low_abundance {microbiome} | R Documentation

## Low Abundance Index

### Description

Calculates the concentration of low-abundance taxa below the indicated detection threshold.

### Usage

    low_abundance(x, detection = 0.2/100)

### Arguments

`x` | `phyloseq-class` object
`detection` | Detection threshold for absence/presence (strictly greater by default).

### Details

The low_abundance index gives the concentration of species at low abundance, or the relative proportion of rare species in [0,1]. The species that are below the indicated detection threshold are considered rare. Note that population prevalence is not considered. If the detection argument is a vector, then a data.frame is returned, one column for each detection threshold.

### Value

A vector of indicators.

### Author(s)

Contact: Leo Lahti microbiome-admin@googlegroups.com

### See Also

core_abundance, rarity, global

### Examples

    data(dietswap)
    d <- low_abundance(dietswap, detection=0.2/100)

[Package microbiome version 1.12.0 Index]