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


##Overview As long-term datasets increase in scope and length, new analytical tools are being developed to capture patterns of species interactions over time. The package codyn includes recently developed metrics of ecological community dynamics. Functions in codyn implement metrics that are explicitly temporal, and include the option to calculate them over multiple replicates. Functions fall into two categories: temporal diversity indices and community stability metrics.

##Temporal Diversity Indices Many traditional measure of community structure represent a ‘snapshot in time’ whereas ecological communities are dynamic and many are experiencing directional change with time. The diversity indices in codyn are temporal analogs to traditional diversity indices such as richness and rank-abundance curves. They include:

##Community Stability Metrics Ecologists have long debated the relationship between species diversity and stability. Unstable species populations may stabilize aggregate community properties if a decrease in one species is compensated for by an increase in another. In a time series, this should be reflected by a pattern in which species negatively covary or fluctuate asynchronously while total community stability remains relatively stable. codyn includes a function to characterize community stability, community_stability, and three metrics to characterize species covariance and asynchrony:


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