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

Value

A tibble joining sample metadata with columns from get_alpha_S(), get_alpha_simpson(), and get_alpha_shannon().

Details

Although this new version removes much of the phyloseq code, running them instead in Vegan or calculating manually, it does still require phyloseq from bioconductor, which is not automatically installed with jakR2.