Error: cannot allocate vector of size 1.2 Gb

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

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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 <jorismeys at 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 <romunov at 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

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