Package: codyn 2.0.5

Matthew B. Jones

codyn: 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. Details of the methods are available in Hallett et al. (2016) <doi:10.1111/2041-210X.12569> and Avolio et al. (2019) <doi:10.1002/ecs2.2881>.

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]

codyn_2.0.5.tar.gz
codyn_2.0.5.zip(r-4.7)codyn_2.0.5.zip(r-4.6)codyn_2.0.5.zip(r-4.5)
codyn_2.0.5.tgz(r-4.6-any)codyn_2.0.5.tgz(r-4.5-any)
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codyn_2.0.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
codyn/json (API)
NEWS

# Install 'codyn' in R:
install.packages('codyn', repos = c('https://dataoneorg.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/nceas/codyn/issues

Datasets:
  • collins08 - Konza data from Collins et al. 2008
  • knz_001d - Data from Konza Prairie, watershed 001d
  • pplots - Phosphorus plots data from Avolio et al. 2014

On CRAN:

Conda:

9.24 score 37 stars 312 scripts 390 downloads 11 mentions 19 exports 9 dependencies

Last updated from:d09e65b2d7. Checks:7 NOTE, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-x86_64NOTE177
source / vignettesOK213
linux-release-x86_64NOTE174
macos-release-arm64NOTE133
macos-oldrel-arm64NOTE111
windows-develNOTE149
windows-releaseNOTE159
windows-oldrelNOTE142
wasm-releaseOK125

Exports:abundance_changeabundance_differencecommunity_diversitycommunity_stabilitycommunity_structurecurve_changecurve_differencecyclic_shiftmean_rank_shiftmultivariate_changemultivariate_differenceRAC_changeRAC_differencerank_shiftrate_changerate_change_intervalsynchronyturnovervariance_ratio

Dependencies:assertthatclusterlatticeMASSMatrixmgcvnlmepermutevegan

codyn: Community Dynamic Metrics

Lauren M. Hallett, Sydney K. Jones, Andrew A. MacDonald, Matthew B. Jones, Dan F. B. Flynn, Peter Slaughter, Corinna Gries, Scott L. Collins

Rendered fromcodyn_overview.Rmdusingknitr::rmarkdownon May 27 2026.

Last update: 2019-04-09
Started: 2015-03-04

Community Stability Metrics

Lauren M. Hallett

Rendered fromCommunity_Stability_Metrics.Rmdusingknitr::rmarkdownon May 27 2026.

Last update: 2020-12-01
Started: 2015-10-07

Temporal Diversity Indices

Lauren M. Hallett, Dan F. B. Flynn, Sydney K. Jones

Rendered fromTemporal_Diversity_Indices.Rmdusingknitr::rmarkdownon May 27 2026.

Last update: 2019-04-09
Started: 2015-10-08