The symmetrized Renyi divergence (RD) is a measure of similarity between two discrete probability distributions which is non negative and symmetric. For details, see the description of function rd or Rempala and Seweryn (2013).
srd(x, alpha = 0.5, CI = 0.95, resample = 100, graph = FALSE, csv_output = FALSE,
PlugIn = FALSE, size = 1, CVG = FALSE, saveBootstrap = FALSE)a matrix containing input populations
Renyi's Divergence index of order alpha must be between 0 and 1, default = 0.5
Renyi's Divergence index of order alpha = coverage. If CVG = TRUE argument alpha is ignored; default = FALSE
Confidence Interval default = 0.95, range (0, 1)
number of repetitions, default = 100
default = FALSE, plots the results of hierarchical clustering of pairwise analysis of Renyi's Divergence; graph = 'fileName' user-defined output file name
save the result of the analysis as .CSV file, default = FALSE; csv_output = 'fileName' user-defined output file name
standard plug-in estimator, default = FALSE
resampled fraction of the population, default = 1 (actual size of populations). The value should not be smaller than 10% of population (size = 0.1)
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
Christoph Sadee, Maciej Pietrzak, Michal Seweryn, Cankun Wang, Grzegorz Rempala
Maintainer: Maciej Pietrzak pietrzak.20@osu.edu
Rempala G.A., Seweryn M. (2013) Methods for diversity and overlap analysis in T-cell receptor populations. J Math Biol 67:1339-68
data(TCR.Data)
result <- srd(x, resample = 20, alpha=0.5)Run the code above in your browser using DataLab