Calculates diversity profile (DP) (Rempala and Seweryn 2013 or Tothmeresz 1995) using the Renyi entropy (Renyi 1961) as a diversity measure. The function calculates the Renyi entropy values for a given range of the Renyi index (the index should be greater than 0). When the index is less then one, the rare counts are up-weighted and when it is greater than one, the rare counts are down-weighted. Since the Renyi entropy is a non-increasing function of the index, the profile plot should be always non-increasing.

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`x` |
a matrix containing input populations |

`alpha` |
a vector containing alpha values, default = seq(0.1, 2, 0.1) |

`CVG` |
a vector containing alpha values multiplied by coverage; default = FALSE |

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

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

`single_graph` |
default = FALSE, plot of the Diversity Profile for each population; |

`pooled_graph` |
default = FALSE, plot of the Diversity Profile for all populations; |

`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

Renyi P. (1961) On measures of information and entropy. In: Proceedings of the 4th Berkeley symposium on mathematics, statistics and probability, pp 547-61

Tothmeresz B. (1995) Comparison of different methods for diversity ordering. J Veget Sci 6:283-90

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