Software

  • A package in development for a while now, for making interactive visualizations, plotly (version 2.0.2), is on CRAN. It is maintained by the Plot.ly team, and Carson Sievert. plotly is an R client for easily translating ggplot2 graphs to an interactive web-based version and/or create other plot types not available in ggplot2. Once uploaded to a plotly account, plotly graphs (and the data behind them) can be viewed and modified in a web browser. See An overview of plotly’s R API for an introduction to the package. Repository on GitHub.
  • A new version (2.1.0) of rfishbase is on CRAN. Repository on GitHub.
  • A new version (0.0.7) of prism is on CRAN. See the NEWS for changes.
  • A new version (0.2.1) of ecoretriever is on CRAN. This version adds a new function get_updates() to update the retriever scripts; a big improvement as it avoids automatically updating the scripts every time the package is imported. See the release notes for changes.
  • A new version (1.0.6) of rusda is on CRAN. Repository on GitHub.
  • A new package (version 0.1.0) brranching is on CRAN. This aims to be an R client for many sources of phylogenies. However, only one source of data is available now: Phylomatic. Other data sources will be added. Some sources of phylogenies already have nice R clients so won’t be included in this one, e.g., Open Tree of Life - rotl. See the README for an introduction to the package. Repository on GitHub.

rOpenSci HQ

Use cases

A few recent papers cite rOpenSci software:

References

  1. Boettiger C, Chamberlain S, Hart E, Ram K. Building Software, Building Community: Lessons from the rOpenSci Project. Journal of Open Research Software. 2015;3(1):e8. http://dx.doi.org/10.5334/jors.bu 

  2. Baden, H. M., Särkinen, T., Conde, D. A., Matthews, A. C., Vandrot, H., Chicas, S., … (2015). A BOTANICAL INVENTORY OF FOREST ON KARSTIC LIMESTONE AND METAMORPHIC SUBSTRATE IN THE CHIQUIBUL FOREST, BELIZE, WITH FOCUS ON WOODY TAXA. Edinburgh Journal of Botany, 1–43. http://dx.doi.org/10.1017/S0960428615000256 

  3. Price, S. A., Friedman, S. T., & Wainwright, P. C. (2015). How predation shaped fish: the impact of fin spines on body form evolution across teleosts. Proceedings of the Royal Society B: Biological Sciences, 282(1819), 20151428–20151428. http://dx.doi.org/10.1098/rspb.2015.1428 

  4. Mindel, B. L., Webb, T. J., Neat, F. C., & Blanchard, J. L. (Accepted). A trait-based metric sheds new light on the nature of the body size-depth relationship in the deep sea. J Anim Ecol. http://dx.doi.org/10.1111/1365-2656.12471 

  5. Muench, D., & Galizia, C. G. (2015). DoOR 2.0 - Comprehensive Mapping of Drosophila melanogaster Odorant Responses. http://dx.doi.org/10.1101/027920