pg.ht: pg.ht Power-Geometric Index with the Horvitz-Thompson...

In divo: Tools for Analysis of Diversity and Similarity in Biological Systems

Description

The Horvitz-Thompson corrected version of the Power Geometric (PG) index (see help for pg). The PG index is a generalization of the Morisita-Horn index as well as the Bhattacharyya's coefficient. It quantifies overlap as cosine of an angle between two exponentially normalized population vectors. For further details and definitions, see Rempala and Seweryn (2013).

Usage

pg.ht(x, alpha = 1, beta=alpha, CI = 0.95, resample = 100, graph = FALSE, 
csv_output = FALSE, PlugIn = FALSE, size = 1, CVG = FALSE, saveBootstrap = FALSE)

Arguments

x	a matrix containing input populations
alpha	PG of order alpha < 1 puts more weight on the rare species and the I Index of order alpha > 1 puts more weight on the abundant ones for first population, default = 1
beta	PG of order beta < 1 puts more weight on the rare species and the I Index of order beta > 1 puts more weight on the abundant ones for second population, default = alpha
CVG	PG of order alpha or beta = coverage. If CVG = TRUE argument alpha is ignored; default = FALSE
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 Power-Geometric 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

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 <- pg.ht(x, PlugIn = TRUE)

divo documentation built on Dec. 18, 2019, 1:51 a.m.