rarity {microbiome}R Documentation

Rarity Index

Description

Calculates the community rarity index.

Usage

rarity(x, index = "all", rarity.detection = 0.2/100,
  rarity.prevalence = 20/100)

Arguments

x

A species abundance vector, or matrix (taxa/features x samples) with the absolute count data (no relative abundances), or phyloseq-class object

index

If the index is given, it will override the other parameters. See the details below for description and references of the standard rarity indices.

rarity.detection

Detection threshold for determining rare taxa.

rarity.prevalence

Prevalence threshold for determining rare taxa.

Details

The rarity index characterizes the concentration of species at low abundance.

The following rarity indices are provided:

Value

A vector of rarity indices

Author(s)

Contact: Leo Lahti microbiome-admin@googlegroups.com

References

Kenneth J. Locey and Jay T. Lennon. Scaling laws predict global microbial diversity. PNAS 2016 113 (21) 5970-5975; doi:10.1073/pnas.1521291113.

Magurran AE, McGill BJ, eds (2011) Biological Diversity: Frontiers in Measurement and Assessment (Oxford Univ Press, Oxford), Vol 12

See Also

global, log_modulo_skewness, noncore_abundance, low_abundance

Examples

data(dietswap)
d <- rarity(dietswap, index='low_abundance')
# d <- rarity(dietswap, index='all')

[Package microbiome version 1.0.2 Index]