ML.Alpha {CooccurrenceAffinity}R Documentation

Maximum likelihood estimate and intervals of alpha, null expectation and p-value of a 2x2 table


This function calculates the maximum likelihood estimate and other quantities computed in AlphInts(), for the log-odds parameter alpha in the Extended Hypergeometric distribution with fixed margins (mA,mB) and table-total N, which is the "log-affinity" index of co-occurrence championed in a paper by Mainali et al. (2022) as an index of co-occurrence-based similarity.


  bound = TRUE,
  scal = log(2 * marg[3]^2),
  lev = 0.95,
  pvalType = "Blaker"



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


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


a boolean parameter which when TRUE replaces the MLE of "+/-Infinity", applicable when x is respectively at the upper extreme min(mA,mB) or the lower extreme max(mA+mB-N,0) of its possible range, by a finite value with absolute value upper-bounding the value of MLEs attainable for values of x not equal to its extremes


an integer parameter (default 2*N^2, capped at 10 within the function) that should be 2 or greater


a confidence level, generally somewhere from 0.8 to 0.95 (default 0.95)


a character string telling what kind of p-value to calculate. ‘Blaker’ or “midP’. If ‘pvalType=Blaker” (the default value), the p-value is calculated according to "Acceptability" function of Blaker (2000). If ‘pvalType=midP’, the p-value is calculated using the same idea as the midP confidence interval.


This function calculates the maximum likelihood estimate of the log-odds paramater alpha within the Extended Hypergeometric distribition (Harkness 1965) based on the count x and fixed table margins (mA,mB) and total N, which is the "affinity" index of co-occurrence championed in the paper of Mainali et al. (2022) as an index of cooccurrence-based similarity, along with the intervals computed in AlphInts, called CI.CP, CI.Balker, CI.midQ and CI.midP. The boolean "bound" parameter is an option to prevent the intervals containing alpha-estimates to extend to plus or minus infinity, based on a Bayesian argument. T he bound substituted for the Infinite endpoints is provably larger than the largest value the MLE can take whenever x avoids the enpoints max(mA+mB-N,0) and min(mA,mB) of its logical range. The recommended confidence interval for alpha is CI.Blaker if a reliably conservative (over-large) coverage probability is desired, and CI.midP otherwise.


This function returns maximum likelihood estimate of alpha, the interval-endpoints of alpha values for which x is a median, and four confidence intervals for alpha, described in detail under documentation for AlphInts(). In addition there are two output list-components for the null-distribution expected co-occurrence count and the p-value for the test of the null hypothesis alpha=0, calculated as in AlphInts.


Eric Slud


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.

Mainali, K., Slud, E., Singer, M. and Fagan, W. (2022), "A better index for analysis of co-occurrence and similarity", Science Advances, to appear.


unlist(ML.Alpha(30,c(50,80,120), lev=0.9))
AlphInts(30,c(50,80,120), lev=0.9)

AlphInts(61,c(80,80,100), lev=0.9)
ML.Alpha(61,c(80,80,100), lev=0.9)

# Alpha capped warning examples
AlphInts(60,c(80,80,100), lev=0.9)
ML.Alpha(60,c(80,80,100), lev=0.9)

AlphInts(80,c(80,80,100), lev=0.9)
ML.Alpha(80,c(80,80,100), lev=0.9)

# impossible x warning examples
AlphInts(81,c(80,80,100), lev=0.9)
ML.Alpha(81,c(80,80,100), lev=0.9)

# Degenerate distribution warning example
AlphInts(80,c(80,100,100), lev=0.9)
ML.Alpha(80,c(80,100,100), lev=0.9)

[Package CooccurrenceAffinity version 1.0 Index]