What formula is used to calculate Chao1 and Chao2?

[colinbrislawn (Colin J Brislawn)]

Hello Jarred,

Many of the diversity indexes are listed, described, and cited in this thread:

Alpha and Beta Diversity Explanations and Commands

About the Alpha and Beta Diversity Analysis Tutorial This Alpha and Beta Diversity Community Tutorial (run using QIIME 2017.12) walks you through analyzing the alpha and beta diversity of a sample dataset. Below you will find a link to a small test dataset to download and use in this tutorial. Files used in tutorial The following files, derived from the Moving Pictures tutorial, are used in this document. table.qza rooted-tree.qza Alpha Diversity Analysis The alpha and alpha-phylogenetic met…

Chao1, Chao2, and ACE are sort of the same thing.

Formula here:
https://rdrr.io/cran/vegan/man/specpool.html

P.S. Does that help answer your question?
P.P.S. Welcome to the forums!