2020-03-16

rOpenSci HQ

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

Software 📦

CRAN: GitHub:

New Packages

The first version (v0.1.0) of ghql is on CRAN - general purpose GraphQL client. Checkout the docs to get started.

New Versions

A new version (v0.3.0) of crminer is on CRAN - Fetch scholarly full text from Crossref. See the release notes for changes. Checkout the README to get started.
A new version (v0.1.1) of rromeo is on CRAN - access publisher copyright & self-archiving policies via the SHERPA/RoMEO API. See the release notes for changes. Checkout the docs to get started.
A new version (v1.1.0) of cyphr is on CRAN - high level encryption wrappers. See the release notes for changes. Checkout the docs to get started.
A new version (v2.2.0) of rgbif is on CRAN - interface to the Global Biodiversity Information Facility API. See the release notes for changes. Checkout the occurrence manual to get started.
A new version (v0.1.5) of baRcodeR is on CRAN - label creation for tracking and collecting data from biological samples. See the release notes for changes. Checkout the docs to get started.
A new version (v1.3) of hydroscoper is on CRAN - interface to the Greek National Data Bank for Hydrological and Meteorological Information http://www.hydroscope.gr/. See the release notes for changes. Checkout the vignettes to get started.
A new version (v1.1.1) of MODISTools is on CRAN - interface to the MODIS Land Products Subsets web services. See the release notes for changes. Checkout the docs to get started.
A new version (v0.5.2) of rdatacite is on CRAN - client for DataCite. See the release notes for changes. Checkout the README to get started.
A new version (v0.5.0) of vcr is on CRAN - record HTTP calls to disk for test caching. See the release notes for changes. Checkout the HTTP testing book to get started.
A new version (v1.2.0) of stats19 is on CRAN - Work with Open Road Traffic Casualty Data from Great Britain. See the release notes for changes. Checkout the docs to get started.
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.
A new version (v0.4.3) of nomisr is on CRAN - access UK official statistics from the Nomis database. See the release notes for changes. Checkout the docs to get started.
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.
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.

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:

SymbiotaR2 > Downloading data from Symbiota2 portals into R
- Author: Austin Koontz
- Issue: ropensci/onboarding#373
- Reviewers: not yet assigned

On the blog

Steffi LaZerte wrote a post on our next community call: Community Call - Maintaining an R Package.

Tech notes

Patrick Schratz wrote a post on using Github Actions with the tic package: Supercharge your GitHub Actions Experience with tic. tic works with many continuous integration (CI) services.

Use Cases

The following 17 works use/cite rOpenSci software:

Loo & Jonge used assertr in their paper Data Validation Infrastructure for R ¹
Marshall & Strine used rgbif and taxize and CoordinateCleaner and rnaturalearth in their paper Exploring snake occurrence records: Spatial biases and marginal gains from accessible social media ²
Cameron used weathercan in their paper Improving passive acoustic monitoring methods for anuran amphibians in ³
Pontes used taxize in their paper Biodiversity informatics-entomological data processing, analysis and visualization ⁴
Tancoigne used rtweet in their paper Invisible brokers: “citizen science” on Twitter ⁵
Hosford & Winters used bikedata in their paper Quantifying the Bicycle Share Gender Gap ⁶
Noecker et al. used biomartr in their paper Defining and evaluating microbial contributions to metabolite variation in microbiome-metabolome association studies ⁷
Ruiz-Sanchez et al. used restez and phylotaR in their paper Datataxa: a new script to extract metadata sequence information from GenBank, the Flora of Bajío as a case study ⁸
Greenhalgh et al. used rtweet in their paper Approaches to Mormon Identity and Practice in the #ldsconf Twitter Hashtag ⁹
Die et al. used rentrez in their paper GeneHummus: A pipeline to define gene families and their expression in legumes and beyond ¹⁰
Maia et al. used magick in their paper pavo 2: new tools for the spectral and spatial analysis of colour in R ¹¹
Mowinckel & Vidal-Piñeiro used magick in their paper Visualisation of Brain Statistics with R-packages ggseg and ggseg3d ¹²
Champagne et al. used taxize in their paper Phytochemicals Involved in Plant Resistance to Leporids and Cervids: a Systematic Review ¹³
Burrows et al. used taxize in their paper Global‐scale species distributions predict temperature‐related changes in species composition of rocky shore communities in Britain ¹⁴
Avdeev used lingtypology in their paper International Collaboration In Higher Education Research: A Gravity Model Approach ¹⁵
Herrera used brranching in their paper Flower traits, habitat, and phylogeny as predictors of pollinator service: a plant community perspective ¹⁶
Kim et al. used taxize in their paper Epibionts associated with floating Sargassum horneri in the Korea Strait ¹⁷

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.

