negLLzero: Likelihood with zero counts

Description Usage Arguments Details Value Warnings References See Also

View source: R/f_likelihoodEqs.R


negLLzero computes the negative log-likelihood based on the unconditional marginal distribution of N (equation 12 in DuMouchel 1999, except taking negative natural log). This function is minimized to estimate the hyperparameters of the prior distribution. Use this function if including zero counts but not squashing data. Generally this function is not recommended (negLLsquash is typically more efficient).


negLLzero(theta, N, E)



A numeric vector of hyperparameters ordered as: α_1, β_1, α_2, β_2, P.


A whole number vector of actual counts from processRaw.


A numeric vector of expected counts from processRaw.


The marginal distribution of the counts, N, is a mixture of two negative binomial distributions. The hyperparameters for the prior distribution (mixture of gammas) are estimated by optimizing the likelihood equation from this marginal distribution.

The hyperparameters are:

This function will not need to be called directly if using exploreHypers or autoHyper.


A scalar negative log-likelihood value.


Make sure N actually contains zeroes before using this function. You should have used the zeroes = TRUE option when calling the processRaw function.

Make sure the data were not squashed before using this function.


DuMouchel W (1999). "Bayesian Data Mining in Large Frequency Tables, With an Application to the FDA Spontaneous Reporting System." The American Statistician, 53(3), 177-190.

See Also

nlm, nlminb, and optim for optimization

Other negative log-likelihood functions: negLLsquash, negLLzeroSquash, negLL

openEBGM documentation built on Aug. 17, 2018, 1:05 a.m.