conting (version 1.4)

sub_model: Compute Posterior Summary Statistics for (Sub-) Models

Description

This function computes posterior summary statistics for (sub-) models using the MCMC output of "bcct" and "bict" objects.

Usage

sub_model(object, formula = NULL, order = 1, n.burnin = 0, thin = 1, 
prob.level = 0.95, statistic = "X2")

Arguments

object

An object of class "bcct" or "bict".

formula

An optional argument of class "formula": a symbolic description of the model of interest. The default value is NULL. If not NULL then this argument takes precedent over order.

order

A scalar argument identifying the model for which to compute summary statistics. The function will compute statistics for the model with the order-th largest posterior model probability. The default value is 1, meaning that, by default,

n.burnin

An optional argument giving the number of iterations to use as burn-in. The default value is 0.

thin

An optional argument giving the amount of thinning to use, i.e. the computations are based on every thin-th value in the MCMC sample. The default value is 1, i.e. no thinning.

prob.level

An optional argument giving the probability content of the highest posterior density intervals (HPDIs). The default value is 0.95.

statistic

An optional argument giving the discrepancy statistic to use for calculating the Bayesian p-value. It can be one of c("X2","FreemanTukey","deviance") which correspond to the different statistics: "X2" = Chi-squared statistic,

Value

• This function will return an object of class "submod" which is a list with the following components. Note that, unless otherwise stated, all components are conditional on the model of interest.
• term
  A vector of term labels for each log-linear parameter.
• post_prob
  A scalar giving the posterior model probability for the model of interest.
• post_mean
  A vector of posterior means for each of the log-linear parameters.
• post_var
  A vector of posterior variances for each of the log-linear parameters.
• lower
  A vector of lower limits for the 100*prob.level% HPDI for each log-linear parameter.
• upper
  A vector of upper limits for the 100*prob.level% HPDI for each log-linear parameter.
• prob.level
  The argument prob.level.
• order
  The ranking of the model of interest in terms of posterior model probabilities.
• formula
  The formula of the model of interest.
• BETA
  A matrix containing the sampled values of the log-linear parameters, where the number of columns is the number of log-linear parameters in the model of interest.
• SIG
  A vector containing the sampled values of sigma^2 under the Sabanes-Bove & Held prior. If the unit information prior is used then the components of this vector will be one.
• If object is of class "bict", then sub_model will also return the following component.
• Y0
  A matrix (with k columns) containing the sampled values of the missing and censored cell counts, where k is the total number of missing and censored cell counts.

Details

If the MCMC algorithm does not visit the model of interest in the thinned MCMC sample, after burn-in, then an error message will be returned. The use of thinning is recommended when the number of MCMC iterations and/or the number of log-linear parameters in the maximal model are/is large, which may cause problems with comuter memory storage.

References

Overstall, A.M. & King, R. (2014) conting: An R package for Bayesian analysis of complete and incomplete contingency tables. Journal of Statistical Software, 58 (7), 1--27. http://www.jstatsoft.org/v58/i07/

See Also

bcct, bict,

Examples

set.seed(1)
## Set seed for reproducibility.

data(AOH)
## Load the AOH data

test1<-bcct(formula=y~(alc+hyp+obe)^3,data=AOH,n.sample=100,prior="UIP")
## Let the maximal model be the saturated model. Starting from the 
## posterior mode of the maximal model do 100 iterations under the unit 
## information prior.

test1sm<-sub_model(object=test1,order=1,n.burnin=10)
## Obtain posterior summary statistics for posterior modal model using a 
## burnin of 10.

test1sm

#Posterior model probability =  0.5
#
#Posterior summary statistics of log-linear parameters:
#            post_mean post_var lower_lim upper_lim
#(Intercept)  2.907059 0.002311   2.81725   2.97185
#alc1        -0.023605 0.004009  -0.20058   0.06655
#alc2        -0.073832 0.005949  -0.22995   0.10845
#alc3         0.062491 0.006252  -0.09635   0.18596
#hyp1        -0.529329 0.002452  -0.63301  -0.43178
#obe1         0.005441 0.004742  -0.12638   0.12031
#obe2        -0.002783 0.004098  -0.17082   0.07727
#NB: lower_lim and upper_lim refer to the lower and upper values of the
#95 % highest posterior density intervals, respectively
#
#Under the X2 statistic 
#
#Summary statistics for T_pred 
#   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
#  11.07   19.76   23.34   24.47   29.04   50.37 
#
#Summary statistics for T_obs 
#   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
#  30.82   34.78   35.74   36.28   37.45   42.49 
#
#Bayesian p-value =  0.0444