JAGS

library("boot")
library(rjags)
library(data.table)
library(tidyverse)
library(stringi)

X <- x

mod1_csim = as.mcmc(do.call(rbind, mod1_sim))

plot(mod1_sim, ask=TRUE)

gelman.diag(mod1_sim)

Potential scale reduction factors:

     Point est. Upper C.I.
b[1]          1          1
b[2]          1          1
b[3]          1          1

Multivariate psrf

1

autocorr.plot(mod1_sim)

effectiveSize(mod1_sim)

    b[1]     b[2]     b[3] 
8195.520 5985.394 7999.867 

#  Geweke diagnostic
geweke.plot(mod1_sim)

• A 3 variables are not a strong predictors of the outcome because they overlap with 0

par(mfrow=c(3,2))
densplot(mod1_csim[,1:3], xlim=c(-3.0,3.0))

colnames(X)

[1] "chr17_150259_C_A" "chr17_150380_C_T" "chr17_151226_C_T" "Label"           

#Find DIC
dic1 = dic.samples(mod1, n.iter=1e3)

  |                                                        
  |                                                  |   0%
  |                                                        
  |*                                                 |   2%
  |                                                        
  |**                                                |   4%
  |                                                        
  |***                                               |   6%
  |                                                        
  |****                                              |   8%
  |                                                        
  |*****                                             |  10%
  |                                                        
  |******                                            |  12%
  |                                                        
  |*******                                           |  14%
  |                                                        
  |********                                          |  16%
  |                                                        
  |*********                                         |  18%
  |                                                        
  |**********                                        |  20%
  |                                                        
  |***********                                       |  22%
  |                                                        
  |************                                      |  24%
  |                                                        
  |*************                                     |  26%
  |                                                        
  |**************                                    |  28%
  |                                                        
  |***************                                   |  30%
  |                                                        
  |****************                                  |  32%
  |                                                        
  |*****************                                 |  34%
  |                                                        
  |******************                                |  36%
  |                                                        
  |*******************                               |  38%
  |                                                        
  |********************                              |  40%
  |                                                        
  |*********************                             |  42%
  |                                                        
  |**********************                            |  44%
  |                                                        
  |***********************                           |  46%
  |                                                        
  |************************                          |  48%
  |                                                        
  |*************************                         |  50%
  |                                                        
  |**************************                        |  52%
  |                                                        
  |***************************                       |  54%
  |                                                        
  |****************************                      |  56%
  |                                                        
  |*****************************                     |  58%
  |                                                        
  |******************************                    |  60%
  |                                                        
  |*******************************                   |  62%
  |                                                        
  |********************************                  |  64%
  |                                                        
  |*********************************                 |  66%
  |                                                        
  |**********************************                |  68%
  |                                                        
  |***********************************               |  70%
  |                                                        
  |************************************              |  72%
  |                                                        
  |*************************************             |  74%
  |                                                        
  |**************************************            |  76%
  |                                                        
  |***************************************           |  78%
  |                                                        
  |****************************************          |  80%
  |                                                        
  |*****************************************         |  82%
  |                                                        
  |******************************************        |  84%
  |                                                        
  |*******************************************       |  86%
  |                                                        
  |********************************************      |  88%
  |                                                        
  |*********************************************     |  90%
  |                                                        
  |**********************************************    |  92%
  |                                                        
  |***********************************************   |  94%
  |                                                        
  |************************************************  |  96%
  |                                                        
  |************************************************* |  98%
  |                                                        
  |**************************************************| 100%

dic1

Mean deviance:  299.8 
penalty 1.46 
Penalized deviance: 301.3