conting: sub_model – R documentation

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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, the function will compute summary statistics for the posterior modal model.
`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, `"FreemanTukey"` = Freeman-Tukey statistic, `"deviance"` = deviance statistic. See Overstall & King (2014), and references therein, for descriptions of these statistics.

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.

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.

Author(s)

Antony M. Overstall A.M.Overstall@soton.ac.uk.

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/

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

conting

Bayesian Analysis of Contingency Tables

v1.7

GPL-2

Authors

Antony M. Overstall

Initial release

2019-04-02