rare_abundance: Rare (Non-Core) Abundance Index

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/rare_abundance.R

Description

Calculates the rare abundance community index.

Usage

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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

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

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