JSD {phyloseq} | R Documentation

## Calculate the Jensen-Shannon Divergence (distance)

### Description

This is a phyloseq-specific implementation of the Jensen-Shannon Divergence for comparing pairs of microbial communities (samples) in an experiment. The expectation is that you have many samples (say. more than two) and you want a distance matrix on which will perform further analysis. `JSD` is intended to be “wrapped” by the more general `distance` function in phyloseq, and it can be invoked using `"jsd"` as the argument to the `method` parameter of `distance`.

### Usage

    JSD(physeq)

### Arguments

`physeq` | (Required). `phyloseq-class`. The phyloseq data on which to compute the pairwise sample distance matrix.

### Details

One of the motivations for providing JSD in phyloseq was its recent use in the analysis of the `enterotype` dataset.

### Value

An object of class “`dist`” suitable for certain ordination methods and other distance-based analyses. See `distance`.

### Author(s)

Susan Holmes susan@stat.stanford.edu. Adapted for phyloseq by Paul J. McMurdie.

### References

Jensen-Shannon Divergence and Hilbert space embedding. Bent Fuglede and Flemming Topsoe University of Copenhagen, Department of Mathematics http://www.math.ku.dk/~topsoe/ISIT2004JSD.pdf

### See Also

`distance`

`enterotype`

http://en.wikipedia.org/wiki/Jensen-Shannon_divergence

### Examples

    # library(doParallel)  # Do this and next line only if you have multi-cores
    # registerDoParallel(cores=6)
    # data(enterotype)
    # # ent.jsd <- JSD(enterotype, TRUE) # internal only
    # ent.jsd <- distance(enterotype, "jsd", parallel=TRUE)
    # ent.PCoA <- ordinate(enterotype, "PCoA", ent.jsd) # Perform principle coordinate analysis
    # p <- plot_ordination(enterotype, ent.PCoA, color="Enterotype", shape="SeqTech")
    # (p <- p + geom_point(size=5, alpha=0.5))

[Package phyloseq version 1.24.2 Index]