Univariate and multivariate temporal and spatial diversity indices, rank abundance curves, and community stability metrics. The functions implement metrics that are either explicitly temporal and include the option to calculate them over multiple replicates, or spatial and include the option to calculate them over multiple time points. Functions fall into five categories: static diversity indices, temporal diversity indices, spatial diversity indices, rank abundance curves, and community stability metrics. The diversity indices are temporal and spatial analogs to traditional diversity indices. Specifically, the package includes functions to calculate community richness, evenness and diversity at a given point in space and time. In addition, it contains functions to calculate species turnover, mean rank shifts, and lags in community similarity between two time points.
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.
From CRAN, the package can be installed using standard tools:
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:
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
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.