evenness: Evenness Index
In microbiome: Microbiome Analytics

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

Various community evenness indices.

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

`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

By default, Pielou's evenness is returned.

The available evenness indices include the following: 1) 'camargo': Camargo's evenness (Camargo 1992) 2) 'simpson': Simpson<e2><80><99>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 <e2><80><93>2001) and a plea for more rigorous use of species richness, species diversity and the <e2><80><98>Shannon<e2><80><93>Wiener<e2><80><99> Index. Spellerberg and Fedor. Alpha Ecology & Biogeography (2003) 12, 177<e2><80><93>197 4) 'evar': Smith and Wilson<e2><80><99>s Evar index (Smith & Wilson 1996) 5) 'bulla': Bulla<e2><80><99>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.

A vector of evenness indices

Contact: Leo Lahti microbiome-admin@googlegroups.com

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.

coverage, core_abundance, rarity, alpha

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