i.in Information Index (I index) for 2-Way Table

Description

The I-index is a measure of overlap in two way tables based on the generalized mutual information statistic. The I-index measures dependence among columns of two-way tables, taking values between 0 and 1. It returns a value of zero when the table columns form an orthogonal system and a value of one when the table columns rank is one. The value of the parameter alpha is related to the structure of dependence, as described in Rempala and Seweryn (2013).

Usage

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i.in(x, alpha = 1, CI = 0.95, resample = 100, PlugIn = FALSE, size = 1, CVG = FALSE, 
saveBootstrap = FALSE)

Arguments

x

a matrix containing input populations

alpha

I index of order alpha, must be between 0 and 1, default = 0.5

CVG

I index of order alpha = 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

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)

Maciej Pietrzak, Michal Seweryn, Grzegorz Rempala
Maintainer: Maciej Pietrzak pietrzak.20@osu.edu

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

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data(TCR.Data)
result <- i.in(x, resample = 50)