Colonization and extinction rates estimated from temporal dynamics of ecological communities: The island r package

The temporal dynamics of ecological communities are inherently complex, as dispersal processes, interspecific biotic interactions and environmental fluctuations interact to shape species assemblages. We developed an r package, island-a community ecology tool to analyse temporal patterns and explore potential drivers of community dynamics. The r package island is inspired by the simplicity of the Theory of Island Biogeography. Our package includes a suite of functions to easily confront models of increasing complexity to community data from the simplest stochastic model underlying Island Biogeography Theory to more elaborate models that include species responses to environmental variables and imperfect detectability, obtained at regular or irregular sampling times, using maximum-likelihood and AIC-based model selection. Models implemented in island should be regarded as simple approximations of true temporal community dynamics. In this sense, we call them effective models which we use to estimate effective parameters. These models are simple, but dynamic, as opposed to purely statistical. We illustrate the concept of dynamic effective models by using an immigration-birth-death stochastic model of population dynamics. We generated simulated community data to demonstrate the correspondence between the underlying true model parameters values and our effective parameter estimates. We present three examples showcasing the uses of our package: detectability estimation and model selection, influence of environmental covariates on community dynamics and estimation of co-occurrence networks. Three detailed vignettes with a full set of examples accompany the r Package island available on CRAN.