jags.parallel - Error in get(name, envir = envir) : invalid first argument

Question

When using jags.parallel, I get the following error:

> out <- jags.parallel(win.data, inits, params, "Poisson.OD.t.test.txt",
+ nc, ni, nb, nt);
Error in get(name, envir = envir) : invalid first argument

The same call using jags function runs OK. I have only found one thread on this topic, but there is only one speculative suggestion that does not apply nor work here.

Reproducible code, taken from Introduction to WinBUGS for ecologists, see chapter 14.1 (slightly modified):

set.seed(123)

### 14.1.2. Data generation
n.site <- 10
x <- gl(n = 2, k = n.site, labels = c("grassland", "arable"))
eps <- rnorm(2*n.site, mean = 0, sd = 0.5)# Normal random effect
lambda.OD <- exp(0.69 +(0.92*(as.numeric(x)-1) + eps) )
lambda.Poisson <- exp(0.69 +(0.92*(as.numeric(x)-1)) ) # For comparison

C.OD <- rpois(n = 2*n.site, lambda = lambda.OD)
C.Poisson <- rpois(n = 2*n.site, lambda = lambda.Poisson)

### 14.1.4. Analysis using WinBUGS
# Define model
sink("Poisson.OD.t.test.txt")
cat("
model {
# Priors
 alpha ~ dnorm(0,0.001)
 beta ~ dnorm(0,0.001)
 sigma ~ dunif(0, 10)   
 tau <- 1 / (sigma * sigma)
 maybe_overdisp <- mean(exp_eps[])

# Likelihood
 for (i in 1:n) {
    C.OD[i] ~ dpois(lambda[i]) 
    log(lambda[i]) <- alpha + beta *x[i] #+ eps[i]
    eps[i] ~ dnorm(0, tau)
    exp_eps[i] <- exp(eps[i])
 }
}
",fill=TRUE)
sink()


# Bundle data
win.data <- list(C.OD = C.OD, x = as.numeric(x)-1, n = length(x))

# Inits function
inits <- function(){ list(alpha=rlnorm(1), beta=rlnorm(1), sigma = rlnorm(1))}

# Parameters to estimate
params <- c("lambda","alpha", "beta", "sigma", "maybe_overdisp")

# MCMC settings
nc <- 3     # Number of chains
ni <- 3000     # Number of draws from posterior per chain
nb <- 1000     # Number of draws to discard as burn-in
nt <- 5     # Thinning rate

require(R2jags)

# THIS WORKS FINE
out <- R2jags::jags(win.data, inits, params, "Poisson.OD.t.test.txt",
    nc, ni, nb, nt);

# THIS PRODUCES ERROR
out <- jags.parallel(win.data, inits, params, "Poisson.OD.t.test.txt",
    nc, ni, nb, nt);

# THIS ALSO PRODUCES ERROR
out <- do.call(jags.parallel, list(win.data, inits, params, "Poisson.OD.t.test.txt",
    nc, ni, nb, nt));

Surfbird

The error occurs because the first argument to get must be a character string naming a function. Use traceback to see which function calls get and produces the error, then debug that function to investigate the objects in the function body. Or you can use options(error=recover) (and turn it off via options(error=NULL)). – Redouble

Thanks @Joshua! So this actually leads to debugging the jags package, not my code, right? If we conclude it is a bug, then maybe I the best strategy is to report to jags developers? – Surfbird

Not sure. I'm not familiar with these packages and didn't run the code, so it could still be one of your functions (e.g. maybe inits should be "inits" in the jags.parallel call?)... but that should be clear to you once you run traceback. – Redouble

Possibly not unrelated: https://mcmap.net/q/600246/-error-in-get-as-character-fun-mode-quot-function-quot-envir-envir/684229 – Surfbird

Answer 1

Jags/R had practically two problems with this line:

out <- jags.parallel(win.data, inits, params, "Poisson.OD.t.test.txt",
    nc, ni, nb, nt);

Both are related to evaluation of function parameters - he is probably not able to resolve parameters which refer to other R variables:

1) The win.data was encoded as variable names as usually for WinBUGS/Jags:

win.data <- list(C.OD = C.OD, x = as.numeric(x)-1, n = length(x))`

but jags.parallel issues the error "Error in get(name, envir = envir) : invalid first argument". He wants the data in this format:

windata <- list("C.OD", "x", "n")

Why? Don't ask me... I discovered this when reading the example of ?jags.

2) The arguments nc, ni, nb, nt in function call are a problem! If I put constants, it is OK, but references to variables are unacceptable for him. Don't ask me why. Remedy found at strange jags.parallel error / avoiding lazy evaluation in function call.

The complete fix looks like:

out <- do.call(jags.parallel, list(names(win.data), inits, params, "Poisson.OD.t.test.txt",
    nc, ni, nb, nt));

Surfbird

Thanks! I can add that the model MUST be a filename. A textConnection(modelString) doesn't work. I used sink(), cat() and file.remove() to handle the file. – Palinode

@Jonas, exactly - I do it like this all the time. – Surfbird

@TMS, a quick question, does jags.parallel actually parallelize? I mean, does it need other packages like snow to do the parallelization, or does it parallelize different chains by itself and we don't need to take care of that part? Thanks! – Vltava

@Vltava I don't actually remember, but I think it actualy parallelizes. But I gave up completely on using R2jags and this function, since there have been many bugs and strange problems like this one. I am using runjags package now and I am satisfied. With the run.jags function you can just specify method = "rjparallel" and the chains will run on separate cores. And the best thing is that it actually works :-) – Surfbird

@TMS & @qkhhly, I think (at least R2jags version 0.5-7) uses the R package parallel to initialize clusters etc. It does have some nice wrappers for exporting objects to the cluster. – Baltoslavic

@TMS, the why this format for windata works might be how the package figures out what to export to the cluster... btw. – Baltoslavic

Answer 2

sometimes this error occurs when you use a vectorized function inside parlapply. I've solved the problem by adding "do.call" and "mapply" functions to cluster.export

Prettypretty

As it’s currently written, your answer is unclear. Please edit to add additional details that will help others understand how this addresses the question asked. You can find more information on how to write good answers in the help center. – Persona