Chao 1984 proposed a nonparametric estimator for species richness that takes the form. Colwell 2009 has released a program for windows called estimates which does exactly. 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. Although the chao 1 estimator works for abundance data, often only occurrence data are available. 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. Evaluating the performance of species richness estimators.
Species richness possesses intuitive mathematical properties, and features prominently in foundational models of community ecology. 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 and lin34 extended the chao1 estimator to deal with data based on. Although rarefaction interpolates data back, nonparametric species estimators. Estimates is a free software application for windows and macintosh operating. 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.
In this case, compute the biascorrected form of chao2 instead. Anne chaos website offers excellent rbased tools to compute most of what. Use the inext package calculate some richness estimators and build the species accumulation curve. Introduction to online program spader speciesrichness prediction and diversity estimation in r by anne chao, k. Species richness and species density are not the same thing. Computes asymmetric logtransformed confidence intervals for chao1 andchao2. Computes a wide range of species richness estimators for. 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. There is another estimator, named conveniently chao 2 chao 1987. The chao calculator returns the chao1 richness estimate for an otu definition. Computes a wide range of species richness estimators for samplebased abundance and incidence presenceabsence data chao, jackknife, ice, ace and others.
Introduction to online program spader speciesrichness. Optimizing performance of nonparametric species richness. Estimating species richness 41 the formula for ice is unde. Although the chao 1 estimator works for abundance data, often only. Species diversity and richness offers a variety of methods for species richness estimation. Computes diversity indices shannon, simpson, fishers alpha, hill numbers. The solid line is the samplebased rarefaction curve for the same data set as in fig 4. The inext package is mainly aimed for comparisons betweenamong sites. Anne chao, national tsing hua university, taiwan 30043. Estimated species richness scores depended both on the estimator. Generally reliable methods are the chao and jackknife techniques.