Kullback.Leibler: Kullback Leibler

In HMP: Hypothesis Testing and Power Calculations for Comparing Metagenomic Samples from HMP

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

	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
	
## End(Not run)

Example output

Loading required package: dirmult

Attaching package: 'HMP'

The following object is masked from 'package:dirmult':

    weirMoM

           Data Set 1 Data Set 2 Data Set 3
Data Set 1     0.0000  355.38839  510.54204
Data Set 2   355.3884    0.00000   21.51607
Data Set 3   510.5420   21.51607    0.00000

HMP documentation built on Aug. 31, 2019, 5:05 p.m.