Anne chaos website offers excellent rbased tools to compute most of what. Species richness estimation based on sampling data has a long history in. The calculations for the biascorrected chao1 richness estimator are implemented as described by chao in the user manual for her program spade and modified by colwell in his program estimates. Hsieh and chunhuo chiu institute of statistics national tsing hua university, taiwan 30043 the program spader is the rbased online version of spade available via the link. Species richness and species density are not the same thing. Species richness possesses intuitive mathematical properties, and features prominently in foundational models of community ecology. The solid line is the samplebased rarefaction curve for the same data set as in fig 4. Computes asymmetric logtransformed confidence intervals for chao1 andchao2. Generally reliable methods are the chao and jackknife techniques. Although the chao 1 estimator works for abundance data, often only. Use the inext package calculate some richness estimators and build the species accumulation curve. Computes diversity indices shannon, simpson, fishers alpha, hill numbers. The chao calculator returns the chao1 richness estimate for an otu definition. Anne chao, national tsing hua university, taiwan 30043.
In this case, compute the biascorrected form of chao2 instead. There are two approaches to infer species richness and make fair comparisons among multiple assemblages based on possibly unequal sampling effort and incomplete samples that miss many species. So, to use it for the aurora data, we need to transform the data into a single site with species abundance just for the sake of this exercise. This means that the data it requires refer to the abundance of individuals belonging to a certain class in a sample. Colwell and coddington 1994, which uses occurrence data from multiple samples in aggregate to estimate the species diversity of the whole. Chao 1984 proposed a nonparametric estimator for species richness that takes the form. Although the chao 1 estimator works for abundance data, often only occurrence data are available. Chao and lin34 extended the chao1 estimator to deal with data based on. Computes a wide range of species richness estimators for. Introduction to online program spader speciesrichness prediction and diversity estimation in r by anne chao, k.