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Dice-Sorensen dissimilarity

Source: R/beta_div.r
sorensen.Rd

A statistic used for comparing the similarity of two samples.

Usage

sorensen(counts, margin = 1L, pairs = NULL, 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

pairs

Which combinations of samples should distances be calculated for? The default value (NULL) calculates all-vs-all. Provide a numeric or logical vector specifying positions in the distance matrix to calculate. See examples.

cpus

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

Details

The Dice-Sorensen dissimilarity is defined as: $$\frac{2J}{(A + B)}$$

Where:

  • \(A\), \(B\) : Number of features in each sample.

  • \(J\) : Number of features in common (intersection).

Base R Equivalent:

x <- ex_counts[1,]
y <- ex_counts[2,]
2 * sum(x & y) / sum(x>0, y>0)

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

Sørensen, T. (1948). A method of establishing groups of equal amplitude in plant sociology based on similarity of species content. Kongelige Danske Videnskabernes Selskab, Biologiske Skrifter, 5, 1-34.

Dice, L. R. (1945). Measures of the amount of ecologic association between species. Ecology, 26(3), 297–302. doi:10.2307/1932409

See also

beta_div(), vignette('bdiv'), vignette('bdiv_guide')

Other Presence/Absence metrics: hamming(), jaccard(), ochiai()

Examples

    sorensen(ex_counts)
#>           Saliva       Gums       Nose
#> Gums  0.11111111                      
#> Nose  0.20000000 0.09090909           
#> Stool 0.33333333 0.20000000 0.09090909