Ecologists seeking to measure temporal dynamics often need to write their own R code from scratch, leading to differences in implementation, as well as inefficiencies from the duplicated work. Hallett et al. published a new article in Methods in Ecology and Evolution that examines how new analytical tools can be applied to long-term data to demonstrate the dynamics of ecological communities over time. The authors developed an associated R package, "codyn" (short for "community dynamics"), to help ecologists easily use these metrics and gain broader insights into ecological community dynamics.
The work leading to "codyn" arose from collaboration between community ecologists and the informatics team at NCEAS under an NSF collaborative research award.
"The codyn R package is an outcome of the growing trend in ecology for supporting open and reproducible science, and it is encouraging to see early career researchers embracing the gains that can be made by sharing software and data as key products of their research."
-Matthew Jones, Director of Informatics at NCEAS
The “codyn” package provides temporal diversity indices, such as species turnover, mean rank shifts, and rate of community change over time. It also calculates community stability metrics, including a null-modeling method to test significance. This package contains vignettes that describe methods and reproduce figures from published papers, which can help users contextualize and apply functions to their own data.
Now, “codyn” fills this niche for published functions that characterize communities over time. As long-term datasets increase in scope and length, new analytical tools like “codyn” can help to deepen our understanding of ecological patterns and processes.
codyn: An R package of community dynamics metrics
L. M. Hallett, S. K. Jones, A. A. A. Macdonald, M. B. Jones, D. F. B. Flynn, J. Ripplinger, P. Slaughter, C. Gries, & S. L. Collins. Methods in Ecology and Evolution, 2 April 2016, Accepted manuscript online. DOI: 10.1111/2041-210X.12569