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• Authors: Lauren Hallett [lauren.m.hallett@gmail.com], Meghan Avolio [meghan.avolio@jhu.edu], Ian T. Carroll [carroll.ian@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]
• Version 1.x:doi:10.5063/F1542KJB
• Version 2.x:doi:10.5063/F1N877Z6
• License:Apache 2
• Package source code on Github
• Submit Bugs and feature requests

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 functionsimplement metrics that are either explicitly temporal and include theoption to calculate them over multiple replicates, or spatial and includethe option to calculate them over multiple time points. Functions fall intofive categories: static diversity indices, temporal diversity indices,spatial diversity indices, rank abundance curves, and community stabilitymetrics. The diversity indices are temporal and spatial analogs totraditional diversity indices. Specifically, the package includes functionsto calculate community richness, evenness and diversity at a given point inspace and time. In addition, it contains functions to calculate speciesturnover, mean rank shifts, and lags in community similarity between twotime points.

For an overview ofcodyn, see:

• Hallett LM, Jones SK, MacDonald AAA, Jones MB, Flynn DFB, Ripplinger J, Slaughter P, Gries C, Collins SL (2016)codyn: An R package of community dynamics metrics. Methods in Ecology and Evolution, 7(10):1146–1151.https://doi.org/10.1111/2041-210X.12569

For a description of the newer spatial methods incodyn v2.x:

• Avolio ML, Carroll IT, Collins SL, Houseman GR, Hallett LM, Isbell F, Koerner SE, Komatsu KJ, Smith MD, Wilcox KR (2019)A comprehensive approach to analyzing community dynamics using rank abundance curves. Ecosphere, 10(10):e02881.https://doi.org/10.1002/ecs2.2881

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

install.packages("codyn")

To simplify the process of runningR CMD check on the package, one can easily run the build and tests usingtherhub package. Userhub::platforms() to get a list of platforms that can be used to build and test.

library(rhub)chks<- check(platform= c("debian-gcc-devel","fedora-gcc-devel"),show_status=FALSE)

and the checks can be run locally using rhub as well using a docker container:

library(rhub)local_check_linux(image="rhub/fedora-gcc-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, and a SESYNC Synthesis Postdoctoral Fellowship to MLA.