Affinity in Co-Occurrence Data
Acceptability Interval
Calculates the "Acceptability Function" used in defining Blaker's (200...
Computes alpha, probability, expected co-occurence, median interval, v...
Maximum likelihood estimate and intervals of alpha, null expectation, ...
Median interval, four confidence intervals, null expectation of cooccu...
Bisections for finding a root of a function
Coverage Probabilities for Confidence Intervals about alpha, for fixed...
Coverage probabilities of the confidence intervals, calculated and plo...
Occurrence matrix (e.g., species by site) data preparation for affinit...
Quantile of the Extended Hypergeometric distribution approximated by t...
Interval of alpha values for which X is a specified q'th quantile
log of Extended Hypergeometric Likelihiood at (X, mA,mB,N, alpha)
MaxX.Int computation
midP.EHyp computation
integer-endpoint of range for which BiasedUrn::pFNCHHypergeo() works w...
MinX.Int computation
Maximum likelihood estimate and intervals of alpha, null expectation a...
Heatmap plot of affinity() output
Computes a novel metric of affinity between two entities based on their co-occurrence (using binary presence/absence data). The metric and its MLE, alpha hat, were advanced in Mainali, Slud, et al, 2021 <doi:10.1126/sciadv.abj9204>. Various types of confidence intervals and median interval were developed in Mainali and Slud, 2022 <doi:10.1101/2022.11.01.514801>. The `finches` dataset is now bundled internally (no longer pulled via the cooccur package, which has been dropped).
Useful links