divergence {microbiome} | R Documentation

## Divergence within a Sample Group

### Description

Quantify microbiota divergence (heterogeneity) within a given sample set with respect to a reference.

### Usage

    divergence(x, y, method = "bray")

### Arguments

`x` | phyloseq object or a vector
`y` | Reference sample. A vector.
`method` | dissimilarity method: any method available via phyloseq::distance function. Note that some methods ("jsd" and 'unifrac' for instance) do not work with the group divergence.

### Details

Microbiota divergence (heterogeneity / spread) within a given sample set can be quantified by the average sample dissimilarity or beta diversity with respect to a given reference sample.

This measure is sensitive to sample size. Subsampling or bootstrapping can be applied to equalize sample sizes between comparisons.

### Value

Vector with dissimilarities; one for each sample, quantifying the dissimilarity of the sample from the reference sample.

### Author(s)

Leo Lahti microbiome-admin@googlegroups.com

### References

To cite this R package, see citation('microbiome')

### See Also

the vegdist function from the vegan package provides many standard beta diversity measures

### Examples

    # Assess beta diversity among the African samples
    # in a diet swap study (see \code{help(dietswap)} for references)
    data(dietswap)
    pseq <- subset_samples(dietswap, nationality == 'AFR')
    reference <- apply(abundances(pseq), 1, median)
    b <- divergence(pseq, reference, method = "bray")

[Package microbiome version 1.12.0 Index]