Help with MCMC fitting in R
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,
mcmc2=0,
mcsave,
mcnoscale=FALSE,
mcgrope=FALSE,
mcmult=1,
mcmcpars=NULL) {
if (missing(mcsave)) mcsave <- pmax(1,floor(mcmc/5000))
if (mcmc2>0) {
if (missing(mcmc)) {
mcmc <- 0
}
if (mcmc>0) stop("may not specify both mcmc and mcmc2>0")
}
r <-
list(mcsave=mcsave,mcnoscale=mcnoscale,mcgrope=mcgrope,mcmult=mcmult,mcmcpars=mcmcpars)
if (mcmc>0) c(list(mcmc=mcmc),r) else c(list(mcmc2=mcmc2),r)
}:
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) Troubleshooting steps include (1) run with 'save.dir' set and inspect output files; (2) change run parameters: see '?admbControl';(3) re-run with debug=TRUE for more information on failure mode In addition: Warning message: running command 'C:\Windows\system32\cmd.exe /c glmmadmb -maxfn 500 -maxph 5 -noinit -shess -mcmc 50000 -mcsave 50 -mcmult 1' had status 1
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. I really hope you can provide some help. Thank you so much for your time! Sincerely, Janelle Sylvester