phyloseq (version 1.16.2)

JSD: 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.

Value

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

Details

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

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))