AcceptAffCI             Acceptability Interval
AcceptAffin             Calculates the "Acceptability Function" used in
                        defining Blaker's (2000) Acceptability Interval
                        and computing the latter in the function
                        AcceptAffCI().
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
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
ML.Alpha                Maximum likelihood estimate and intervals of
                        alpha, null expectation and p-value of a 2x2
                        table
MaxX.Int                MaxX.Int computation
MinX.Int                MinX.Int computation
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
dataprep                Occurrence matrix (e.g., species by site) data
                        preparation for affinity() function
finches                 Darwin’s finches presence–absence data
logLikExtHyp            log of Extended Hypergeometric Likelihiood at
                        (X, mA,mB,N, alpha)
midP.EHyp               midP.EHyp computation
minmaxAlpha.pFNCH       integer-endpoint of range for which
                        BiasedUrn::pFNCHHypergeo() works without error
plotgg                  Heatmap plot of affinity() output
