JSD.Rd 2.05 KB
 Andreas Tille committed Sep 22, 2017 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 % Generated by roxygen2: do not edit by hand % Please edit documentation in R/distance-methods.R \name{JSD} \alias{JSD} \title{Calculate the Jensen-Shannon Divergence (distance)} \usage{ JSD(physeq) } \arguments{ \item{physeq}{(Required). \code{\link{phyloseq-class}}. The phyloseq data on which to compute the pairwise sample distance matrix.} } \value{ An object of class \code{\link{dist}}'' suitable for certain ordination methods and other distance-based analyses. See \code{\link{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. \code{JSD} is intended to be wrapped'' by the more general \code{\link{distance}} function in phyloseq, and it can be invoked using \code{"jsd"} as the argument to the \code{method} parameter of \code{\link{distance}}. } \details{ One of the motivations for providing JSD in phyloseq was its recent use in the analysis of the \code{\link{enterotype}} dataset. } \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)) } \references{ Jensen-Shannon Divergence and Hilbert space embedding. Bent Fuglede and Flemming Topsoe University of Copenhagen, Department of Mathematics \url{http://www.math.ku.dk/~topsoe/ISIT2004JSD.pdf} } \seealso{ \code{\link{distance}} \code{\link{enterotype}} \url{http://en.wikipedia.org/wiki/Jensen-Shannon_divergence} }  Andreas Tille committed Nov 11, 2017 55 56 57 58 \author{ Susan Holmes \email{susan@stat.stanford.edu}. Adapted for phyloseq by Paul J. McMurdie. }  Andreas Tille committed Sep 22, 2017 59 \keyword{internal}