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)

Arguments

x

phyloseq-class object

detection

Detection threshold for absence/presence (strictly greater by default).

prevalence

Prevalence threshold (in [0, 1]; strictly greater 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 1.0.2 Index]