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Margalef's Richness Index

Source: R/alpha_div.r
margalef.Rd

A richness metric that normalizes the number of species by the log of the total sample size.

Usage

margalef(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

Margalef's index is defined as: $$\frac{n - 1}{\ln{X_T}}$$

Where:

  • \(n\) : The number of features.

  • \(X_T\) : Total of all counts (sequencing depth).

Base R Equivalent:

x <- ex_counts[1,]
(sum(x > 0) - 1) / log(sum(x))

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

Margalef, R. (1958). Information theory in ecology. General Systems, 3, 36-71.

Gamito, S. (2010). Caution is needed when applying Margalef diversity index. Ecological Indicators, 10(2), 550-551. doi:10.1016/j.ecolind.2009.07.006

See also

alpha_div(), vignette('adiv')

Other Richness metrics: ace(), chao1(), menhinick(), observed(), squares()

Examples

    margalef(ex_counts)
#>    Saliva      Gums      Nose     Stool 
#> 0.5133870 0.5893866 0.7226796 0.6228956