richness {microbial}

calculat the richness for the phyloseq object

Description

calculat the richness for the phyloseq object

Usage

richness(physeq, method = c("Observed", "Simpson", "Shannon"))

Arguments

physeq

A phyloseq object containing merged information of abundance, taxonomic assignment, sample data including the measured variables and categorical information of the samples, and / or phylogenetic tree if available.

method

A list of character strings specifying method to be used to calculate for alpha diversity in the data. Available methods are: "Observed","Chao1","ACE","Richness", "Fisher", "Simpson", "Shannon", "Evenness","InvSimpson".

Value

data.frame of alpha diversity

Author(s)

Kai Guo

Examples

{
data("Physeq")
rich <-richness(physeq,method=c("Simpson", "Shannon"))
}