rOpenSci HQ

  • rOpenSci’s community is increasingly international and multilingual. While we have operated primarily in English, we now receive submissions of packages from authors whose primary language is not. As we expand our community in this way, we want to learn from the experience of other organizations. How can we manage our peer-review process and open-source projects to be welcoming to non-native English speakers? Share your perspective in the public discussion and join our Community Call on Involving Multilingual Communities on Friday, June 28th. No RSVP needed.


Software 📦

CRAN: GitHub:

New packages

  • The first version (v0.1) of git2rdata is on CRAN - store and retrieve data.frames in a Git repository. Checkout the docs to get started. git2rdata git2rdata

New Versions

  • A new version (v0.3.3) of auk is on CRAN - eBird data extraction and processing. See the release notes for changes. Checkout the docs to get started. auk

    fixes to auk_date(), auk_protocol(), and auk_set_awk_path()

  • A new version (v1.3.9) 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

    fixes bug causing crashes on MOD14A1 product; adds support for product MCD12Q2

  • A new version (v1.21) of rtika is on CRAN - R Interface to Apache Tika. See the release notes for changes. Checkout the docs to get started. rtika rtika
  • A new version (v1.0.7) of skimr is on CRAN - compact and flexible summaries of data. See the release notes for changes. Checkout the vignettes to get started. skimr skimr

    stop assignment of foreign functions in namesspace at build time

  • A new version (v3.0.9) 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

    small fixes following updates to the Open Tree of Life API

  • A new version (v2.0.0) 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

    get_tiff_tags_reference() -> tif_tags_reference() & count_imgs() -> count_frames(); now can read certain frames of a TIFF image w/ read_tif()



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 two packages recently went through our software-review process and have been approved:



On the blog

Scott Chamberlain, Maëlle Salmon, and Noam Ross wrote about Taking over maintenance of a software package. This blog post is about trying to give guidance to software contributors, and to rOpenSci editors, on how to deal with software maintainer changes.


Stefanie Butland wrote about our next community call: Community Call - Involving Multilingual Communities - coming up on June 28th.


Stefanie Butland wrote the first of a semi-monthly summary of the rOpenSci Newsletter including software reviews, packages on CRAN, use cases, posts from staff and community, and events - 2 Months in 2 Minutes - rOpenSci News, June 2019



Use Cases

The following 16 works use/cite rOpenSci software:



Call For Contributors

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.



BoF event at SciPy2019 discussing the brand new @pyOpenSci, an open community to promote python best practices, Thurs 7/11 6-7pm



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.

Ben Marwick started a discussion thread recently titled Teaching with the TIER protocol and replication assignments using R. All are welcome to contribute to the discussion.






Keep up with rOpenSci


Footnotes

  1. Płaczek, A., Płuciennik, A., Pach, M., Jarząb, M., & Mrozek, D. (2019). The Role of Feature Selection in Text Mining in the Process of Discovering Missing Clinical Annotations – Case Study. Communications in Computer and Information Science, 248–262. https://doi.org/10.1007/978-3-030-19093-4_19 

  2. Germon, A., Jourdan, C., Bordron, B., Robin, A., Nouvellon, Y., Chapuis-Lardy, L., … Laclau, J.-P. (2019). Consequences of clear-cutting and drought on fine root dynamics down to 17 m in coppice-managed eucalypt plantations. Forest Ecology and Management, 445, 48–59. https://doi.org/10.1016/j.foreco.2019.05.010 

  3. Chambault, P., Baudena, A., Bjorndal, K. A., AR Santos, M., Bolten, A. B., & Vandeperre, F. (2019). Swirling in the ocean: immature loggerhead turtles seasonally target old anticyclonic eddies at the fringe of the North Atlantic gyre. Progress in Oceanography. https://doi.org/10.1016/j.pocean.2019.05.005 

  4. Kadereit, J. W., Lauterbach, M., Kandziora, M., Spillmann, J., & Nyffeler, R. (2019). Dual colonization of European high-altitude areas from Asia by Callianthemum (Ranunculaceae). Plant Systematics and Evolution. https://doi.org/10.1007/s00606-019-01583-5 

