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

[Ben Bolker]

glenda mendieta <glendamendieta at ...> writes:

> I have being trying to fit a glmm on binary and poisson data and when I 
> run this model, with poisson data, the error below shows up. But still 
> gives me results. 

  Be very careful.  It probably means that the results are left over
from some previous run that you tried that did work.  An Error
results should *not* give any result.  Try re-running in a clean
R session, with just the minimal stuff you need loaded (see below).

> 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))

  Your random effect specification is not sensible (I think): it asks for an
estimate of the variation of the species effect across trees, which
is more or less impossible because every tree belongs only to a single
species.  Did you mean (1|spp/tree) or (1|spp)+(1|tree) ?

> Error: cannot allocate vector of size 183 Kb

  [snip]

> 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.

   Take a look at the R for Windows FAQ entries on memory use.
   Can you give the results of sessionInfo()?  If you can, you
may need to switch to a 64-bit OS.

>  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

  This does not seem like a particularly huge dataset, so I'm
a bit surprised you're running into trouble (with the exception
of the weird RE specification ...) are your predictor variables
all continuous?

> 
> Thanks to anyone who can shed some light on this,
> 
> Glenda Mendieta-Leiva
> PhD candidate
> University of Oldenburg
>