[R-sig-ME] Binomial glmmadmb error message

Wed Aug 12 10:03:44 CEST 2015

Hi

pj
Paul Johnson
http://pj.freefaculty.org
On Aug 2, 2015 2:25 PM, "Scott McCain" <jspmccain at gmail.com> wrote:
>
> Hello,
>
> I'm trying to fit a hurdle mixed effects model, looking at cod abundance
> (cod0, cod1, and cod2). Because of the overdispersion and zero-inflation,
> I'm trying to use a hurdle model with the first stage as a binomial GLMM
> and the second stage a negative binomial GLMM. We have chosen site to be a
> random effect. Here is a summary of the data I'm working with:
>
> str(div.3a)
> 'data.frame': 325 obs. of  21 variables:
>  $ beach           : Factor w/ 56 levels "1","2","3","4",..: 1 1 1 1 1 1 1
> 1 1 7 ...
>  $ shannons        : num  1.017 1.014 1.302 0.853 1.325 ...
>  $ year            : Factor w/ 12 levels "59","60","61",..: 3 5 4 7 11 6 9
> 10 8 7 ...
>  $ region          : Factor w/ 6 levels "Bonavista Bay",..: 5 5 5 5 5 5 5
5
> 5 5 ...
>  $ species.rich    : int  6 7 6 7 6 5 6 4 6 3 ...
>  $ year.range      : Factor w/ 2 levels "1960-1964","1992-1996": 1 1 1 2 2
> 1 2 2 2 2 ...
>  $ sum.tfish       : num  137 120 157 84 73 56 20 5 320 96 ...
>  $ evenness        : num  0.568 0.521 0.726 0.439 0.74 ...
>  $ cod0            : int  24 43 0 0 0 3 0 0 0 9 ...
>  $ cod1            : int  47 10 48 0 0 8 0 0 1 0 ...
>  $ cod2            : int  0 0 5 0 0 0 0 0 0 0 ...
>  $ beach.name      : Factor w/ 56 levels "Admirals Beach",..: 26 26 26 26
> 26 26 26 26 26 52 ...
>  $ site.no         : Factor w/ 42 levels "1","2","5","6",..: 1 1 1 1 1 1 1
> 1 1 5 ...
>  $ depth           : num  4 4 4 4 4 4 4 4 4 3 ...
>  $ vegetation      : Factor w/ 2 levels "0","1": 2 2 2 2 2 2 2 2 2 2 ...
>  $ eelgrass        : int  1 1 1 1 1 1 1 1 1 0 ...
>  $ kelp            : int  0 0 0 0 0 0 0 0 0 1 ...
>  $ cod0nz          : num  1 1 0 0 0 1 0 0 0 1 ...
>  $ cod1nz          : num  1 1 1 0 0 1 0 0 1 0 ...
>  $ cod2nz          : num  0 0 1 0 0 0 0 0 0 0 ...
>
> (I'm using likelihood ratio tests using anova() by adding one term at a
> time). First fitting the binomial glmmadmb:
>
> cod1b.1 <- glmmadmb(data=div.3a, cod1nz ~ (1|site.no), family="binomial")
>
> #works fine
>
> cod1b.2 <- glmmadmb(data=div.3a, cod1nz ~ year.range + (1|site.no),
> family="binomial")
>
> ## the above returns the following error message:
>
> Parameters were estimated, but not standard errors were not: the most
> likely problem is that the curvature at MLE was zero or negative
>
> Error in glmmadmb(data = div.3a, cod1nz ~ year.range + (1 | site.no),  :
>   The function maximizer failed (couldn't find STD file) Troubleshooting
> steps include (1) run with 'save.dir' set and inspect output files; (2)
> change run parameters: see '?admbControl'
>
> In addition: Warning message:
> running command 'C:\Windows\system32\cmd.exe /c
>
"C:/Users/Scott/Documents/R/win-library/3.2/glmmADMB/bin/windows64/glmmadmb.exe"
> -maxfn 500 -maxph 5' had status 1
>
> ################
>
> So looking at this error message, I first attempted to inspect the output
> files but was quickly lost. I then looked into admbControl() and tried the
> following:

I suspect quasi-complete separation here. For one year.range value, there
is no diversity. That generally gives back this kind of error.

If I were you, i'd get table(div.3a, year.range, site.no) to see.
>
> cod1b.2 <- glmmadmb(data=div.3a, cod1nz ~ year.range + (1|site.no),
> family="binomial", admb.opts=admbControl(noinit=FALSE, shess=FALSE))
>
> #This unfortunately returns the exact same error message.
>
> What's quite strange is when I add in the next term I want to do null
> hypothesis testing on ("region"), I don't get an error.
>
> cod1b.3 <- glmmadmb(data=div.3a, cod1nz ~ year.range + region + (1|site.no
),
> family="binomial")
>
> However when I add the next term, "vegetation", I get this error:
>
> cod1b.4 <- glmmadmb(data=div.3a, cod1nz ~ year.range + region + vegetation
> + (1|site.no), family="binomial")
>
> Warning message:
> In glmmadmb(data = div.3a, cod1nz ~ year.range + region + vegetation +  :
>   Convergence failed:log-likelihood of gradient= -0.0434684
>
> If anybody has any insight about these error messages, please let me know!
>
> Here is my sessionInfo():
>
> R version 3.2.1 (2015-06-18)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> Running under: Windows 8 x64 (build 9200)
>
> locale:
> [1] LC_COLLATE=English_Canada.1252  LC_CTYPE=English_Canada.1252
>  LC_MONETARY=English_Canada.1252 LC_NUMERIC=C
> [5] LC_TIME=English_Canada.1252
>
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets  methods
> base
>
> other attached packages:
>  [1] glmmADMB_0.8.0     matrixStats_0.14.2 beepr_1.2
lmtest_0.9-34
>      zoo_1.7-12         gridExtra_2.0.0    pscl_1.4.9
>  [8] MASS_7.3-40        mgcv_1.8-7         nlme_3.1-120
> statmod_1.4.21     tweedie_2.2.1      lme4_1.1-8         Matrix_1.2-1
> [15] xtable_1.7-4       mvabund_3.10.4     ggplot2_1.0.1
stringr_1.0.0
>      vegan_2.3-0        lattice_0.20-31    permute_0.8-4
> [22] reshape2_1.4.1     dplyr_0.4.2
>
> loaded via a namespace (and not attached):
>  [1] Rcpp_0.12.0      R2admb_0.7.5.3   nloptr_1.0.4     plyr_1.8.3
> tools_3.2.1      digest_0.6.8     gtable_0.1.2     DBI_0.3.1
>  [9] parallel_3.2.1   proto_0.3-10     cluster_2.0.1    R6_2.1.0
> minqa_1.2.4      magrittr_1.5     scales_0.2.5     splines_3.2.1
> [17] assertthat_0.1   colorspace_1.2-6 stringi_0.5-5    lazyeval_0.1.10
>  munsell_0.4.2    audio_0.1-5
>
> Thanks!
>
> Scott
>
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