R help - Jun 2009 - Problem with storing a sequence of lmer() model fit into a list

Dear R-helpers:
May I ask a question related to storing a number of lmer model fit into a
list.

Basically, I have a for-loop (see towards the bottom of this email)
in the loop, I am very sure that the i-th model fit (i.e.,fit_i) is
successfully generated and the character string (i.e., tmp_i) is created
correctly.
The problem stems from the following line in the for-loop
#trouble making line below
fit.list[[tmp_i]] <- fit_i


I tried the following example which stores glm() model fit without a
problem.
#the following code can store glm() model fit into a list
---------------------------------------------------
x1<-runif(200)
x2<-rnorm(200)
y<-x1+x2
testdf<-data.frame(y=y, x1=x1, x2=x2)
indepvec<-c("x1","x2")
fit.list<-NULL
fit_1<-glm(y~x1,data=testdf)
fit_2<-glm(y~x2,data=testdf)
fit.list[[paste('fit_',indepvec[1],sep='')]]<-fit_1
fit.list[[paste('fit_',indepvec[12],sep='')]]<-fit_2
----------------------------------------------------
so why cannot I store lmer() model fit in a list?
Would someone kindly explain to me what the R error message(last line of
this email) really means?
Your kind help will be highly appreciated!

-Sean

#the following for-loop intends to store lmer() random poisson model output
into list (fit.list), it does not work
---------------------------------------------------------------------------
fit.list<-NULL
for (i in seq_along(depvar_vec))
    {
      #I found that s_sex, ses1 and race are not useful
      fit_i <- lmer(as.formula(gen.ranpoisson.fml.jh(depvar_vec[i],
offsetvar ,factorindepvars,  nonfactorindepvars ,ranintvar )),
family=quasipoisson(link="log"),verbose=F, data=indf)
      tmp_i<-paste('ranpoi_', depvar_vec[i], sep='')
      fit.list[[tmp_i]] <- fit_i
      #assign also does not work
      #assign(fit.list$parse(text = tmp_i), fit_i)
     }
---------------------------------------------------------------


#R gives the following error message.

Error in fit.list[[tmp_i]] <- fit_i : invalid type/length (S4/0) in vector
allocation

	[[alternative HTML version deleted]]

(a) Your code is unnecessarily convoluted.

(b) The example of things *not* working is not reproducible.  (Read  
the posting guide!!!)

(c) Nonetheless the phenomenon you describe is weird/interesting.

On my system, the following runs without error:

fit.list <- NULL
a <- factor(rep(1:10,each=20))
set.seed(42)
for(i in 1:10) {
         x1<-runif(200)
         x2<-rnorm(200)
         y <- x1+x2
         testdf<-data.frame(y=y, x1=x1)
         fit <- lm(y~x1+a,data=testdf)
         fit.list[[i]] <- fit
}


However if the call to lm() is replace by a call to lmer()

library(lme4)
fit.list <- NULL
a <- factor(rep(1:10,each=20))
set.seed(42)
for(i in 1:10) {
         x1<-runif(200)
         x2<-rnorm(200)
         y <- x1+x2
         testdf<-data.frame(y=y, x1=x1)
         fit <- lmer(y~x1 + (1|a),data=testdf)
         fit.list[[i]] <- fit
}

I get the same error that you reported, namely

Error in fit.list[[i]] <- fit :
   invalid type/length (S4/0) in vector allocation

Finally if fit.list is initialized to an empty list (which is the way  
it *should*
be initialized anyway) rather than to NULL, then things appear to  
work smoothly even
with a call to lmer():

library(lme4)
fit.list <- list()
a <- factor(rep(1:10,each=20))
set.seed(42)
for(i in 1:10) {
         x1<-runif(200)
         x2<-rnorm(200)
         y <- x1+x2
         testdf<-data.frame(y=y, x1=x1)
         fit <- lmer(y~x1 + (1|a),data=testdf)
         fit.list[[i]] <- fit
}

So a ``fix'' for the problem would seem to be to start with fit.list  
being an empty list,
rather than NULL.

But why the problem shows up only with calls to lmer() is completely  
mysterious to me.
Perhaps others will be able to shed light.

HTH

	cheers,

		Rolf Turner

On 23/06/2009, at 6:34 AM, Sean Zhang wrote:
> Dear R-helpers:
> May I ask a question related to storing a number of lmer model fit  
> into a
> list.
>
> Basically, I have a for-loop (see towards the bottom of this email)
> in the loop, I am very sure that the i-th model fit (i.e.,fit_i) is
> successfully generated and the character string (i.e., tmp_i) is  
> created
> correctly.
> The problem stems from the following line in the for-loop
> #trouble making line below
> fit.list[[tmp_i]] <- fit_i
>
>
> I tried the following example which stores glm() model fit without a
> problem.
> #the following code can store glm() model fit into a list
> ---------------------------------------------------
> x1<-runif(200)
> x2<-rnorm(200)
> y<-x1+x2
> testdf<-data.frame(y=y, x1=x1, x2=x2)
> indepvec<-c("x1","x2")
> fit.list<-NULL
> fit_1<-glm(y~x1,data=testdf)
> fit_2<-glm(y~x2,data=testdf)
> fit.list[[paste('fit_',indepvec[1],sep='')]]<-fit_1
> fit.list[[paste('fit_',indepvec[12],sep='')]]<-fit_2
> ----------------------------------------------------
> so why cannot I store lmer() model fit in a list?
> Would someone kindly explain to me what the R error message(last  
> line of
> this email) really means?
> Your kind help will be highly appreciated!
>
> -Sean
>
> #the following for-loop intends to store lmer() random poisson  
> model output
> into list (fit.list), it does not work
> ---------------------------------------------------------------------- 
> -----
> fit.list<-NULL
> for (i in seq_along(depvar_vec))
>     {
>       #I found that s_sex, ses1 and race are not useful
>       fit_i <- lmer(as.formula(gen.ranpoisson.fml.jh(depvar_vec[i],
> offsetvar ,factorindepvars,  nonfactorindepvars ,ranintvar )),
> family=quasipoisson(link="log"),verbose=F, data=indf)
>       tmp_i<-paste('ranpoi_', depvar_vec[i], sep='')
>       fit.list[[tmp_i]] <- fit_i
>       #assign also does not work
>       #assign(fit.list$parse(text = tmp_i), fit_i)
>      }
> ---------------------------------------------------------------
>
>
> #R gives the following error message.
>
> Error in fit.list[[tmp_i]] <- fit_i : invalid type/length (S4/0) in  
> vector
> allocation
######################################################################
Attention:\ This e-mail message is privileged and confid...{{dropped:9}}