Update 2016-01-05

rOpenSci HQ

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Software

A new package (version 0.1.0) binomen is on CRAN. binomen provides various taxonomic classes for defining a single taxon, multiple taxa, and a taxonomic data.frame. It is designed as a companion to taxize, where you can get taxonomic data on taxonomic names from the web. See vignette for an introduction to the package. Repository on GitHub.
A new version (version 0.0.4) of webchem is on CRAN. See release notes for changes. Repository on GitHub.
A new version (0.13.1) of git2r is on CRAN. See the NEWS for changes. Repository on GitHub.
A new version (2.0.16) of plotly is on CRAN. See the NEWS for changes. Repository on GitHub.
A new version (0.3.6) of gistr is on CRAN. See the release notes for changes. Repository on GitHub.
A new version (0.2.0) of rdryad is on CRAN. See the release notes for changes. Repository on GitHub.
A new version (2.0.5) of RNeXML is on CRAN. See the NEWS for changes. Repository on GitHub.
A new version (0.2.0) of USAboundaries is on CRAN. See the NEWS for changes. Repository on GitHub.

CRAN dependencies

rfigshare has a new package that imports it on CRAN: zoon - for reproducible and remixable species distribution modelling.
A suite of packages (some older, some new) use git2r: archivist, spm12r, nat.templatebrains, and , Rcereal.

Use cases

Eight recent papers cite rOpenSci software:

Cimiano et al., in a project proposal titled Continuous quality control for research data to ensure reproducibility: an institutional approach mentions rOpenSci ¹
Crouzier in a European Commission report titled Science Ecosystem 2.0: how will change occur? mentions rOpenSci
Vandepitte et al. have a paper in Journal of Marine Science and Engineering titled How Aphia—the platform behind several online and taxonomically oriented databases—can serve both the taxonomic community and the field of biodiversity informatics in which they cite taxize ²
Bevan has a paper in Antiquity titled The data deluge in which he mentions rOpenSci ³
Pilaar Birch & Graham have a letter in Bioscience titled A stable isotope data repository as part of neotoma, a paleoecological database in which they cite neotoma ⁴
Schaefer et al. have a paper in Transactions of the American Fisheries Society titled Dynamics of near-coastal fish assemblages following the deepwater horizon oil spill in the northern gulf of mexico in which they cite rfishbase ⁵
Zizka & Antonelli have a pre-print in Biorxiv titled speciesgeocodeR: An R package for linking species occurrences, user-defined regions and phylogenetic trees for biogeography, ecology and evolution in which they cite rgbif ⁶
Westcott & Schloss have a paper in PeerJ titled De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units in which they cite rentrez ⁷

References

Cimiano, Philipp, and Ing Gerhard Sagerer. “Continuous quality control for research data to ensure reproducibility: an institutional approach.” https://doi.org/10.5281/zenodo.31298 ↩
Vandepitte, Leen, et al. “How Aphia—The Platform behind Several Online and Taxonomically Oriented Databases—Can Serve Both the Taxonomic Community and the Field of Biodiversity Informatics.” Journal of Marine Science and Engineering 3.4 (2015): 1448-1473. https://doi.org/10.3390/jmse3041448 ↩
Bevan, Andrew. “The data deluge.” Antiquity 89.348 (2015): 1473-1484. https://doi.org/10.15184/aqy.2015.102 ↩
Birch, Suzanne E. Pilaar, and Russell W. Graham. “A Stable Isotope Data Repository as Part of Neotoma, a Paleoecological Database.” BioScience (2015): biv133. https://doi.org/10.1093/biosci/biv133 ↩
Schaefer, Jacob, Nkrumah Frazier, and Jonathan Barr. “Dynamics of Near-Coastal Fish Assemblages following the Deepwater Horizon Oil Spill in the Northern Gulf of Mexico.” Transactions of the American Fisheries Society 145.1 (2015): 108-119. https://doi.org/10.1080/00028487.2015.1111253 ↩
Zizka, Alexander, and Alexandre Antonelli. “speciesgeocodeR: An R package for linking species occurrences, user-defined regions and phylogenetic trees for biogeography, ecology and evolution.” bioRxiv (2015): 032755. https://doi.org/10.1101/032755 ↩
Westcott, Sarah L., and Patrick D. Schloss. “De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units.” PeerJ 3 (2015): e1487. https://doi.org/10.7717/peerj.1487 ↩