AcceptAffCI |
Acceptability Interval |

AcceptAffin |
Calculates the "Acceptability Function" used in defining Blaker's (2000) Acceptability Interval and computing the latter in the function AcceptAffCI(). |

affinity |
Computes alpha, probability, expected co-occurence, median interval, various confidence intervals, other indices of affinity, etc. |

affinity2by2 |
Maximum likelihood estimate and intervals of alpha, null expectation, p-value and traditional indices from a 2x2 table |

AlphInts |
Median interval, four confidence intervals, null expectation of cooccurrence count, and p-value |

Bisect |
Bisections for finding a root of a function |

Covrg |
Coverage Probabilities for Confidence Intervals about alpha, for fixed true alpha |

dataprep |
Occurrence matrix (e.g., species by site) data preparation for affinity() function |

EHypMidP |
Quantile of the Extended Hypergeometric distribution approximated by the midP distribution function |

EHypQuInt |
Interval of alpha values for which X is a specified q'th quantile |

logLikExtHyp |
log of Extended Hypergeometric Likelihiood at (X, mA,mB,N, alpha) |

MaxX.Int |
MaxX.Int computation |

midP.EHyp |
midP.EHyp computation |

minmaxAlpha.pFNCH |
integer-endpoint of range for which BiasedUrn::pFNCHHypergeo() works without error |

MinX.Int |
MinX.Int computation |

ML.Alpha |
Maximum likelihood estimate and intervals of alpha, null expectation and p-value of a 2x2 table |

plotgg |
Heatmap plot of affinity() output |