rare_abundance: Rare (Non-Core) Abundance Index

In microbiome/microbiome: Microbiome Analytics

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 [e-mail]

See Also

core_abundance, rarity, diversity

Examples

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

microbiome/microbiome documentation built on Aug. 22, 2023, 7:12 a.m.