Community Dynamics Metrics

A toolbox of ecological community dynamics metrics that are explicitly temporal. Functions fall into two categories: temporal diversity indices and community stability metrics. The diversity indices are temporal analogs to traditional diversity indices such as richness and rank-abundance curves. Specifically, functions are provided to calculate species turnover, mean rank shifts, and lags in community similarity between time points. The community stability metrics calculate overall stability and patterns of species covariance and synchrony over time.


  • Authors:Lauren Hallett [lauren.m.hallett@gmail.com], Sydney K. Jones [syd@sevilleta.unm.edu], Andrew A. MacDonald [a.a.m.macdonald@gmail.com], Dan F. B. Flynn [flynn@fas.harvard.edu], Peter Slaughter [slaughter@nceas.ucsb.edu], Julie Ripplinger [julie.ripplinger@asu.edu], Scott L. Collins [scollins@sevilleta.unm.edu], Corinna Gries [cgries@wisc.edu], Matthew B. Jones [jones@nceas.ucsb.edu]
  • doi:10.5063/F1542KJB
  • License: Apache 2
  • Package source code on Github
  • Submit Bugs and feature requests

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:

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")

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.

News

NEW FEATURES

  • Add S3 class for cyclic_shift *#66)
  • add an alias for temporal_torus_translation (#65)

BUG FIXES

  • selectively import from stats and assertthat (#64)
  • adjustments to coding consistency (#63)
  • import 'stats' and 'permute' package methods (#69)
  • Improved function and parameter names

BUG FIXES

  • Fixed bug to ensure data frames are ordered before unlisting (#58)
  • Fixed bug in temporal_torus_translation to correctly recognize numeric data (#59)
  • Fixed bug in synchrony (Gross) with only 1 spp in a plot (#60)
  • Fixed bug in calculating variance ratio if species counts are constant (#61)

NEW FEATURES

  • Initial version (see help topic for 'codyn', e.g. "?codyn")
  • Includes functions for temporal community dynamics analysis

NEW FUNCTIONS

  • turnover: Calculates species turnover between time periods
  • mean_rank_shift: Calculates the mean relative change in species rank abundances
  • rate_change: Calculates the rate change in a community over time
  • rate_change_interval: Produces a data frame containing differences in species composition between samples at increasing time intervals
  • community_stability: Calculates community stability over time
  • variance_ratio: Computes the ratio of the variance of aggregate species abundances in a community
  • synchrony: Calculates the degree synchrony in species abundances
  • temporal_torus_translation: Calculates a null test statistic using a temporal modification of the torus translation
  • temporal_torus_translation_CI: Returns confidence intervals calculated from a temporal modification of the torus translation

Reference manual

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install.packages("codyn")

1.1.0 by Matthew B. Jones, a year ago


https://github.com/laurenmh/codyn/


Report a bug at https://github.com/laurenmh/codyn/issues


Browse source code at https://github.com/cran/codyn


Authors: Lauren Hallett [aut], Sydney K. Jones [aut], A. Andrew M. MacDonald [aut], Dan F. B. Flynn [aut], Peter Slaughter [aut], Julie Ripplinger [aut], Scott L. Collins [aut], Corinna Gries [aut], Matthew B. Jones [aut, cre]


Documentation:   PDF Manual  


Apache License (== 2.0) license


Imports assertthat, stats, permute

Suggests testthat, knitr, ggplot2, reshape2, devtools, dplyr, rmarkdown


See at CRAN