core_abundance {microbiome} | R Documentation

## Core Abundance

### Description

Calculates the community core abundance index.

### Usage

    core_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

The core abundance index gives the relative proportion of the core species (in [0,1]). The core taxa are defined as those that exceed the given population prevalence threshold at the given detection level.

### Value

A vector of core abundance indices

### Author(s)

Contact: Leo Lahti microbiome-admin@googlegroups.com

### See Also

rarity

### Examples

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

[Package microbiome version 1.12.0 Index]