Hi Joris,
thanks for spotting that one. This little mistake has gotten in when I was
trying desperate things with the analysis (factor1 is used in diversitycomp).
Nevertheless, here is the result:
> poacc2 <- accumcomp(PoCom, y=PoEnv, factor="HM_sprem", method="exact")
Error in if (p == 1) { : argument is of length zero
And the traceback():
> traceback()
3: specaccum(x, method = method, permutations = permutations, conditioned =
conditioned,
gamma = gamma, ...)
2: accumresult(x, y, factor, level = levels[i], scale = scale, method =
method,
permutations = permutations, conditioned = conditioned, gamma =
gamma)
1: accumcomp(PoCom, y = PoEnv, factor = "HM_sprem", method = "exact")
Best wishes,
Roman
On Mon, Oct 12, 2009 at 1:56 PM, joris meys <jorism...@gmail.com> wrote:
> Hi Roman,
>
> that throws a different light on the problem. It goes wrong from the
> start, so it has little to do with the bootstrap or jackknife
> procedures. R.huge won't help you either.
>
> Likely your error comes from the fact that "factor1" is not an
> argument of the function accumcomp. the argument is "factor". As R
> doesn't find this, it'll try to tabulate the complete environmental
> dataset, and this gives the memory overflow.
>
> Try :
>
> poacc2 <- accumcomp(PoCom, y=PoEnv, factor="HM_sprem", method="exact")
>
> That should work. I can't try it out without dataset off course. If it
> doesn't work, post the traceback again, I'll take another look.
>
> Kind regards
> Joris
>
> On Mon, Oct 12, 2009 at 1:07 PM, romunov <romu...@gmail.com> wrote:
> > 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.
> >> >
> >
> >
>
[[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.
