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]

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NEWS

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

Peer review:

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:

9.03 score 33 stars 217 scripts 429 downloads 11 mentions 19 exports 9 dependencies

Last updated 4 years agofrom:d09e65b2d7. Checks:OK: 3 NOTE: 4. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 10 2024
R-4.5-winNOTENov 10 2024
R-4.5-linuxNOTENov 10 2024
R-4.4-winNOTENov 10 2024
R-4.4-macNOTENov 10 2024
R-4.3-winOKNov 10 2024
R-4.3-macOKNov 10 2024

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 Nov 10 2024.

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

Community Stability Metrics

Lauren M. Hallett

Rendered fromCommunity_Stability_Metrics.Rmdusingknitr::rmarkdownon Nov 10 2024.

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 Nov 10 2024.

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