The Morisita-Horn index is a popular angular overlap measure used both in ecological and immunological literature. It quantifies overlap as cosine of an angle between two standardized population vectors. It ranges between zero (no overlap) and one (perfect overlap). MH tends to be over-sensitive to abundant species. For details see Rempala and Seweryn (2013) or Magurran (2005).

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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 Morisita-Horn 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

Magurran A.E. (2005) Biological diversity. Curr Biol 15:R116-8

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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