rarity: Rarity Index

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

View source: R/rarity.R

Description

Calculates the community rarity index.

Usage

1
rarity(x, index = "all", detection = 0.2/100, prevalence = 20/100)

Arguments

x

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.

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.

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

alpha, log_modulo_skewness, rare_abundance, low_abundance

Examples

1
2
3
data(dietswap)
d <- rarity(dietswap, index='low_abundance')
# d <- rarity(dietswap, index='all')

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