I want to account for differences in communities using species turnover and nestedness. I have seen this done using stacked bar plots but am not sure how to get there from the betapart package in R.
Hello. We have done this following Baselga´s (2010) approach.
First, we calculated multisite total β-diversity using Sørensen´s index (βSOR), and decomposed it into two additive components: β-diversity resulting from turnover (using Simpson´s index, βSIM) and β-diversity resulting from nestedness (βNES). These indices were calculated with the ‘beta.multi’ function of the betapart 1.5.1 package in R (Baselga & Orme 2012). Because βNES is a measure of “dissimilarity caused by nestedness” and not a direct estimation (Baselga 2010), we also calculated the nestedness metric based on overlap and decreasing fill (NODF, Almeida-Neto et al. 2008). The significance of the NODF index was analyzed comparing the observed value with the average of 9999 null model simulations implemented with the Sim3 algorithm (in which the species numbers per site are fixed, Gotelli 2000). NODF and its significance were computed with the ‘oecosimu’ function of the package vegan 2.5-3 (Oksanen et al. 2018). These analyses were all performed using RStudio v. 1.1.463 (RStudio Team 2016).
Hope this helps!
Best,
Luis Daniel.
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