The Sorensen similarity (overlap) index measures the overlap between two populations by taking the ratio of the number of species shared between the two populations, relative to the number of species in both populations. The index varies between zero (no overlap) and one (perfect overlap). It is closely related to the Jaccard index of similarity (implemented in function `ji`

).

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`x` |
a matrix containing input populations |

`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 Sorensen 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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