tabledap() overlays on gridded maps now work for ggplot2



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 submitted:

The following package recently went through our software-review process and has been approved:



On the blog

It’s time for another installment of … 2 Months in 2 Minutes - rOpenSci News, February 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)


Julia Stewart Lowndes cross-posted a blog post on our blog: rOpenSci’s Leadership in #rstats Culture. In it she reflects on her experience at the 2020 RStudio conference as well as her experience at the 2015 rOpenSci Unconference.


Software Review:

Malcom Morgan wrote about his recently rOpenSci reviewed package opentripplanner: opentripplanner: Fast and Easy Multimodal Trip Planning in R with OpenTripPlanner. Malcom discusses the design of the package, and how to use opentripplanner.



Use Cases

The following 15 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.

Peter Desmet asked a good question that many R package maintainers run in to: What if raw data in package is too large?



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. Checkout our Contributing Guide for why and how to contribute to rOpenSci.

We’ve had six recent examples of maintainer transitions within rOpenSci:

We don’t have any packages looking for new maintainers - if you are a maintainer and want to hand over that role to someone else get in touch with us.






Keep up with rOpenSci


Footnotes

  1. Godfrey, J. M., Riggio, J., Orozco, J., Guzmán‐Delgado, P., Chin, A. R. O., & Zwieniecki, M. A. (2020). Ray fractions and carbohydrate dynamics of tree species along a 2750 m elevation gradient indicate climate response, not spatial storage limitation. New Phytologist, 225(6), 2314–2330. https://doi.org/10.1111/nph.16361 

  2. Zhong, B. (2019). Towards Developing a Double Cropping System Between Winter Barley and Soybean in the Upper Midwest. http://bit.ly/3co35Es 

  3. Betts, M. G., Wolf, C., Pfeifer, M., Banks-Leite, C., Arroyo-Rodríguez, V., Ribeiro, D. B., … Ewers, R. M. (2019). Extinction filters mediate the global effects of habitat fragmentation on animals. Science, 366(6470), 1236–1239. https://doi.org/10.1126/science.aax9387 

  4. Kim, K. W., Allen, D. W., Briese, T., Couper, J. J., Barry, S. C., … Colman, P. G. (2020). Higher frequency of vertebrate‐infecting viruses in the gut of infants born to mothers with type 1 diabetes. Pediatric Diabetes, 21(2), 271–279. https://doi.org/10.1111/pedi.12952 

  5. Atalah, J., & Forrest, B. (2019). Forecasting mussel settlement using historical data and boosted regression trees. Aquaculture Environment Interactions, 11, 625–638. https://doi.org/10.3354/aei00337 

  6. Karakülah, G., Arslan, N., Yandım, C., & Suner, A. (2019). TEffectR: an R package for studying the potential effects of transposable elements on gene expression with linear regression model. PeerJ, 7, e8192. https://doi.org/10.7717/peerj.8192 

  7. Yusri, S., Siregar, V. P., & Suharsono. (2019). Distribution Modelling of Porites (Poritidae) in Indonesia. IOP Conference Series: Earth and Environmental Science, 363, 012025. https://doi.org/10.1088/1755-1315/363/1/012025 

  8. Clark, T. J., & Luis, A. D. (2019). Nonlinear population dynamics are ubiquitous in animals. Nature Ecology & Evolution, 4(1), 75–81. https://doi.org/10.1038/s41559-019-1052-6 

  9. Ekroos, J., Kleijn, D., Batáry, P., Albrecht, M., Báldi, A., Blüthgen, N., … Smith, H. G. (2020). High land-use intensity in grasslands constrains wild bee species richness in Europe. Biological Conservation, 241, 108255. https://doi.org/10.1016/j.biocon.2019.108255 

  10. Lysne, V. (2019). Biomarkers of one-carbon metabolism and B-vitamin status: Targeted metabolomics in rats and humans exploring the effects of PPARα-activation and dietary composition. http://bit.ly/3crBane 

  11. Vitale, O., Preste, R., Palmisano, D., & Attimonelli, M. (2019). A data and text mining pipeline to annotate human mitochondrial variants with functional and clinical information. Molecular Genetics & Genomic Medicine, 8(2). https://doi.org/10.1002/mgg3.1085 

  12. Wcisel, D. J., III, J. T. H., Yoder, J. A., & Dornburg, A. (preprint) Transcriptome Ortholog Alignment Sequence Tools (TOAST) for Phylogenomic Dataset Assembly. https://doi.org/10.21203/rs.2.16269/v3 

  13. Sansone, A., Cignarelli, A., Ciocca, G., Pozza, C., Giorgino, F., Romanelli, F., & Jannini, E. A. (2019). The Sentiment Analysis of Tweets as a New Tool to Measure Public Perception of Male Erectile and Ejaculatory Dysfunctions. Sexual Medicine, 7(4), 464–471. https://doi.org/10.1016/j.esxm.2019.07.001 

  14. Finnegan, A., Sao, S. S., & Huchko, M. J. (2019). Using a Chord Diagram to Visualize Dynamics in Contraceptive Use: Bringing Data Into Practice. Global Health: Science and Practice, 7(4), 598–605. https://doi.org/10.9745/ghsp-d-19-00205 

  15. Kim, J., Plitman, E., Iwata, Y., Nakajima, S., Mar, W., Patel, R., … Graff-Guerrero, A. (2020). Neuroanatomical profiles of treatment-resistance in patients with schizophrenia spectrum disorders. Progress in Neuro-Psychopharmacology and Biological Psychiatry, 99, 109839. https://doi.org/10.1016/j.pnpbp.2019.109839