On 26Jul 2018, at 22:03, Bansal, Udita <udita.bansal17 at imperial.ac.uk> wrote:
I am measuring breeding success as number of chicks produced out of number of eggs laid. So, the values range from 0 to 1 including decimal values. Although, that was just a warning. Should I be too concerned about that?
My model statement is as follows:
m_admb <- glmmadmb( breeding.success ~ laying.date.julian.day.zscale + tmean.zscale + (1|YEAR) ,
data = hungary_breeding, zeroInflation = TRUE, family = "nbinom", link = "logit")
Summary for relevant columns of my data:
YEAR No.of.chicks Clutch.size laying_date tmean prec
1988:16 Min. :0.000 Min. :2.000 Min. :1988-04-22 Min. : 3.45 Min. : 0.000
1989:25 1st Qu.:0.000 1st Qu.:3.000 1st Qu.:1990-05-07 1st Qu.:11.35 1st Qu.: 0.000
1990:45 Median :0.000 Median :3.000 Median :1991-05-09 Median :15.12 Median : 0.000
1991:65 Mean :1.021 Mean :2.946 Mean :1991-05-24 Mean :14.62 Mean : 2.285
1992:46 3rd Qu.:3.000 3rd Qu.:3.000 3rd Qu.:1992-05-15 3rd Qu.:17.95 3rd Qu.: 1.050
1993:24 Max. :3.000 Max. :3.000 Max. :1994-06-16 Max. :27.05 Max. :55.200
1994:19
breeding.success clutch.volume laying.date.julian.day tmean.zscale.V1 prec.zscale.V1
Min. :0.0000 Min. :15.82 Min. : 82.0 Min. :-2.5607265 Min. :-0.559014
1st Qu.:0.0000 1st Qu.:24.60 1st Qu.:115.0 1st Qu.:-0.7638887 1st Qu.:-0.559014
Median :0.0000 Median :25.89 Median :129.0 Median : 0.0947269 Median :-0.559014
Mean :0.3438 Mean :25.52 Mean :132.3 Mean :-0.0190444 Mean : 0.006583
3rd Qu.:1.0000 3rd Qu.:27.06 3rd Qu.:148.2 3rd Qu.: 0.7372670 3rd Qu.: 0.209975
Max. :1.0000 Max. :29.83 Max. :186.0 Max. : 2.8070422 Max. : 3.762186
laying.date.julian.day.zscale.V1
Min. :-2.2850626
1st Qu.:-0.7846733
Median :-0.1481445
Mean : 0.0000000
3rd Qu.: 0.7270826
Max. : 2.4434370
I will try glmmTMB as well now.
Thanks
Udita
On 26/07/18, 7:41 PM, "R-sig-mixed-models on behalf of Ben Bolker" <r-sig-mixed-models-bounces at r-project.org on behalf of bbolker at gmail.com> wrote:
The first thing that pops out is the "non-integer response values in
discrete family" warning. How are you measuring breeding success? Can
you show us your whole glmmadmb() statement, and maybe a summary() of
the relevant columns of your data set?
I'll also make the now-blanket statement that you may have better
luck moving forward with glmmTMB.
cheers
Ben Bolker
On 2018-07-26 12:57 PM, Bansal, Udita wrote:
Hi all,
I was trying to use the glmmADMB package but ran into some errors. I?ve
noticed that other people have run into similar errors but there doesn?t
seem to be a solution online. It would be great help if anyone could
provide any insights on it.
I am using it for running a zero-inflated mixed-effects binomial model.
The errors are as follows:
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(breeding.success ~ laying.date.julian.day.zscale +
tmean.zscale + :
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 messages:
1: In glmmadmb(breeding.success ~ laying.date.julian.day.zscale +
tmean.zscale + :
non-integer response values in discrete family
2: running command './glmmadmb -maxfn 500 -maxph 5 -noinit -shess' had
status 1
Any kind of help will be greatly appreciated.
Bests
Udita Bansal
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