[R-sig-Geo] memory allocation problem with envelope function in spatstat

[Dan Putler]

Hi Erika,

Yes, R's classic warning that you don't have enough memory. I've done K
function analysis with much larger (19,000 point) data sets on a machine
with 3.5GB (running 32 bit Linux), so what you are doing should be
possible. One thought is to create a new R workspace with only your
point data set in it. R wants to hold the workspace in memory, so if you
have a lot of stuff lying around your workspace, you could run into
problems.

Dan

On Fri, 2010-05-07 at 13:06 -0700, Erika Mudrak wrote:
> Hi everyone-  I am trying to fit an inhomogenous K function based to a large(ish) dataset.  I have successfully executed this code on data sets with a smaller n. 
> 
> 
> 
> > SPECIES.ppp
>  planar point pattern: 1598 points 
> window: rectangle = [564320, 564320] x [228490, 228500] units 
> > lambda=density(SPECIES.ppp)
> > Lin=envelope(SPECIES.ppp,Linhom,nsim=5,simulate=expression(rpoispp(lambda)),
> + correction="border")
> Error: cannot allocate vector of size 244.5 Mb
> 
> I am working on a Windows Vista OS with 3GB RAM, and I have attempted to increase the memory size using  memory.limit(2000) within R and by adding --max-vsize=2000M  to the end of the Target field in the shortcut tab of the R properties dialog box. 
> 
> I have also tried making a list of simulated patterns ahead of time, but I get the same error:
> 
> > simpatterns=list()
> > for (i in 1:5)simpatterns[[i]]=rpoispp(lambda)
> > Lin=envelope(SPECIES.ppp,Linhom,nsim=5,simulate=simpatterns,
> + correction="border")
> Error: cannot allocate vector of size 244.5 Mb
> 
> The spatstat FAQ suggest that a complete analysis should be feasible on a data set up of to 4000 points. 
> 
> Can anyone suggest ways to increase my memory limit or to modify my code to make this possible? I don't know what else to try!! Ideally, I would like to be able to make nsim=200, but I am trying to make it work with small numbers for now.  
> 
> Thank you,
> 
> Erika Mudrak
> 
> 
-- 
Dan Putler
Sauder School of Business
University of British Columbia