Affinity in Co-Occurrence Data

Documentation for package ‘CooccurrenceAffinity’ version 1.0

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