Man pages for CooccurrenceAffinity
Affinity in Co-Occurrence Data
| AcceptAffCI | Acceptability Interval |
| AcceptAffin | Calculates the "Acceptability Function" used in defining... |
| affinity | Computes alpha, probability, expected co-occurence, median... |
| affinity2by2 | Maximum likelihood estimate and intervals of alpha, null... |
| AlphInts | Median interval, four confidence intervals, null expectation... |
| Bisect | Bisections for finding a root of a function |
| Covrg | Coverage Probabilities for Confidence Intervals about alpha,... |
| CovrgPlot | Coverage probabilities of the confidence intervals,... |
| dataprep | Occurrence matrix (e.g., species by site) data preparation... |
| EHypMidP | Quantile of the Extended Hypergeometric distribution... |
| EHypQuInt | Interval of alpha values for which X is a specified q'th... |
| logLikExtHyp | log of Extended Hypergeometric Likelihiood at (X, mA,mB,N,... |
| MaxX.Int | MaxX.Int computation |
| midP.EHyp | midP.EHyp computation |
| minmaxAlpha.pFNCH | integer-endpoint of range for which... |
| MinX.Int | MinX.Int computation |
| ML.Alpha | Maximum likelihood estimate and intervals of alpha, null... |
| plotgg | Heatmap plot of affinity() output |
