add_alpha_diversity: Adds alpha diversity metrics to a 'phyloseq' object.

In DanielSprockett/reltools: Microbiome Amplicon Analysis and Visualization

Description

This function adds several alpha diversity metrics to the sample_data of a phyloseq object. This function largely a reimplementation of estimate_richness.

Usage

add_alpha_diversity(ps)

Arguments

ps	A phyloseq object that contains sample_data. If there is a tree in the phy_tree slot, this function will also add Faith's Phylogenetic Diversity (1992) as implemented in picante with the pd function.

Value

This function returns the input phyloseq object with Observed, Chao1, ACE, Shannon, Simpson, InvSimpson, Fisher, and Faiths_PD columns in the sample_data().

Examples

ps <- add_alpha_diversity(ps)

DanielSprockett/reltools documentation built on May 5, 2019, 12:27 p.m.