Description Usage Arguments Author(s) References Examples

The Power Geometric (PG) index is a geometric angular overlap measure parameterized by a two-dimensional vector (alpha, beta). The PG index is a generalization of the Morisita-Horn index as well as the Bhattacharyya's coefficient. It allows for increasing or decreasing the relative contribution of the rare species to the overall overlap and may be therefore used to account for the species undersampling. It quantifies overlap as cosine of an angle between two exponentially normalized population vectors. For further details and definition, see Rempala and Seweryn (2013).

1 2 3 |

`x` |
a matrix containing input populations |

`alpha` |
PG of order |

`beta` |
PG of order |

`CVG` |
PG of order |

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

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

`graph` |
default = FALSE, plot the results of hierarchical clustering of pairwise analysis of Power-Geometric 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 |

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

1 2 |

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.