Emilio Bruna asked recently: What is best practice when a dependency is removed from CRAN?

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 eight 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
mregions: in process of moving to maintenance by VLIZ
rWBclimate: now maintained by Sergio Ibarra-Espinosa and Amanda Rehbein

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.

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

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Footnotes

van der Loo, M. P., & de Jonge, E. (2019). Data Validation Infrastructure for R. arXiv preprint arXiv:1912.09759. https://arxiv.org/pdf/1912.09759.pdf ↩
Marshall, B. M., & Strine, C. T. (2019). Exploring snake occurrence records: Spatial biases and marginal gains from accessible social media. PeerJ, 7, e8059. https://doi.org/10.7717/peerj.8059 ↩
Cameron, J. (2019). Improving passive acoustic monitoring methods for anuran amphibians in northern Alberta, Canada. https://era.library.ualberta.ca/items/82cf4970-7243-49cc-88ac-cbef893cd062 ↩
Pontes, L. F. V. A. (2019). Biodiversity informatics-entomological data processing, analysis and visualization (Doctoral dissertation) https://repositorio.ul.pt/bitstream/10451/40544/1/ulfc125176_tm_Leonor_Pontes.pdf ↩
Tancoigne, E. (2019). Invisible brokers: “citizen science” on Twitter. Journal of Science Communication, 18(06). https://doi.org/10.22323/2.18060205 ↩
Hosford, K., & Winters, M. 2019. Quantifying the Bicycle Share Gender Gap. Transport Findings, November. https://doi.org/10.32866/10802 ↩
Noecker, C., Chiu, H. C., McNally, C. P., & Borenstein, E. (2019). Defining and evaluating microbial contributions to metabolite variation in microbiome-metabolome association studies. mSystems, 4(6). https://doi.org/10.1128/mSystems.00579-19 ↩
Ruiz-Sanchez, E., Maya-Lastra, C. A., Steinmann, V. W., Zamudio, S., Carranza, E., Murillo, R. M., & Rzedowski, J. (2019). Datataxa: a new script to extract metadata sequence information from GenBank, the Flora of Bajío as a case study. Botanical Sciences, 97(4), 754–760. https://doi.org/10.17129/botsci.2226 ↩
Greenhalgh, S. P., Willet, K. B. S., & Koehler, M. J. (2019). Approaches to Mormon Identity and Practice in the #ldsconf Twitter Hashtag. Journal of Media and Religion, 18(4), 122–133. https://doi.org/10.1080/15348423.2019.1696121 ↩
Die, J. V., Elmassry, M. M., LeBlanc, K. H., Awe, O. I., Dillman, A., & Busby, B. (2018). GeneHummus: A pipeline to define gene families and their expression in legumes and beyond. https://doi.org/10.1101/436659 ↩
Maia, R., Gruson, H., Endler, J. A., & White, T. E. (2018). pavo 2: new tools for the spectral and spatial analysis of colour in R. https://doi.org/10.1101/427658 ↩
Mowinckel, A. M., & Vidal-Piñeiro, D. (2019). Visualisation of Brain Statistics with R-packages ggseg and ggseg3d. arXiv preprint arXiv:1912.08200 https://arxiv.org/abs/1912.08200 ↩
Champagne, E., Royo, A. A., Tremblay, J.-P., & Raymond, P. (2019). Phytochemicals Involved in Plant Resistance to Leporids and Cervids: a Systematic Review. Journal of Chemical Ecology, 46(1), 84–98. https://doi.org/10.1007/s10886-019-01130-z ↩
Burrows, M. T., Hawkins, S. J., Moore, J. J., Adams, L., Sugden, H., Firth, L., & Mieszkowska, N. (2020). Global‐scale species distributions predict temperature‐related changes in species composition of rocky shore communities in Britain. Global Change Biology, 26(4), 2093–2105. https://doi.org/10.1111/gcb.14968 ↩
Avdeev, S. (2019). International Collaboration In Higher Education Research: A Gravity Model Approach. Higher School of Economics Research Paper No. WP BRP, 54. https://wp.hse.ru/data/2019/12/18/1523102390/54EDU2019.pdf ↩
Herrera, C. M. (2020). Flower traits, habitat, and phylogeny as predictors of pollinator service: a plant community perspective. Ecological Monographs. https://doi.org/10.1002/ecm.1402 ↩
Kim, H. M., Jo, J., Park, C., Choi, B.-J., Lee, H.-G., & Kim, K. Y. (2019). Epibionts associated with floating Sargassum horneri in the Korea Strait. ALGAE, 34(4), 303–313. https://doi.org/10.4490/algae.2019.34.12.10 ↩