Description Usage Arguments Author(s) References Examples

The Renyi divergence (RD) is a measure of similarity between two discrete probability distributions. The Renyi divergence is non-negative, not symmetric, and is not defined when there is no common support between two distributions RD is parameterized by a single non-negative parameter which may be used to adjust the relative contributions of small and large probabilities to its overall value. RD is a generalization of the Kullback-Leibler divergence. For details, see Rempala and Seweryn (2013).

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`x` |
a matrix containing input populations |

`alpha` |
Renyi's Divergence index of order |

`CVG` |
Renyi's Divergence index of order |

`CI` |
Confidence Interval default = 0.95, range (0, 1) |

`resample` |
number of repetitions, default = 100 |

`graph` |
default = FALSE, plots the results of hierarchical clustering of pairwise analysis of Renyi's Divergence; |

`csv_output` |
save the result of the analysis as .CSV file, default = FALSE; |

`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 |

Christoph Sadee, Maciej Pietrzak, Michal Seweryn, Grzegorz Rempala

Maintainer: Maciej Pietrzak [email protected]

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

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