CODEWITHSUNDEEP
jagsr2jags
Thomas C
Thomas C

Reputation: 31

JAGS Beginner - Receiving and Understanding Output

When using JAGS, how does one receive output from a model in the format:

Inference for Bugs model at "model.txt", fit using jags,
3 chains, each with 10000 iterations (first 5000 discarded)
n.sims = 15000 iterations saved
mu.vect sd.vect 2.5% 25% 50% 75% 97.5% Rhat n.eff
mu 9.950 0.288 9.390 9.755 9.951 10.146 10.505 1.001 11000
sd.obs 3.545 0.228 3.170 3.401 3.534 3.675 3.978 1.001 13000
deviance 820.611 3.460 818.595 819.132 819.961 821.366 825.871 1.001 15000

I assumed, as with BUGS, it would appear when the model completes however I only get something in the format:

Compiling model graph
   Resolving undeclared variables
   Allocating nodes
Graph information:
   Observed stochastic nodes: 1785
   Unobserved stochastic nodes: 1843
   Total graph size: 61542

Initializing model

  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100%

Apologies for the basic question. If anyone can provide useful JAGS introductory material that would also be useful.

Kind regards.

Upvotes: 1

Views: 525

Answers (1)

user3767071
user3767071

Reputation: 109

If you only get the 'plus' signs, it means you only initialized the model. When jags really runs, it typically produces '***' signs after. So you are missing a line here (would have been nice to see your code). For instance if you use r2jags, you would write:

out <- jags(data = data, parameters.to.save = params, n.chains = 3, n.iter = 90000,n.burnin = 5000,
                      model.file = modFile)
out.upd <- update(abundance.out.mod, n.iter=10000)

Upvotes: 1

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