Chao1-index

What does the Chao1 index estimate? - Studybuff

00-Magurran-Prelims.dvi (uvm.edu)

Blockquote Shannon-Weaver and Simpson Diversity Indices

A definition of biodiversity is widely cited as follows:

“Biological diversity means the variability among living

organisms from the ecological complexes of which

organisms are part, and it is defined as species richness and

relative species abundance in space and time” [14]. A

variety of approaches have been used to quantify biological

diversity. Two main factors, richness and evenness, should

be taken into account when measuring the diversity of

certain samples. A measure of the number of different

kinds of organisms present in a particular community is

defined as richness; thus, species richness refers to the

number of different species present in a certain niche. If

more species are present in “A” than “B”, “A” is richer

than “B”. When it comes to species richness, it does not

consider the number of individuals of each species present

(Figs. 1A and 1B). Nevertheless, diversity depends not only

on richness, but also on evenness. Evenness compares the

uniformity of the population size of each of the species

https://www.researchgate.net/post/How-to-interpret-Chao1-and-Chao2-values

https://cran.r-project.org/web/packages/iNEXT/vignettes/Introduction.pdf

https://besjournals.onlinelibrary.wiley.com/doi/10.1111/2041-210X.12613

**Chao1 is an estimator based on abundance.** This means that the data it requires refer to the abundance of individuals belonging to a certain class in a sample. A sample is any list of species in a site, location, quadrant, country, unit of time, trap, etcetera. As we know, there are many species that are only represented by a few individuals in a sample (rare species), compared to the common species, which can be represented by numerous individuals. The Chao1 estimator is based on the presence of the former. That is, we need to know how many species are represented by only one individual in the sample (singletons), and how many species are represented by exactly two individuals (doubletons): Sest = Sobs + F2 / 2G, where: Sest is the number of classes ( in this case, number of species) that we want to know, Sobs is the number of species observed in a sample, F is the number of singletons and G is the number of doubletons. In the programEstimates a corrected formula has also been integrated for this model, which is applied when the number of doubletons is zero: Sest = Sobs + ((F2 / 2G + 1) - (FG / 2 (G + 1) 2)).

**Chao2 is the estimator based on the incidence.** This means that it needs presence-absence data of a species in a given sample, that is, only if the species is present and how many times is that species in the sample set: Sest = Sobs + (L2 / 2M), where: L is the number of species that occur only in one sample (“unique” species), and M is the number of species that occur in exactly two samples (“double” or “duplicate” species). For example, if we have a set of grids, we need to know how many species are in a grid and how many species are in two. The formula corrected in Estimates, which is applied when the number of doubles is zero, is: Sest = Sobs + ((L2 / 2M + 1) - (LM / 2 (M + 1) 2)). To use both estimators in ESTIMATES, data in the form of a matrix is needed, where rows and columns can represent samples and species indistinctly; it is necessary to establish the order once the program has started. Estimates also allows the calculation of the standard deviation of the two estimators. Once several randomisations are made (50 recommended, but can be 100 or more), with or without replacement, and when the total number of samples has been used, the final value of the estimator is obtained and the results can be plotted. The number of samples is presented on the x axis, and the number of species in the dependent variable. Thus, the Sest and the Sobs can be compared. But the final graph is interpreted differently from the conventional one: when you have the total number of samples, there is a certain separation between the curve of the Sest and the Sobs. That separation would be indicating how many species are missing to register in that community. The more separated they are, we would expect that the total number of species that contains the place is greater than the one that we currently know.

For additional information please read the following chapter Estimating species richness in the following link:

https://www.uvm.edu/~ngotelli/manuscriptpdfs/Chapter%204.pdf