Hello joris,
this is the traceback() output. Hopefully you can make some sense out of it.
Thank you for the tips as well (R.huge looks promising)!
> traceback()
7: vector("integer", length)
6: integer(nbins)
5: tabulate(bin, pd)
4: as.vector(data)
3: array(tabulate(bin, pd), dims, dimnames = dn)
2: table(y[, factor])
1: accumcomp(PoCom, y = PoEnv, factor1 = "HM_sprem", method = "exact")
Cheers,
Roman
On Mon, Oct 12, 2009 at 12:52 PM, joris meys <jorism...@gmail.com> wrote:
> Dear Roman,
>
> could you give us the trace given by traceback() ? I suspect the error
> is resulting from the permutations and/or jackknife procedure in the
> underlying functions specaccum and specpool.
>
> You can take a look at the package R.huge, but that one is deprecated
> already. There are other packages around too, but I have no experience
> with them. You find some more tips here :
> http://www.matthewckeller.com/html/memory.html
>
> This should give you a place to start looking.
> Kind regards
> Joris
>
> On Mon, Oct 12, 2009 at 11:39 AM, romunov <romu...@gmail.com> wrote:
> > Dear List,
> >
> > today I turn to you with a next problem. I'm trying to compare species
> > richness between various datasets (locations) using species accumulation
> > curves (Chapter 4, page 54 in Tree diversity
> > analysis<
> http://www.worldagroforestry.org/treesandmarkets/tree_diversity_analysis.asp
> >by
> > Kindt & Coe). To accomplish this I'm using package
> > BiodiversityR. My data is comprised of species community (PoCom) (10
> > locations with 83 species) and environmental factors (PoEnv) (10
> locations
> > with 17 factors).
> > In attempt to calculate the function (accumcomp) I receive the following
> > error. I can not imagine how a 10x83+10x17 matrix can grow to a GB or
> more.
> > Unless I'm missing something? How can I combat this?
> >
> >> poacc2 <- accumcomp(PoCom, y=PoEnv, factor1="HM_sprem", method="exact")
> > Error: cannot allocate vector of size 1.2 Gb
> > In addition: Warning messages:
> > 1: In vector("integer", length) :
> > Reached total allocation of 1023Mb: see help(memory.size)
> > 2: In vector("integer", length) :
> > Reached total allocation of 1023Mb: see help(memory.size)
> > 3: In vector("integer", length) :
> > Reached total allocation of 1023Mb: see help(memory.size)
> > 4: In vector("integer", length) :
> > Reached total allocation of 1023Mb: see help(memory.size)
> >
> >
> > Cheers,
> > Roman
> >
> > [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-help@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.
> >
>
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