core_abundance: Core Abundance

In microbiome: Microbiome Analytics

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 [e-mail]

See Also

rarity

Examples

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

microbiome documentation built on Nov. 8, 2020, 5:08 p.m.