R help - Nov 2013 - Error running MuMIn dredge function using glmer models

Dear list, 
I am trying to use MuMIn to compare all possible mixed models using the dredge
function on binomial data but I am getting an error message that I cannot
decode. This error only occurs when I use glmer. When I use an lmer analysis on
a different response variable every works great.

Example using a simplified glmer model
global model: 
mod<- glmer(cbind(st$X2.REP.LIVE, st$X2.REP.DEAD) ~ DOMESTICATION*GLUC +
(1|PAIR), data=st, na.action=na.omit , family=binomial)

The response variables are the number of survival and dead insects (successes
and failures)
DOMESTICATION is a 2 level factor.
GLUC is a continuous variable.
PAIR is coded as a factor or character (both ways fail).

This model functions correctly but when I try it with dredge() I get an error. 

g<- dredge(mod, beta=F, evaluate=F, rank='AIC')
Error in sprintf(gettext(fmt, domain = domain), ...) : 
  invalid type of argument[1]: 'symbol'

When I try with another rank the same thing happens:
chat<- deviance(mod)/58
g<- dredge(mod, beta=F, evaluate=F, rank='QAIC', chat=chat)
Error in sprintf(gettext(fmt, domain = domain), ...) : 
  invalid type of argument[1]: 'symbol'

Any suggestions would be greatly appreciated

thanks

Martin Turcotte, Ph. D.
mart.turcotte@gmail.com





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Martin Turcotte <mart.turcotte <at> gmail.com> writes:
> Dear list, 
> I am trying to use MuMIn to compare all possible mixed models 
> using the dredge function on binomial data but I
> am getting an error message that I cannot decode. This error 
> only occurs when I use glmer. When I use an lmer
> analysis on a different response variable every works great. 
> 
> Example using a simplified glmer model
> global model: 
> mod<- glmer(cbind(st$X2.REP.LIVE, st$X2.REP.DEAD) ~ 
> DOMESTICATION*GLUC + (1|PAIR), data=st,
> na.action=na.omit , family=binomial) 
> 
> The response variables are the number of survival and dead insects
> (successes and failures)
> DOMESTICATION is a 2 level factor.
> GLUC is a continuous variable.
> PAIR is coded as a factor or character (both ways fail).
> 
> This model functions correctly but when I try it with dredge()
> I get an error. 
> 
> g<- dredge(mod, beta=F, evaluate=F, rank='AIC')
> Error in sprintf(gettext(fmt, domain = domain), ...) : 
>   invalid type of argument[1]: 'symbol'
> 
> When I try with another rank the same thing happens:
> chat<- deviance(mod)/58
> g<- dredge(mod, beta=F, evaluate=F, rank='QAIC', chat=chat)
> Error in sprintf(gettext(fmt, domain = domain), ...) : 
>   invalid type of argument[1]: 'symbol'
> 
> Any suggestions would be greatly appreciated
> 
> thanks
> 
> Martin Turcotte, Ph. D.
> mart.turcotte <at> gmail.com
* Please send follow-ups to r-sig-mixed-models at r-project.org
* I think we need a reproducible example: it works OK for the
first two binomial GLMMs I tried:

library(lme4)
library(MuMIn)
gm1 <- glmer(cbind(incidence, size - incidence) ~ period + (1 | herd),
                   data = cbpp, family = binomial)
dredge(gm1)
dredge(gm1,beta=FALSE,evaluate=FALSE)

library(mlmRev)
gm2 <- glmer(use ~ urban+age+livch+(1|district), Contraception, binomial)
dredge(gm2)
dredge(gm2,beta=FALSE,evaluate=FALSE)

* It might be worth removing the 'st$' from  your response variable,
e.g.

mod<- glmer(cbind(X2.REP.LIVE, X2.REP.DEAD) ~  DOMESTICATION*GLUC + (1|PAIR),
            data=st,family=binomial) 

* What are the results of traceback()?  sessionInfo() ?

There is indeed a glitch in 'dredge' that prevents you from seeing the
actual error message. It is explained in "?dredge", in section
"Missing
values". (it's been corrected now in 1.9.14, on R-forge)

kamil



On 2013-11-08 11:00, r-help-request at r-project.org
wrote:
> ------------------------------
>
> Message: 26
> Date: Thu, 7 Nov 2013 11:55:50 -0500
> From: Martin Turcotte<mart.turcotte at gmail.com>
> To:r-help at r-project.org
> Subject: [R] Error running MuMIn dredge function using glmer models
> Message-ID:<1E4F5497-CCB4-4E8B-A23A-8AA5E1136DAE at gmail.com>
> Content-Type: text/plain
>
> Dear list,
> I am trying to use MuMIn to compare all possible mixed models using the
dredge function on binomial data but I am getting an error message that I cannot
decode. This error only occurs when I use glmer. When I use an lmer analysis on
a different response variable every works great.
>
> Example using a simplified glmer model
> global model:
> mod<- glmer(cbind(st$X2.REP.LIVE, st$X2.REP.DEAD) ~ DOMESTICATION*GLUC +
(1|PAIR), data=st, na.action=na.omit , family=binomial)
>
> The response variables are the number of survival and dead insects
(successes and failures)
> DOMESTICATION is a 2 level factor.
> GLUC is a continuous variable.
> PAIR is coded as a factor or character (both ways fail).
>
> This model functions correctly but when I try it with dredge() I get an
error.
>
> g<- dredge(mod, beta=F, evaluate=F, rank='AIC')
> Error in sprintf(gettext(fmt, domain = domain), ...) :
>    invalid type of argument[1]: 'symbol'
>
> When I try with another rank the same thing happens:
> chat<- deviance(mod)/58
> g<- dredge(mod, beta=F, evaluate=F, rank='QAIC', chat=chat)
> Error in sprintf(gettext(fmt, domain = domain), ...) :
>    invalid type of argument[1]: 'symbol'
>
> Any suggestions would be greatly appreciated
>
> thanks
>
> Martin Turcotte, Ph. D.
> mart.turcotte at gmail.com




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