  5. Ktenioudaki, A., O’Donnell, C. P., & do Nascimento Nunes, M. C. (2019). Modelling the biochemical and sensory changes of strawberries during storage under diverse relative humidity conditions. Postharvest Biology and Technology, 154, 148–158. https://doi.org/10.1016/j.postharvbio.2019.04.023 

  6. Adeola, A. M., Botai, J. O., Mukarugwiza Olwoch, J., DeW. Rautenbach, H. C. J., Adisa, O. M., De Jager, C., … Aaron, M. (2019). Predicting malaria cases using remotely sensed environmental variables in Nkomazi, South Africa. Geospatial Health, 14(1). https://doi.org/10.4081/gh.2019.676 

  7. Salazar, P. C., Navarro-Cerrillo, R. M., Cruz, G., Grados, N., & Villar, R. (2019). Variability in growth and biomass allocation and the phenotypic plasticity of seven Prosopis pallida populations in response to water availability. Trees. https://doi.org/10.1007/s00468-019-01868-9 

  8. Best, B. D., & Halpin, P. N. (2019). Minimizing wildlife impacts for offshore wind energy development: Winning tradeoffs for seabirds in space and cetaceans in time. PLOS ONE, 14(5), e0215722. https://doi.org/10.1371/journal.pone.0215722 

  9. Mann, C. M., Martínez-Gálvez, G., Welker, J. M., Wierson, W. A., Ata, H., Almeida, M. P., … Dobbs, D. (2019). The Gene Sculpt Suite: a set of tools for genome editing. Nucleic Acids Research. https://doi.org/10.1093/nar/gkz405 

  10. da Silva, L. T., de Oliveira, I. L., Dantas, T., & Miranda, V. G. 2019. Studies of new data sources and techniques to improve CPI compilation in Brazil. 16th meeting of the Ottawa Group, Rio de Janeiro, Brazil. https://eventos.fgv.br/sites/eventos.fgv.br/files/arquivos/u161/study_of_new_data_sources_snipc_lincoln_da_silva.pdf 

  11. Lin, B. Y., Chan, P. P., & Lowe, T. M. (2019). tRNAviz: explore and visualize tRNA sequence features. Nucleic Acids Research. https://doi.org/10.1093/nar/gkz438 

  12. Salecker, Jan; Dislich, Claudia; Wiegand, Kerstin; Meyer, Katrin M.; Pe’er,Guy (2019) : EFForTS-LGraf: A landscape generator for creating smallholder-driven land-use mosaics, EFForTS Discussion Paper Series, No. 29, Collaborative Research Centre990 - EFForTS, Ecological and Socioeconomic Functions of Tropical Lowland RainforestTransformation Systems. https://www.econstor.eu/bitstream/10419/196610/1/1665217219.pdf 

  13. Comrie, B. (2019). Mapping the World’s Languages: From Data via Purpose to Representation. Handbook of the Changing World Language Map, 1–16. https://doi.org/10.1007/978-3-319-73400-2_131-1 

  14. Sporbert, M., Bruelheide, H., Seidler, G., Keil, P., Jandt, U., Austrheim, G., … Welk, E. (2019). Assessing sampling coverage of species distribution in biodiversity databases. Journal of Vegetation Science. https://doi.org/10.1111/jvs.12763 

  15. Vantas, K., Sidiropoulos, E., & Loukas, A. (2019). Robustness Spatiotemporal Clustering and Trend Detection of Rainfall Erosivity Density in Greece. Water, 11(5), 1050. https://doi.org/10.3390/w11051050 

  16. Schubert, M., Marcussen, T., Meseguer, A. S., & Fjellheim, S. (2019). The grass subfamily Pooideae: Cretaceous–Palaeocene origin and climate‐driven Cenozoic diversification. Global Ecology and Biogeography. https://doi.org/10.1111/geb.12923