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Berger-Parker Index

Source: R/alpha_div.r
berger.Rd

A measure of the numerical importance of the most abundant species.

Usage

berger(counts, margin = 1L, cpus = n_cpus())

Arguments

counts

A numeric matrix of count data (samples \(\times\) features). Typically contains absolute abundances (integer counts), though proportions are also accepted.

margin

The margin containing samples. 1 if samples are rows, 2 if samples are columns. Ignored when counts is a special object class (e.g. phyloseq). Default: 1

cpus

How many parallel processing threads should be used. The default, n_cpus(), will use all logical CPU cores.

Details

The Berger-Parker index is defined as the proportional abundance of the most dominant feature: $$\max(P_i)$$

Where:

  • \(P_i\) : Proportional abundance of the \(i\)-th feature.

Base R Equivalent:

x <- ex_counts[1,]
p <- x / sum(x)
max(p)

Input Types

The counts parameter is designed to accept a simple numeric matrix, but seamlessly supports objects from the following biological data packages:

  • phyloseq

  • rbiom

  • SummarizedExperiment

  • TreeSummarizedExperiment

For large datasets, standard matrix operations may be slow. See vignette('performance') for details on using optimized formats (e.g. sparse matrices) and parallel processing.

References

Berger, W. H., & Parker, F. L. (1970). Diversity of planktonic foraminifera in deep-sea sediments. Science, 168(3937), 1345-1347. doi:10.1126/science.168.3937.1345

See also

alpha_div(), vignette('adiv')

Other Dominance metrics: mcintosh()

Examples

    berger(ex_counts)
#>    Saliva      Gums      Nose     Stool 
#> 0.5217391 0.8950339 0.4925816 0.9934959