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.simp...@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]] ______________________________________________ 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.
