Diversity Estimators

Using eight estimators developed in the ecological literature, we calculated diversity from replicate samples and tested estimator accuracy. These estimators were recently reviewed [23] and compared in [32] and include the ACE and ICE coverage estimators [29], Chao 1 and Chao 2 [27], and a maximum likelihood estimator of parameters of the Michaelis-Menten model (MM) [94]. The Jackknife and Bootstrap estimators [32] were also evaluated. All estimators were calculated by EstimateS (version 6.0b1, available at viceroy.eeb.uconn.edu/estimates).

Of the eight estimators, two warrant particular attention for reasons detailed below, in Section 3.4.1: Chao 1 and ACE. The Chao 1 estimator was first described in [27]. It is defined as $\hat{S}_{Chao1} = S_{obs} + [f^2(1)/2f(2)]$, where $S_{obs}$ is the observed sample diversity, $f(1)$ is the observed number of singletons (only a single individual is observed), and $f(2)$ is the observed number of duplicates. The ACE (which is an acronym for ``abundance coverage estimator'') calculation is described in [29]. Its advantage is the use of sample coverage information, or the sum of relative abundance probabilities in a sample, to refine estimates over purely non-parametric estimators [29,32].