rarity: Rarity Index

In microbiome/microbiome: Microbiome Analytics

Rarity Index

Description

Calculates the community rarity index.

Usage

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:

• log_modulo_skewness Quantifies the concentration of the least abundant species by the log-modulo skewness of the arithmetic abundance classes (see Magurran & McGill 2011). These are typically right-skewed; to avoid taking log of occasional negative skews, we follow Locey & Lennon (2016) and use the log-modulo transformation that adds a value of one to each measure of skewness to allow logarithmization. The values q=0.5 and n=50 are used here.

• low_abundance Relative proportion of the least abundant species, below the detection level of 0.2%. The least abundant species are determined separately for each sample regardless of their prevalence.

• rare_abundance Relative proportion of the non-core species, exceed the given detection level (default 20 at the given prevalence (default 20 This is complement of the core with the same thresholds.

Value

A vector of rarity indices

Author(s)

Contact: Leo Lahti [e-mail]

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

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

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