Description Usage Arguments Value Author(s) References See Also Examples
This function performs Bayesian variable selection for
logistic regression data in a nonparallel fashion. It does not contain any
preprocessing step or variable initialization. Moreover it does not have
the feature to be run in parallel for performing the coupling algorithm.
Therefore in general, it is NOT recommended to be used unless the user
knows how to initialize all the parameters. However, this function is
called by bvs
function, the recommended way to run Bayesian
variable selection for such datasets.
1 2  logreg_bvs(exmat, chain1, nf, tau, r, nlptype, a, b, in_cons, loopcnt, cplng,
chain2)

exmat 
An extended matrix where the first column is binary resonse
vector and the rest is the design matrix which has its first column all 1
to account for the intercept in the model and is the output of

chain1 
The first chain or initial model where the MCMC algorithm
starts from. Note that the first 
nf 
The number of fixed covariates that do not enter the selection procedure. 
tau 
The paramter 
r 
The paramter 
nlptype 
Determines the type of nonlocal prior that is used in the
analyses. 
a 
The first parameter in beta distribution used as prior on model size. This parameter is equal to 1 when uinformbinomial prior is used. 
b 
The second paramter in beta distribution used as prior on model size. This parameter is equal to 1 when uinformbinomial prior is used. 
in_cons 
The average model size. This value under certain conditions
and when 
loopcnt 
Number of iterations for MCMC procedure. 
cplng 
A boolean variable indicating the coupling algorithm to be performed or not. 
chain2 
Second chain or model for starting the MCMC procedure. This
parameter is only used when 
It returns a list containing following objects:
max_chain 
A 
beta_hat 
The coefficient vector for the selected model. The first one is always for the intercept. 
max_prop 
The unnormalized probability of the model with highest posterior probability. 
num_iterations 
The number of MCMC iterations that are executed.
This is used when 
cplng_flag 
This is used when 
num_vis_models 
Number of visited models in search for the highest probability model. This contains redundant models too and is not the number of unique models. 
hash_key 
This is only used when 
hash_prob 
This is only used when 
vis_covs 
This is only used when 
Amir Nikooienejad
Nikooienejad, A., Wang, W., and Johnson, V. E. (2016). Bayesian
variable selection for binary outcomes in high dimensional genomic studies
using nonlocal priors. Bioinformatics, 32(9), 13381345.
Nikooienejad, A., Wang, W., and Johnson, V. E. (2017). Bayesian Variable
Selection in High Dimensional Survival Time Cancer Genomic Datasets using
Nonlocal Priors. arXiv preprint, arXiv:1712.02964.
Johnson, V. E., and Rossell, D. (2010). On the use of nonlocal prior
densities in Bayesian hypothesis tests. Journal of the Royal Statistical
Society: Series B (Statistical Methodology), 72(2), 143170.
Johnson, V. E. (1998). A couplingregeneration scheme for
diagnosing convergence in Markov chain Monte Carlo algorithms. Journal of
the American Statistical Association, 93(441), 238248.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47  ### Initializing parameters
n < 200
p < 40
set.seed(123)
Sigma < diag(p)
full < matrix(c(rep(0.5, p*p)), ncol=p)
Sigma < full + 0.5*Sigma
cholS < chol(Sigma)
Beta < c(1.7,1.8,2.5)
X < matrix(rnorm(n*p), ncol=p)
X < X%*%cholS
colnames(X) < paste("gene_",c(1:p),sep="")
beta < numeric(p)
beta[c(1:length(Beta))] < Beta
XB < X%*%beta
probs < as.vector(exp(XB)/(1+exp(XB)))
y < rbinom(n,1,probs)
exmat < cbind(y,X)
tau < 0.5; r < 1; a < 3; b < pa; in_cons < a;
loopcnt < 100; cplng < FALSE;
initProb < in_cons/p
### Initializing Chains
schain < p
while (schain > in_cons  schain == 0) {
chain1 < rbinom(p, 1, initProb)
schain < sum(chain1)
}
chain1 < as.numeric(c(1, chain1))
chain2 < chain1
nlptype < 0 ## PiMOM nonlocal prior
nf < 0 ### No fixed columns
### Running the function
bvsout < logreg_bvs(exmat,chain1,nf,tau,r,nlptype,a,b,in_cons,loopcnt,cplng,chain2)
### Number of visited models for this specific run:
bvsout$num_vis_models
### The selected model:
which(bvsout$max_chain > 0)
### Estimated coefficients:
bvsout$beta_hat
### The unnormalized probability of the selected model:
bvsout$max_prob

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