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

# Install 'codyn' in R:
install.packages('codyn', repos = c('https://nceas.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:

9.23 score 38 stars 293 scripts 1.0k downloads 11 mentions 19 exports 9 dependencies

Last updated from:d09e65b2d7. Checks:7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64NOTE167
source / vignettesOK225
linux-release-x86_64NOTE192
macos-release-arm64NOTE112
macos-oldrel-arm64NOTE111
windows-develNOTE132
windows-releaseNOTE142
windows-oldrelNOTE129
wasm-releaseOK124

Exports:abundance_changeabundance_differencecommunity_diversitycommunity_stabilitycommunity_structurecurve_changecurve_differencecyclic_shiftmean_rank_shiftmultivariate_changemultivariate_differenceRAC_changeRAC_differencerank_shiftrate_changerate_change_intervalsynchronyturnovervariance_ratio

Dependencies:assertthatclusterlatticeMASSMatrixmgcvnlmepermutevegan

Community Stability Metrics
Overview | Example dataset | Community stability | Species covariance | Variance ratio | Calculating the variance ratio | Significance testing | General cyclic shift function | Variance ratio and species richness | Species synchrony | Synchrony Option 1: "Loreau" | Synchrony Option 2: "Gross" | Citations
Rendered fromCommunity_Stability_Metrics.Rmdusingknitr::rmarkdown

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

codyn: Community Dynamic Metrics
Rendered fromcodyn_overview.Rmdusingknitr::rmarkdown

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

Temporal Diversity Indices
Overview | Species turnover | Total turnover | Appearances and disappearances | Turnover at Konza | Species rank shifts | Rank clocks: visualizing species rank shifts | Rank clocks at Konza | Mean rank shifts | Rank shifts at Konza | Rate of community change | Rate change at Konza | Citations
Rendered fromTemporal_Diversity_Indices.Rmdusingknitr::rmarkdown

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