refit with binomial model (lme4)

Dear R users,

I'm trying to use function 'refit' from lme4
and I get this error that I can't understand:
refit(dolo4.model4,cbind(uu,50-uu))
Error in function (classes, fdef, mtable)  : 
  unable to find an inherited method for function "refit", for signature
"mer", "matrix"

if I try:
refit(dolo4.model4,uu)
Error in asMethod(object) : matrix is not symmetric [1,2]

I get this error message that I can no more
understand but which suggests that refit expects
two columns.

the initial model was:
dolo4.model4 at call
glmer(formula = cbind(sortis, restes) ~ mean.co2 + (1 | sujet), 
    data = dollo4.df, family = binomial)

R version 2.9.0 (2009-04-17)

and

Package: lme4
Version: 0.999375-28
Date: 2008-12-13

thank you in advance

e.e.
This is related to using the matrix form of the response for a
binomial glmm.  The refit method for a model fit by lmer is based on a
numeric vector response.

Is it possible to use the expanded form (i.e. a vector of 0/1 values)
of the responses instead of the matrix form?
Dear R users,

I'm trying to use function 'refit' from lme4
and I get this error that I can't understand:

refit(dolo4.model4,cbind(uu,50-uu))
Error in function (classes, fdef, mtable) ?:
?unable to find an inherited method for function "refit", for signature
"mer", "matrix"

if I try:

refit(dolo4.model4,uu)
Error in asMethod(object) : matrix is not symmetric [1,2]

I get this error message that I can no more
understand but which suggests that refit expects
two columns.

the initial model was:

dolo4.model4 at call
glmer(formula = cbind(sortis, restes) ~ mean.co2 + (1 | sujet),
? ?data = dollo4.df, family = binomial)

R version 2.9.0 (2009-04-17)

and

Package: lme4
Version: 0.999375-28
Date: 2008-12-13

thank you in advance

e.e.

______________________________________________
R-help at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

This is related to using the matrix form of the response for a
binomial glmm.  The refit method for a model fit by lmer is based on a
numeric vector response.

thank you for this explanation.
Is it possible to use the expanded form (i.e. a vector of 0/1 values)
of the responses instead of the matrix form?

yes I could but I found that I could use the
probability/weights form, at least in my case 
where I am simulating new binomial data with
the observed number of trials.

Eric Elguero
On Mon, Apr 27, 2009 at 7:20 AM, Eric Elguero <Eric.Elguero at mpl.ird.fr> wrote:
Dear R users,

I'm trying to use function 'refit' from lme4
and I get this error that I can't understand:

refit(dolo4.model4,cbind(uu,50-uu))
Error in function (classes, fdef, mtable)  :
 unable to find an inherited method for function "refit", for signature
"mer", "matrix"

if I try:

refit(dolo4.model4,uu)
Error in asMethod(object) : matrix is not symmetric [1,2]

I get this error message that I can no more
understand but which suggests that refit expects
two columns.

the initial model was:

dolo4.model4 at call
glmer(formula = cbind(sortis, restes) ~ mean.co2 + (1 | sujet),
   data = dollo4.df, family = binomial)

R version 2.9.0 (2009-04-17)

and

Package: lme4
Version: 0.999375-28
Date: 2008-12-13

thank you in advance

e.e.

______________________________________________
R-help at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

I think the following works, but use with caution -- I just
wrote it last night.

setMethod("refit", signature(object = "mer", newresp = "matrix"),
          function(object, newresp, ...)
      {
        ## newresp <- as.double(newresp[!is.na(newresp)])
        wts <- rowSums(newresp)
        newresp <- newresp[,1]/wts
        stopifnot(length(newresp) == object at dims["n"])
        object at y <- newresp
        object at pWt <- wts
        lme4:::mer_finalize(object)
      })

  Ben Bolker
View this message in context: http://www.nabble.com/refit-with-binomial-model-%28lme4%29-tp23255224p23276751.html
Sent from the R help mailing list archive at Nabble.com.
Thanks for sending that, Ben.  I have incorporated a slightly modified
version, with attribution, in the lme4 sources.

I think the following works, but use with caution -- I just
wrote it last night.

setMethod("refit", signature(object = "mer", newresp = "matrix"),
? ? ? ? ?function(object, newresp, ...)
? ? ?{
? ? ? ?## newresp <- as.double(newresp[!is.na(newresp)])
? ? ? ?wts <- rowSums(newresp)
? ? ? ?newresp <- newresp[,1]/wts
? ? ? ?stopifnot(length(newresp) == object at dims["n"])
? ? ? ?object at y <- newresp
? ? ? ?object at pWt <- wts
? ? ? ?lme4:::mer_finalize(object)
? ? ?})