Dear Gavin,

Thanks for your reply. I am trying to get the permanova for 5 species, the
first one has 7670 + 1693 (unbalanced factor) with a total of 9363 rows.

In windows the proccess directly cracks, but in linux the process will be
working days but no ends.

I agree with you, I think that the problem is about the RAM memory used. I
am not sure if there is any way of optimize the process.

Thanks in advance,

Paloma
2010/4/14 Gavin Simpson <gavin.simpson@ucl.ac.uk>

>  > Dear all,
> >
> > I am trying to get a PERMANOVA with quite large data set. I am reading a
> lot
> > about this question, but I do not get the answer about it. Although I
> know
> > that the R function is adonis () (vegan package), it does not work:
> >
> > adonis(Pha.env~SPha, data=Pha, permutations=10)
> >
> > The error message:
> >  Error: cannot allocate vector of size 334.2 Mb
> > In addition: Warning messages:
> > 1: In vegdist(lhs, method = method, ...) :
> >   Reached total allocation of 1535Mb: see help(memory.size)
> > 2: In vegdist(lhs, method = method, ...) :
> >   Reached total allocation of 1535Mb: see help(memory.size)
> > 3: In vegdist(lhs, method = method, ...) :
> >   Reached total allocation of 1535Mb: see help(memory.size)
> > 4: In vegdist(lhs, method = method, ...) :
> >   Reached total allocation of 1535Mb: see help(memory.size)
> >
> > When I have received this message from R usually it is due to an
> incorrect
> > introduction of the function elements (i.e., memory message errors).
> > However, I've just checked my matrix (Pha.env is a data.frame with num or
> > int variables, and, Pha is a data.frame with factor variables) and the
> > length of matrices is the same. I know that I'm wrong somewhere
> specifying
> > the matrices in adonis(), but I can't fix it.
>
> That error is coming from the calculation of the dissimilarity matrix
> and you've exhausted the 1.5GB of (allocated) RAM on your system. How
> many samples (rows) are you trying that on?
>
> G
>
> >
> > Thanks in advance,
> >
> > Paloma
> >
> >       [[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<http://www.r-project.org/posting-guide.html>
> > and provide commented, minimal, self-contained, reproducible code.
>
> --
> %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
>  Dr. Gavin Simpson             [t] +44 (0)20 7679 0522
>  ECRC, UCL Geography,          [f] +44 (0)20 7679 0565
>  Pearson Building,             [e] gavin.simpsonATNOSPAMucl.ac.uk<http://gavin.simpsonatnospamucl.ac.uk/>
>  Gower Street, London          [w] http://www.ucl.ac.uk/~ucfagls/
>  UK. WC1E 6BT.                 [w] http://www.freshwaters.org.uk
> %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
>
>

	[[alternative HTML version deleted]]

