Alpha-Diversity Measures

An extension of the phyloseq `estimate_richness` function to include Shannon's Evenness and sample depth. It also combines the normal estimate_richness output with the sample data dataframe.

Usage

get_alpha_diversity(p, id_col = "SAMPLE")

Arguments

p

A phyloseq object

id_col

The name of the column with sample IDs

Details

The new version removes much of the phyloseq code, running them instead in Vegan or calculating manually.