Island LAB Azorean Biodiversity Group

Biodiversity Applications for R

GAMBIN R PACKAGE

The species abundance distribution (SAD) has been a central focus of community ecology for over fifty years, and is currently the subject of widespread renewed interest.The gambin model has recently been proposed as a model that provides a superior fit to commonly preferred SAD models. It has also been argued that the model’s single parameter (α) presents a potentially informative ecological diversity metric, because it summarizes the shape of the SAD in a single number. Despite this potential, few empirical tests of the model have been undertaken,  because the necessary methods and software for fitting the model have not existed. As part of my PhD I (with the help of colleagues) have derived a maximum likelihood method to fit the model. The functions and computational code to fit the model are incorporated in a newly developed free-to-download R package (gambin).

In an empirical evaluation of the model using a number of different datasets we found that that gambin almost universally provided a better fit to the data than popular SAD models (e.g. Poisson lognormal, logseries and zero-sum multinomial). We also demonstrated how α can be used to differentiate intelligibly between community structures of Azorean arthropods sampled in different land use types; thus providing a useful index of SAD form in its single fitted parameter.

R package available from CRAN: http://cran.r-project.org/web/packages/gambin/index.html

Reference: Matthews, T.J., Borregaard, M.K., Ugland, K., Borges, P.A.V., Rigal, F., Cardoso, P. & Whittaker, R.J. (2014). The gambin model provides a superior fit to species abundance distributions with a single free parameter: evidence, implementation and interpretation. Ecography, 37: 1002–1011, DOI: 10.1111/ecog.00861 (IF2013:4.207; Q1 Ecology)

 

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