I got the following error from JAGS:
Error in node Y[107]
Invalid parent values
From this mere information it is very difficult to find out what is happening there. It is caused by this part of code:
pi[j,1] <- 1 - M[site[j]] * phi[j] * (1 - (1 - q[j])^6)
pi[j,2] <- M[site[j]] * phi[j] * (1 - q[j])^interval[j] * q[j]
pi[j,3] <- 1 - pi[j,1] - pi[j,2]
Y[j] ~ dcat(pi[j,])
It would have been very useful to print out the parent values of node Y[107], i.e. the nodes pi[107,]! That would give me very clear feedback where to look for the error! Is there such a way in JAGS?
In Chapter 3.2 of the JAGS manual, JAGS is speaking about leaving some useful jags.dumpN.R files:
If a model compiles and initializes correctly, but an error occurs during updating, then the current state of the model will be dumped to a le named jags.dumpN.R where N is the chain number. You should then load the dumped data into R to inspect the state of each chain when the error occurred.
however, I am not sure if this applies to my case. So I tried to get the dump files. Since I am using runjags::run.jags() to run JAGS, I tried to run it in the debugging mode:
R> outRJ <- run.jags("tmp_bugs_model.txt", params, win.data, nc, inits,
nb, ni - nb, thin = 1, summarise=TRUE, plot=FALSE, adapt = adapt,
modules = "glm",
keep.jags.files = TRUE, method = "interruptible",
jags = "c:/Program Files/JAGS/JAGS-3.4.0/i386/bin/")
Running the simulation using the simple method... (output will be displayed once the
simulation has termianted)
Welcome to JAGS 3.4.0 on Thu Nov 27 10:33:49 2014
JAGS is free software and comes with ABSOLUTELY NO WARRANTY
Loading module: basemod: ok
Loading module: bugs: ok
. Loading module: glm: ok
. . Reading data file data.txt
. Compiling model graph
Resolving undeclared variables
Allocating nodes
Graph Size: 2451
WARNING: Unused variable(s) in data table:
desetiminutovka
. Reading parameter file inits1.txt
. Reading parameter file inits2.txt
. Reading parameter file inits3.txt
. Initializing model
Error in node Y[107]
Invalid parent values
Deleting model
. Updating 500
-------------------------------------------------| 500
Can't update. No model!
. Can't set monitor. No model!
. Can't set monitor. No model!
. Can't set monitor. No model!
. Can't set monitor. No model!
. Can't set monitor. No model!
. Can't set monitor. No model!
. Updating 500
-------------------------------------------------| 500
Can't update. No model!
. No model
. No model
. No model
. Can't dump CODA output. No model!
. Updating 0
Can't update. No model!
Can't update. No model!
. Deleting model
.
Error in runjags.readin(directory = startinfo$directory, copy = (keep.jags.files & :
The simulation appears to have crashed - check the model output in failedjags$output for clues
In addition: Warning messages:
1: running command '"TASKLIST"' had status 1
2: Parallel and interruptible methods aren't available on your machine because testing the TASKLIST system command produced an error; switching to the simple method
JAGS files were saved to the 'runjagsfiles_3' folder in your current working
directory
Unfortunatelly, there are no dumps or files with any useful information in the runjagsfiles_3 directory.
Is there any way to get those "Invalid parent values" out of JAGS?
I am using JAGS 3.4.0.
PS: I intentionally do not submit my full model code here. My question is general about JAGS, not why my model doesn't work.
I'm afraid there is no way to dump any values from your model. The key line you quoted from the JAGS manual is 'and initialises correctly' - this didn't happen for your model, so there is nothing to dump out, sorry. You will have to manually specify sensible initial values for the (stochastic) parents of Y[] as @nicola suggests.
Incidentally - I am interested in the failure of TASKLIST on your system - can you give me some details of your platform?