I am trying to fit GLMM's to my data using the glmer function available in R's lme4 package. The data is available at: https://onedrive.live.com/redir?resid=1B727FC7180E87DF%21118

I keep getting warning messages. Can anybody help me get rid of them.

I am re-posting this from stackoverflow after someone's kind suggestion. The suggesty also suggested that the main of the issue may be low number of virus positive samples n=12. Which I suspected. But I am also wandering if linear seperation could be an issue, as all the virus positives occur in the low food group. Can these problems be resolved using GLMMs or should I think of other statistical tests.

Tried fitting the model:
`Food_Treatment.glmer<-glmer(Virus_DNA~Food*Treatment+(1|Set),family=binomial,data=data,method = "ML")`

to get the warning messages
"Warning messages:

1: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, : Model failed to converge with max|grad| = 0.001101 (tol = 0.001, component 3)

2: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, : Model failed to converge: degenerate Hessian with 4 negative eigenvalues"

After running code with more iterations of the model, I still get the same warning messages: `Food_Treatment.glmer<-glmer(Virus_DNA~Food*Treatment+(1|Set),data=data,family=binomial,control=glmerControl(optCtrl=list(maxfun=1e9)))`

I then looked on-line and that people had similar problems and tried the otmizer "bobyqa": `Food_Treatment.glmer<-glmer(Virus_DNA~Food*Treatment+(1|Set),data=data,family=binomial,                            control=glmerControl(optimizer="bobyqa",optCtrl=list(maxfun=1e9)))` I then got the very similar warning messages:

"Warning messages:

1: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, : Model failed to converge with max|grad| = 0.00393532 (tol = 0.001, component 2)

2: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, : Model failed to converge: degenerate Hessian with 2 negative eigenvalues"

I then thought of simplifying the model and tried no interactions between explanatory variables, with the codes:  `Food.Plus.Treatment.glmer<-glmer(Virus_DNA~Food+Treatment+(1|Set),family=binomial,data=data)`
and `Food.Plus.Treatment.glmer<-glmer(Virus_DNA~Food+Treatment+(1|Set),family=binomial,data=data,control=glmerControl(optCtrl=list(maxfun=1e9)))`
Only to get the warning messages :

"Warning messages:

1: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, : Model failed to converge with max|grad| = 0.00248016 (tol = 0.001, component 2)

2: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, : Model failed to converge: degenerate Hessian with 1 negative eigenvalues"

So I tried this simplified model with the opimizers "bobyqa" and "Nelder_Mead", as well as the otimzers "nlminb" and "L-BFGS-B" from the package optimx.

All but the "bobyqa" opimzers produce variations on the 2 warning messages. "bobyqa" otpimzer produces the 1 warning message:

"warning message:

In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, : Model failed to converge with max|grad| = 0.00139574 (tol = 0.001, component 2)

P.S. This is my first post on here I hope I have provided enough information without being verbose and it is correctly formatted.