The I-index is a measure of overlap in two way tables based on the generalized mutual information statistic. This function implements a special case of table with two columns only. In general, the I-index measures dependence in any 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).

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`x` |
a matrix containing input populations |

`alpha` |
I index of order |

`CVG` |
I index of order |

`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 I Index; |

`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 |

Maciej Pietrzak, Michal Seweryn, 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

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