dominance {microbiome} | R Documentation

## 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 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

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)

[Package microbiome version 1.6.0 Index]