mh {divo}

mh Morisita-Horn Index

Description

The Morisita-Horn index is a popular angular overlap measure used both in ecological and immunological literature. It quantifies overlap as cosine of an angle between two standardized population vectors. It ranges between zero (no overlap) and one (perfect overlap). MH tends to be over-sensitive to abundant species. For details see Rempala and Seweryn (2013) or Magurran (2005).

Usage

mh(x, CI = 0.95, resample = 100, graph = FALSE, csv_output = FALSE, 
PlugIn = FALSE, size = 1, saveBootstrap = FALSE)

Arguments

x

a matrix containing input populations

CI

Confidence Interval default = 0.95, range (0, 1)

resample

set number of repetitions, default = 100

graph

default = FALSE, plot the results of hierarchical clustering of pairwise analysis of Morisita-Horn Index; graph = 'fileName' user-defined output file name

csv_output

save the result of the analysis as .CSV file, default = FALSE; csv_output = 'fileName' user-defined output file name

PlugIn

standard plug-in estimator, default = FALSE

size

resampled fraction of the population, default = 1 (actual size of populations). The value should not be smaller than 10% of population (size = 0.1)

saveBootstrap

Saves bootstrap result to a file. Use saveBootstrap = TRUE to save bootstrap results to a Bootstrap folder in current directory; saveBootstrap = 'FolderName' - saves bootstrap results to user-named folder

Author(s)

Christoph Sadee, Maciej Pietrzak, Michal Seweryn, Cankun Wang, Grzegorz Rempala
Maintainer: Maciej Pietrzak [e-mail]

References

Magurran A.E. (2005) Biological diversity. Curr Biol 15:R116-8

Rempala G.A., Seweryn M. (2013) Methods for diversity and overlap analysis in T-cell receptor populations. J Math Biol 67:1339-68

Examples

data(TCR.Data)
result <- mh(x, PlugIn = TRUE)