resample-estimates.RmdAlpha diversity metrics, such as Shannon and Simpson indices, are unknown parameters of the microbial communities that we study. Like any other parameter of a population, they need to be estimated based on data, and the estimates should be accompanied by standard errors. Unfortunately this is not practised in the case of alpha diversity indices in microbial ecology.
breakaway focuses on species richness estimates. The package DivNet is for alpha and beta diversity estimates. Please go to github.com/adw96/DivNet to get DivNet.