rarity {microbiome} | R Documentation

## 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 detection level of 0.2% at 50% prevalence at most. This is complement of the core with the same thresholds.

- rare_abundance Relative proportion of the rare taxa in [0,1] - the rare taxa are detected with less than 20% prevalence, regardless of abundance.

### 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

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

[Package microbiome version 1.8.0 Index]