codyn - Community Dynamics Metrics

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A package to analyze long-term ecological community datasets.

The functions in codyn implement metrics that are explicitly temporal, and include the option to calculate them over multiple replicates. Functions fall into two categories: temporal diversity indices and community stability metrics. The diversity indices in codyn are temporal analogs to traditional diversity indices such as richness and rank-abundance curves. Specifically, codyn includes functions to calculate species turnover, mean rank shifts and lags in community similarity between time points. The community stability metrics in codyn calculate overall stability and patterns of species covariance and synchrony over time. Finally, codyn contains vignettes that describe methods and reproduce figures from published papers to help users contextualize and apply functions to their own data.

Installation

From CRAN, the package can be installed using standard tools:

install.packages("codyn")

Releases and pre-releases of the software are also available from the NCEAS drat repository, and can be installed after drat has been installed using:

drat::addRepo("NCEAS")
install.packages("codyn")

Automated R CMD check with Docker

To simplify the process of running R CMD check on the package, the source distribution on GitHub includes configuration files to use Docker to download and build standard Debian-based images for the current release of R and the current development branch of R. Assuming you already have docker and docker-compose installed, these Docker configuration files allow a clean environment to be built and tested with a single command. Checks can be run against the current stable release of R using:

$ docker-compose run --rm r-check-stable

and the checks can be run against the current unstable development version of R using:

$ docker-compose run --rm r-check-devel

Acknowledgements

Work on this package was supported by NSF-ABI grant #1262458 to C. Gries, M. Jones, and S. Collins. Additional support was provided for working group collaboration by the National Center for Ecological Analysis and Synthesis, a Center funded by the University of California, Santa Barbara, and the State of California.