Affinity in Co-Occurrence Data

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Documentation for package ‘CooccurrenceAffinity’ version 1.0

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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