rare_abundance {microbiome} | R Documentation

## Rare (Non-Core) Abundance Index

### Description

Calculates the rare abundance community index.

### Usage

    rare_abundance(x, detection = 0.1/100, prevalence = 50/100,
      include.lowest = FALSE)

### Arguments

`x` | `phyloseq-class` object
`detection` | Detection threshold for absence/presence (strictly greater by default).
`prevalence` | Prevalence threshold (in [0, 1]). The required prevalence is strictly greater by default. To include the limit, set include.lowest to TRUE.
`include.lowest` | Include the lower boundary of the detection and prevalence cutoffs. FALSE by default.

### Details

This index gives the relative proportion of rare species (ie. those that are not part of the core microbiota) in the interval [0,1]. This is the complement (1-x) of the core abundance. The rarity function provides the abundance of the least abundant taxa within each sample, regardless of the population prevalence.

### Value

A vector of indices

### Author(s)

Contact: Leo Lahti microbiome-admin@googlegroups.com

### See Also

core_abundance, rarity, diversity

### Examples

    data(dietswap)
    d <- rare_abundance(dietswap, detection=0.1/100, prevalence=50/100)

[Package microbiome version 1.8.0 Index]