CODYN: AnR package of community dynamics metrics

TitleCODYN: AnR package of community dynamics metrics
Publication TypeJournal Article
Year of Publication2016
AuthorsHallett, L. M., Jones S. K., MacDonald A. A. M., Jones M. B., Flynn D. F. B., Ripplinger J., Slaughter P., Gries C., and Collins S. L.
JournalMethods in Ecology and Evolution
Volume7
Issue10
Number of Pages1146-1151
Date PublishedOct
Type of ArticleArticle
Reprint Number2041-210X
LTER Accession NumberWOS:000387670700002
Keywordsbiodiversity analysis; cyclic shift; long-term data; mean rank shift; R, ecological communities; biodiversity; stability; variability;, package; rank clock; synchrony; temporal analysis; turnover; variance, productivity; associations; population; mechanisms; synchrony; diversity, ratio
Abstract

1. New analytical tools applied to long-term data demonstrate that ecological communities are highly dynamic over time. We developed an R package, library("codyn"), to help ecologists easily implement these metrics and gain broader insights into ecological community dynamics. 2. library("codyn") provides temporal diversity indices and community stability metrics. All functions are designed to be easily implemented overmultiple replicates. 3. Temporal diversity indices include species turnover, mean rank shifts and rate of community change over time. Community stability metrics calculate overall stability and patterns of species covariance and synchrony over time, and include a null-modellingmethod to test significance. 4. Finally, library("codyn") contains vignettes that describe methods and reproduce figures from published papers to help users contextualize and apply functions to their own data.

DOI10.1111/2041-210X.12569
Print Copy LocationMethods Ecol. Evol.