richness {microbiome} | R Documentation

## Richness Index

### Description

Community richness index.

### Usage

    richness(x, detection = NULL)

### Arguments

`x` | A species abundance vector, or matrix (taxa/features x samples) with the absolute count data (no relative abundances), or `phyloseq-class` object
`detection` | Detection threshold.

### Details

By default, returns the richness for multiple detection thresholds defined by the data quantiles. If the detection argument is provided, returns richness with that detection threshold.

### Value

A vector of richness indices

### Author(s)

Contact: Leo Lahti microbiome-admin@googlegroups.com

### See Also

global

### Examples

    data(dietswap)
    d <- richness(dietswap, detection=0)

[Package microbiome version 1.2.1 Index]