dominance: Dominance Index

In microbiome/microbiome: Microbiome Analytics

Dominance Index

Description

Calculates the community dominance index.

Usage

dominance(x, index = "all", rank = 1, relative = TRUE, aggregate = TRUE)

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	If the index is given, it will override the other parameters. See the details below for description and references of the standard dominance indices. By default, this function returns the Berger-Parker index, ie relative dominance at rank 1.
rank	Optional. The rank of the dominant taxa to consider.
relative	Use relative abundances (default: TRUE)
aggregate	Aggregate (TRUE; default) the top members or not. If aggregate=TRUE, then the sum of relative abundances is returned. Otherwise the relative abundance is returned for the single taxa with the indicated rank.

Details

The dominance index gives the abundance of the most abundant species. This has been used also in microbiomics context (Locey & Lennon (2016)). The following indices are provided:

• 'absolute' This is the most simple variant, giving the absolute abundance of the most abundant species (Magurran & McGill 2011). By default, this refers to the single most dominant species (rank=1) but it is possible to calculate the absolute dominance with rank n based on the abundances of top-n species by tuning the rank argument.

• 'relative' Relative abundance of the most abundant species. This is with rank=1 by default but can be calculated for other ranks.

• 'DBP' Berger–Parker index, a special case of relative dominance with rank 1; This also equals the inverse of true diversity of the infinite order.

• 'DMN' McNaughton’s dominance. This is the sum of the relative abundance of the two most abundant taxa, or a special case of relative dominance with rank 2

• 'simpson' Simpson's index ($sum(p^2)$) where p are relative abundances has an interpretation as a dominance measure. Also the version ($sum(q * (q-1)) / S(S-1)$) based on absolute abundances q has been proposed by Simpson (1949) but not included here as it is not within [0,1] range, and it is highly correlated with the simpler Simpson dominance. Finally, it is also possible to calculated dominances up to an arbitrary rank by setting the rank argument

• 'core_abundance' Relative proportion of the core species that exceed detection level 0.2% in over 50% of the samples

• 'gini' Gini index is calculated with the function inequality.

By setting aggregate=FALSE, the abundance for the single n'th most dominant taxa (n=rank) is returned instead the sum of abundances up to that rank (the default).

Value

A vector of dominance 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

coverage, core_abundance, rarity, alpha

Examples

data(dietswap)
# vector
d <- dominance(abundances(dietswap)[,1], rank=1, relative=TRUE)
# matrix
# d <- dominance(abundances(dietswap), rank=1, relative=TRUE)
# Phyloseq object
# d <- dominance(dietswap, rank=1, relative=TRUE)

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