R: Affinity in Co-Occurrence Data

# Affinity in Co-Occurrence Data

## Documentation for package ‘CooccurrenceAffinity’ version 2.0.0

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

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
finches | Darwin’s finches presence–absence data
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