Help with MCMC fitting in R
Janelle Sylvester <jsylves92 at ...> writes:
Hi, I found this email address from the R-Forge website and was hoping you could help me with a problem I am having. I keep getting an error message every time I try to preform a *post hoc* Markov chain on my zero-inflated, neg. binomial mixed model. Below is my code and the error message I keep getting. If I can't make this work, can you recommend any other ways of validating my model? I really can't find anything on this topic. glmmNB<- glmmadmb(CON_XAL~Treatment+(1|Site), data = SR.year.raw,
zeroInflation = TRUE, family = "nbinom")
summary(glmmNB) #Summary output is attached to this email as a picture
fit_glmmNB <- glmmadmb(CON_XAL~Treatment+(1|Site),
data=SR.year.raw,
zeroInflation=TRUE, save.dir = "TMP",
family="nbinom",
mcmc=TRUE,
mcmc.opts=mcmcControl(mcmc=5000))
And the error message I get: Error in R2admb::read_psv(file_name) : no PSV file found
In addition: Warning messages: 1: In glmmadmb(CON_XAL ~ Treatment + (1 | Site), data = SR.year.raw, : file glmmadmb.std exists: overwriting 2: running command 'C:\Windows\system32\cmd.exe /c glmmadmb -maxfn 500 -maxph 5 -noinit -shess -mcmc 1000 -mcsave 1 -mcmult 1' had status 42
I tried running this: mcmc.control <- function(mcmc=50000,
snip
}:
But then when I run my model again, I get this error message: Parameters were estimated, but standard errors were not: the most likely
problem is that the curvature at MLE was zero or negative Error in glmmadmb(CON_XAL ~ Treatment + (1 | Site),
data = SR.year.raw, :
The function maximizer failed (couldn't find parameter file)
snip
I've tried for weeks to fix this problem and I just don't know what to do. If my data is just not suitable enough for this *post hoc* procedure, can you please recommend another way to validate my model so I can ensure that it fits well? I attached my data and would be happy to send any other information that may help figure out a solution. I am looking at the "Treatment" effect on seed abundances of 11 species (ignore ALL_PSI). Site is my random factor. I am looking at species separately.
[snip] It's possible that you're just having problems with an out-of-date binary: some people reported difficulty like this, and solved it using instructions at: https://stat.ethz.ch/pipermail/r-sig-mixed-models/2016q1/024490.html Data and figures get stripped by the mailing list software, so we haven't seen that (you could send it to me, but I can't guarantee I'll have time to take a look at it). I'm not sure what you're up to with defining mcmc.control there ... As far as other solutions go: do you absolutely need the post-hoc MCMC? It is nice, but I would generally say that if you do standard model diagnostics (examine residuals and model predictions, ideally graphically) it's not an ironclad requirement. (Among other things, most other non-Bayesian model-fitting methods don't offer this feature ...) Other ways to go to cross-check your model would be: - fit a zero-inflated Poisson-logNormal with MCMCglmm (a bit of a nuisance, but doable: search for "owls NCEAS bolker" to find an example) - use the relatively new/experimental glmmTMB package (install via devtools::install_github("glmmTMB/glmmTMB",sub="glmmTMB") , then library("glmmTMB"); ?Owls for an example) Ben Bolker