poisson.zellner.prior {BoomSpikeSlab}R Documentation

Zellner Prior for Poisson Regression


A Zellner-style spike and slab prior for Poisson regression models. See 'Details' for a definition.


    counts = NULL,
    exposure = NULL,
    prior.event.rate = NULL,
    expected.model.size = 1,
    prior.information.weight = .01,
    diagonal.shrinkage = .5,
    optional.coefficient.estimate = NULL,
    max.flips = -1,
    prior.inclusion.probabilities = NULL)



The design matrix for the regression problem. No missing data is allowed.


The vector of responses, This is only used to obtain the empirical overall event rate, so it can be left NULL if prior.event.rate is specified.


A vector of the same length as counts, giving the "exposure time" for each observation. This can also be NULL, signifying that exposure = 1.0 for each observation.


An a priori guess at the overall event rate. Used in two places: to set the prior mean of the intercept (if optional.coefficient.estimate is NULL) and to weight the information matrix in the "slab" portion of the prior.


A positive number less than ncol(x), representing a guess at the number of significant predictor variables. Used to obtain the 'spike' portion of the spike and slab prior.


A positive scalar. Number of observations worth of weight that should be given to the prior estimate of beta.


The conditionally Gaussian prior for beta (the "slab") starts with a precision matrix equal to the information in a single observation. However, this matrix might not be full rank. The matrix can be made full rank by averaging with its diagonal. diagonal.shrinkage is the weight given to the diaonal in this average. Setting this to zero gives Zellner's g-prior.


If desired, an estimate of the regression coefficients can be supplied. In most cases this will be a difficult parameter to specify. If omitted then a prior mean of zero will be used for all coordinates except the intercept, which will be set to mean(y).


The maximum number of variable inclusion indicators the sampler will attempt to sample each iteration. If negative then all indicators will be sampled.


A vector giving the prior probability of inclusion for each variable. If NULL then a default set of probabilities is obtained by setting each element equal to min(1, expected.model.size / ncol(x)).


A Zellner-style spike and slab prior for Poisson regression. Denote the vector of coefficients by beta, and the vector of inclusion indicators by gamma. These are linked by the relationship beta[i] != 0 if gamma[i] = 1 and beta[i] == 0 if gamma[i] = 0. The prior is

beta | gamma ~ N(b, V),

gamma ~ Bernoulli(pi)

where pi is the vector of prior.inclusion.probabilities, and b is the optional.coefficient.estimate. Conditional on gamma, the prior information matrix is

V^{-1} = kappa * ((1 - alpha) * x^Twx / n + alpha * diag(x^Twx/n))

The matrix x^Twx is, for suitable choice of the weight vector w, the total Fisher information available in the data. Dividing by n gives the average Fisher information in a single observation, multiplying by kappa then results in kappa units of "average" information. This matrix is averaged with its diagonal to ensure positive definiteness.

In the formula above, kappa is prior.information.weight, alpha is diagonal.shrinkage, and w is a diagonal matrix with all elements set to prior.success.probability * (1 - prior.success.probability). The vector b and the matrix V^{-1} are both implicitly subscripted by gamma, meaning that elements, rows, or columsn corresponding to gamma = 0 should be omitted.


Returns an object of class PoissonZellnerPrior, which is a list with data elements encoding the selected prior values. It inherits from PoissonPrior and from SpikeSlabGlmPrior, which implies that it contains an element prior.success.probability.

This object is intended for use with poisson.spike.


Steven L. Scott


Hugh Chipman, Edward I. George, Robert E. McCulloch, M. Clyde, Dean P. Foster, Robert A. Stine (2001), "The Practical Implementation of Bayesian Model Selection" Lecture Notes-Monograph Series, Vol. 38, pp. 65-134. Institute of Mathematical Statistics.

[Package BoomSpikeSlab version 1.2.4 Index]