evenness: Evenness Index

In microbiome/microbiome: Microbiome Analytics

Evenness Index

Description

Various community evenness indices.

Usage

evenness(x, index = "all", zeroes = TRUE, detection = 0)

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	Evenness index. See details for options.
zeroes	Include zero counts in the evenness estimation.
detection	Detection threshold

Details

By default, Pielou's evenness is returned.

The available evenness indices include the following: 1) 'camargo': Camargo's evenness (Camargo 1992) 2) 'simpson': Simpson’s evenness (inverse Simpson diversity / S) 3) 'pielou': Pielou's evenness (Pielou, 1966), also known as Shannon or Shannon-Weaver/Wiener/Weiner evenness; H/ln(S). The Shannon-Weaver is the preferred term; see A tribute to Claude Shannon (1916 –2001) and a plea for more rigorous use of species richness, species diversity and the ‘Shannon–Wiener’ Index. Spellerberg and Fedor. Alpha Ecology & Biogeography (2003) 12, 177–197 4) 'evar': Smith and Wilson’s Evar index (Smith & Wilson 1996) 5) 'bulla': Bulla’s index (O) (Bulla 1994)

Desirable statistical evenness metrics avoid strong bias towards very large or very small abundances; are independent of richness; and range within [0,1] with increasing evenness (Smith & Wilson 1996). Evenness metrics that fulfill these criteria include at least camargo, simpson, smith-wilson, and bulla. Also see Magurran & McGill (2011) and Beisel et al. (2003) for further details.

Value

A vector of evenness indices

Author(s)

Contact: Leo Lahti [e-mail]

References

Beisel J-N. et al. A Comparative Analysis of Evenness Index Sensitivity. Internal Rev. Hydrobiol. 88(1):3-15, 2003. URL: https://portais.ufg.br/up/202/o/2003-comparative_evennes_index.pdf

Bulla L. An index of evenness and its associated diversity measure. Oikos 70:167–171, 1994

Camargo, JA. New diversity index for assessing structural alterations in aquatic communities. Bull. Environ. Contam. Toxicol. 48:428–434, 1992.

Locey KJ and Lennon JT. Scaling laws predict global microbial diversity. PNAS 113(21):5970-5975, 2016; doi:10.1073/pnas.1521291113.

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

Pielou, EC. The measurement of diversity in different types of biological collections. Journal of Theoretical Biology 13:131–144, 1966.

Smith B and Wilson JB. A Consumer's Guide to Evenness Indices. Oikos 76(1):70-82, 1996.

See Also

coverage, core_abundance, rarity, alpha

Examples

data(dietswap)
# phyloseq object
#d <- evenness(dietswap, 'pielou')
# matrix
#d <- evenness(abundances(dietswap), 'pielou')
# vector
d <- evenness(abundances(dietswap)[,1], 'pielou')

microbiome/microbiome documentation built on Dec. 12, 2024, 2:45 p.m.