- 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.
- The first version (
git2rdatais on CRAN - store and retrieve data.frames in a Git repository. Checkout the docs to get started.
- A new version (
aukis on CRAN - eBird data extraction and processing. See the release notes for changes. Checkout the docs to get started.
- A new version (
MODIStspis on CRAN - Automate Download and Preprocessing of MODIS Land Products Data. See the release notes for changes. Checkout the docs to get started.
fixes bug causing crashes on MOD14A1 product; adds support for product MCD12Q2
- A new version (
rtikais on CRAN - R Interface to Apache Tika. See the release notes for changes. Checkout the docs to get started.
- A new version (
skimris on CRAN - compact and flexible summaries of data. See the release notes for changes. Checkout the vignettes to get started.
stop assignment of foreign functions in namesspace at build time
- A new version (
rotlis on CRAN - an interface to the Open Tree of Life API. See the release notes for changes. Checkout the vignettes to get started.
small fixes following updates to the Open Tree of Life API
- A new version (
ijtiffis 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.
count_frames(); now can read certain frames of a TIFF image w/
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:
- UCSCXenaTools > Download and Explore Datasets from UCSC Xena Data Hubs
The following two packages recently went through our software-review process and have been approved:
- gitignore > Create useful .gitignore files for your project
- tidypmc > Parse full text XML documents from PMC
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
The following 16 works use/cite rOpenSci software:
- Płaczek et al. used tokenizers in their paper The Role of Feature Selection in Text Mining in the Process of Discovering Missing Clinical Annotations – Case Study 1
- Germon et al. used plotly in their paper Consequences of clear-cutting and drought on fine root dynamics down to 17 m in coppice-managed eucalypt plantations 2
- Chambault et al. used clifro in their paper Swirling in the ocean: immature loggerhead turtles seasonally target old anticyclonic eddies at the fringe of the North Atlantic gyre 3
- Kadereit et al. used rgbif in their paper Dual colonization of European high-altitude areas from Asia by Callianthemum (Ranunculaceae) 4
- Ktenioudaki et al. used writexl in their paper Modelling the biochemical and sensory changes of strawberries during storage under diverse relative humidity conditions 5
- Adeola et al. used MODIStsp in their paper Predicting malaria cases using remotely sensed environmental variables in Nkomazi, South Africa 6
- Salazar et al. used magick in their paper Variability in growth and biomass allocation and the phenotypic plasticity of seven Prosopis pallida populations in response to water availability 7
- Best & Halpin used plotly in their paper Minimizing wildlife impacts for offshore wind energy development: Winning tradeoffs for seabirds in space and cetaceans in time 8
- Mann et al. used rentrez in their paper The Gene Sculpt Suite: a set of tools for genome editing 9
- da Silva et al. used RSelenium in their conference paper Studies of new data sources and techniques to improve CPI compilation in Brazil 10
- Lin et al. used taxize in their paper tRNAviz: explore and visualize tRNA sequence features 11
- Salecker et al. used nlrx in their paper EFForTS-LGraf: A landscape generator for creating smallholder-driven land-use mosaics 12
- Comrie used lingtypology in their work Mapping the World’s Languages: From Data via Purpose to Representation 13
- Sporbert et al. used taxize in their paper Assessing sampling coverage of species distribution in biodiversity databases 14
- Vantas et al. used hydroscoper in their paper Robustness Spatiotemporal Clustering and Trend Detection of Rainfall Erosivity Density in Greece 15
- Schubert et al. used rgbif in their paper The grass subfamily Pooideae: Cretaceous–Palaeocene origin and climate‐driven Cenozoic diversification 16
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:
- RSelenium: now maintained by Ju Kim
- chromer: now maintained by Paula Andrea
- qualtRics: now maintained by Julia Silge
- rsnps: now maintained by Julia Gustavsen and Sina Rüeger
- rdpla: now maintained by Alyssa Columbus
- webchem: now maintained by Erik Sapper
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.
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
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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 ↩
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 ↩
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 ↩
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 ↩
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 ↩
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 ↩
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 ↩
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 ↩
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 ↩
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 ↩
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 ↩
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 ↩
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 ↩
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 ↩