HMP (version 2.0.1)

Kullback.Leibler: Kullback Leibler

Description

Calculates Kullback Leibler divergence for all pairs of the datasets.

Usage

Kullback.Leibler(group.data, plot = TRUE, main="Kullback Leibler Divergences", 
		parallel = FALSE, cores = 3)

Arguments

group.data

A list where each element is a matrix of taxonomic counts(columns) for each sample(rows).

plot

When 'TRUE' a heatmap of the results will also be generated.

main

A string to be used as the plots title.

parallel

When this is 'TRUE' it allows for parallel calculation of the KL distances. Requires the package doParallel.

cores

The number of parallel processes to run if parallel is 'TRUE'.

Value

A matrix of Kullback Leibler divergence values and a heatmap if plot is TRUE.

References

Kotz S, Johnson N.L (1981) Encyclopedia Of Statistical Sciences

Examples

# NOT RUN {
	data(saliva)
	data(throat)
	data(tonsils)
	
	### Combine the data sets into a single list
	group.data <- list(saliva, throat, tonsils)
	
	
# }
# NOT RUN {
		kl <- Kullback.Leibler(group.data)
		kl
	
# }