Community Dynamics Metrics

Univariate and multivariate temporal and spatial diversity indices, rank abundance curves, and community stability measures. The functions implement measures 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 measures. 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.


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A package to analyze long-term ecological community datasets.

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.

For an overview of codyn, see:

Installation

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

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, and a SESYNC Synthesis Postdoctoral Fellowship to MLA.

News

Version 2.0.2

BUG FIXES

  • use codyn::Evar rather than codyn::EQ in RAC_difference
  • fixes for breaking change in testthat (PR #111)

Version 2.0.1

DOCUMENTATION

  • use @inheritParams to reduce redundancy

BUG FIXES

  • elminate unverifiable centroid calculation in vegan::betadisper (#306)
  • better error message (#108)
  • fix handling of Null arguments (#95)

Version 2.0.0

NEW FUNCTIONS

  • community_structure: Calculates richness and evenness (using specified metric) for a replicate
  • community_diversity: Calculates diversity (using specified metric) for a replicate
  • RAC_change: Calculates changes in species richness, evenness, species' ranks, gain, and losses for a replicate over time
  • abundance_change: For each species in a replicate, calculates changes in abundance over time
  • curve_change: Calculates changes in the shape of the RAC curve for each replicate over time
  • multivariate_change: Calculates changes in community composition and dispersion over time
  • RAC_difference: Calculates differences in species richness, evenness, species' ranks, shared species between paired samples at a single point in time
  • abundance_difference: Calculates differences in abundance for each species in paired samples at a single point in time
  • curve_difference: Calculates differences in the shape of the RAC between paired samples at a single point in time
  • multivariate_difference: Calculates differences in community composition and dispersion of all replicates between treatments at a single point in time

BUG FIXES

Previous warnings have been changed to errors.

Version 1.1.0

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

Version 1.0.1

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)

Version 1.0.0

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")

2.0.2 by Matthew B. Jones, a month ago


https://github.com/NCEAS/codyn/


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


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


Authors: Lauren Hallett [aut] , Meghan L. Avolio [aut] , Ian T. Carroll [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, vegan

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


See at CRAN