logLikExtHyp {CooccurrenceAffinity}

log of Extended Hypergeometric Likelihiood at (X, mA,mB,N, alpha)

Description

This function calculates the logarithm of the Extended Hypergeometric likelihood at specified x and alpha, with marginal totals mA, mB, N fixed.

Usage

logLikExtHyp(x, marg, alpha)

Arguments

x

integer co-occurrence count that should properly fall within the closed interval [max(0,mA+mB-N), min(mA,mB)]

marg

a 3-entry integer vector (mA,mB,N) consisting of the first row and column totals and the table total for a 2x2 contingency table

alpha

a real number, the log odds ratio or affinity parameter for the 2x2 contingency table

Details

This is simply the logarithm of the Extended Hypergeometric (Harkness 1965) or Fisher noncentral Hypergeometric, as calculated by the R package BiasedUrn. The formula is log(pFNCHypergeo(x,mA,N-mA,mB,exp(alpha))

Value

scalar loglikelihood value

Author(s)

Eric Slud

References

Fog, A. (2015), BiasedUrn: Biased Urn Model Distributions. R package version 1.07.

Harkness, W. (1965), “Properties of the extended hypergeometric distribution“, Annals of Mathematical Statistics, 36, 938-945.

Examples

require(BiasedUrn)
c(logLikExtHyp(30,c(50,80,120),1),  log(dFNCHypergeo(30,50,70,80,exp(1))))