[R-sig-ME] taking in account results of a gmml in despite of error warning about memory?

[glenda mendieta]

Hi to everyone,

I have being trying to fit aglmm on binay and poisson data and when I 
run this model, with poisson data, the error below shows up. But still 
gives me results. Does this means that those are only partial results 
and shouldn't be taking into account, because the model didn't run fully?

>  glmmab.FMv<-glmer(abundance~c.census*avail.surface*abundance.prev +(0+spp|tree), data=db.e_St, family=poisson(link=log))
Error: cannot allocate vector of size 183 Kb
In addition:Warning messages:
1: In structure(list(message = as.character(message), call = call),  :
   Reached total allocation of 4061Mb: see help(memory.size)
2: In structure(list(message = as.character(message), call = call),  :
   Reached total allocation of 4061Mb: see help(memory.size)


I am using the latest version of R and R studio. As I have seen before 
that some complicated models don't run at all if I had already many 
other models as objects in the workspace, I did run this one with the 
minimum use of memory (just the database as an object). I also read that 
R is suppose to do not have memory problems any more, but I don't really 
know how to expand the use of memory by R on my pc. For what I observed 
with mem.limits() it appears unlimited (NA), but then if I type 
mem.limit(), 4061 shows up. Does that mean that I can not run those 
models in my pc at al?.
Here, some more info in the data:

Number of obs: 23407, groups:tree,89


Thanks to anyone who can shed some light on this,

Glenda Mendieta-Leiva
PhD candidate
University of Oldenburg


On 28/11/2011 12:00, r-sig-mixed-models-request at r-project.org wrote:
> Send R-sig-mixed-models mailing list submissions to
> 	r-sig-mixed-models at r-project.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
> 	https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
> or, via email, send a message with subject or body 'help' to
> 	r-sig-mixed-models-request at r-project.org
>
> You can reach the person managing the list at
> 	r-sig-mixed-models-owner at r-project.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of R-sig-mixed-models digest..."
>
>
> Today's Topics:
>
>     1. Population fit with glm works fine: totally off with	glmer
>        (Dieter Menne)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 28 Nov 2011 08:21:44 +0000 (UTC)
> From: Dieter Menne<dieter.menne at menne-biomed.de>
> To: r-sig-mixed-models at r-project.org
> Subject: [R-sig-ME] Population fit with glm works fine: totally off
> 	with	glmer
> Message-ID:<loom.20111128T091939-576 at post.gmane.org>
> Content-Type: text/plain; charset=us-ascii
>
> Ben Bolker<bbolker at ...>  writes:
>
>>    This (using the aforementioned Dorie package)
>>
>> library(blme)
>> (fitbglmer<-   summary(g3<- bglmer(Satiated~MealVol*Group+(1|Subject),
>>                           family=binomial, data=sdata)))
>>
>> ## requires LATEST version of coefplot2 from r-forge:
>> ##  packages won't be rebuilt until tomorrow, probably
>> library(coefplot2)
>> coefplot2(list(gf1,gf2,gf3),col=c(1,2,4))
>> coefplot2(list(gf1,gf2,gf3),xlim=c(-0.05,0.15))
>>
> Thanks, Ben, I had already started with MCMCglmm, but did not know about blme.
>
> Dieter
>
>
>
> ------------------------------
>
> _______________________________________________
> R-sig-mixed-models mailing list
> R-sig-mixed-models at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>
>
> End of R-sig-mixed-models Digest, Vol 59, Issue 39
> **************************************************