Error in glmmADMB
Boris Berkhout <b.berkhout at ...> writes:
Dear list members, I am trying to fit a glmmADMB model on my data, but even after trying several things and reading different posts on forums I can't seem to fix the problem I am encountering. My response variable is the proportion of individuals surviving at a certain timepoint. The model looks like this: glmmSing8 =
glmmadmb(survF~temperature*snail*tank*plate+(1|plate:replicate)+(1|week), data=SurvSing8, family="binomial", zeroInflation=TRUE)
If you want to fit a binomial model, you need to specify the _number_ surviving and the total (denominator), as in glmmadmb(cbind(nSurv,nTotal) ~ ....) in your case this might? be cbind(dead_cc,total) ? otherwise I'm afraid the results won't make sense. (glmer() has syntax proportion~..., weights=nTotal , so that you can use the proportion as the response variable, but I haven't implemented a similar syntax for glmmADMB ... Are you sure you need zero-inflation in the binomial? Did you try it first with zeroInflation=FALSE? I'm also afraid that with snail crossed with everything else you'll be overfitting your model: what is ncol(model.matrix(~temperature*snail*tank*plate,data=SurvSing8)) ? In this case you are fitting the _interaction_ between snail and the three-way interaction of temperature, tank, plate. Was each snail really measured in all combinations of temperature, tank, and plate??? [snip]
'snail' is a fixed effect, because I want to distinguish between snails and 'plate' and 'tank' are fixed effects, because they only have two and three levels respectively. A summary of my data looks like this:
summary(SurvSing8)
snail temperature plate tank week
replicate time
Y33 : 59 Min. :15.00 1:287 1:189 13 : 97 7 : 77
Min. :8
Y64 : 59 1st Qu.:15.00 2:285 2:218 16 : 92 8 : 75
1st Qu.:8
Y40 : 55 Median :20.00 3:165 5 : 81 2 : 74
Median :8
Y48 : 53 Mean :17.53 6 : 73 3 : 73
Mean :8
Y30 : 45 3rd Qu.:20.00 7 : 64 4 : 71
3rd Qu.:8
Y51 : 45 Max. :20.00 8 : 64 1 : 69
Max. :8
(Other):256 (Other):101
(Other):133
total dead_cc survF
Min. :10.0 Min. : 0.00 Min. :0.0000
1st Qu.:13.0 1st Qu.: 6.75 1st Qu.:0.3820
Median :20.0 Median :10.00 Median :0.5410
Mean :22.9 Mean :11.83 Mean :0.5346
3rd Qu.:29.0 3rd Qu.:16.00 3rd Qu.:0.7037
Max. :78.0 Max. :53.00 Max. :1.0000
Kind regards, Boris Berkhout [[alternative HTML version deleted]]