I am fitting models to investigate the relationship between herbicide
treatment and species response using the R package glmmADMB with 2 fixed
(treatment, year) and 2 random (block, plot) effects. I would like to use
MCMC to improve estimates and confidence limits. Model fit and output is
sensible without mcmc, but when mcmc=TRUE, the response is simply 'no PSV
file found', i.e., no output, and model output is not produced. When I run
the executable from the cmd prompt, I receive an invalid-index error.
For example, using the Owls data set that comes with the package, the
following model from Getting Started with glmmADMB by Bolker et al., and
this same process, the error is: Invalid index 11 used for array range [1,
10] in "double& dvector::operator [] (int i)":
OwlModel_nb1_bs <- glmmadmb(NCalls ~ (FoodTreatment + ArrivalTime) *
SexParent +
BroodSize + (1 | Nest), data = Owls,
zeroInflation = TRUE,
family = "nbinom1",
mcmc = TRUE, mcmc.opts =
mcmcControl(mcmc=25000, mcsave=25),
debug=TRUE,
admb.opts=admbControl(run=TRUE,
noinit=FALSE, shess=FALSE),
save.dir = "C:/Temp/glmm")
I would appreciate any recommendations on how I might avoid this error.
Peggy
My sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] pastecs_1.3-18 boot_1.3-17 MCMCglmm_2.21 ape_3.3
coda_0.17-1 Matrix_1.2-2 ggplot2_1.0.1
[8] glmmADMB_0.8.3.3 MASS_7.3-43
loaded via a namespace (and not attached):
[1] Rcpp_0.11.6 magrittr_1.5 munsell_0.4.2 colorspace_1.2-6
lattice_0.20-33 stringr_1.0.0 plyr_1.8.3
[8] tools_3.2.1 grid_3.2.1 gtable_0.1.2 nlme_3.1-121
corpcor_1.6.8 htmltools_0.2.6 yaml_2.1.13
[15] digest_0.6.8 tensorA_0.36 R2admb_0.7.5.3 reshape2_1.4.1
rmarkdown_0.8 stringi_0.5-5 scales_0.2.5
[22] proto_0.3-10