breakaway is the premier package for statistical analysis of taxonomic richness. breakaway implements a wide variety of estimates of taxonomic richness, as well as methods for modeling diversity is a function of covariates.

corncob is an R package for modeling relative abundance and testing hypotheses about the effect of covariates on relative abundance. The corncob methodology was specifically developed for modelling microbial abundances based on high throughput sequencing data, such as 16S or whole-genome sequencing. Check out the paper for more details.

paramedic is a R package for estimating microbial concentration. paramedic uses information from 16S count data (compositional data on all taxa) and absolute data on a subset of taxa (e.g., qPCR or flow cytometry) to estimate the absolute abundance of all taxa. The method accounts for differing taxon detection efficiencies between the two methods, and produces prediction and confidence intervals as well as point estimates of the absolute abundance of all taxa. Check out the preprint for more details.

DivNet is an R package for estimating alpha and beta diversity in ecological communities, including the Shannon, Simpson, Bray-Curtis, and Euclidean indices. Unlike other methods, DivNet utilizes covariate and replicate information ("metadata") and models taxa in the ecosystem interacting and co-occuring. Check out the paper for more details.