Brian thanks for answer me, The idea is to make a hierarchical cluster of 138037 pixels of 1 km^2 from a study area of colombian Andes as a biogeographical regionalization . I have distributions models for 89 species so i have a matrix with the pixels in the rows and is full with absence(0)/presence(1) of each species per pixel. Also for agglomeration method in hierarchical cluster i need the hole matrix so it can´t be divided I made some profs with smaller area and it works, the code:
MODELOS=stack(list.files(pattern="*.tif$") DF=as.data.frame(MODELOS) DF=na.omit(DF) DISTAN=vegdist(DF[,2:ncol(DF)],"jaccard") E1=hclust(DISTAN,"ward") Thanks a lot for helping me in my problem i think this is exceeding my programing capacities =( Carolina Bello 2013/2/9 Prof Brian Ripley <rip...@stats.ox.ac.uk> > Suppose N = 138037 (you haven't really told us). A dissimilarity > half-matrix would have 9 billlion elements. The maximum size of a vector > in current versions of R is 2 billion. > > You will be able to get further in R-devel (3.0.0-to-be) with a 64-bit > version of R, although as you appear to be using Windows it will be very > slow and 32GB of RAM is not enough to even store that object. > > What do you propose to do with a distance matrix on 140,000 objects? I > think you need to re-think whatever that is. > > > > On 08/02/2013 23:25, Carolina Bello wrote: > >> ---------- Forwarded message ---------- >> From: <r-help-ow...@r-project.org> >> Date: 2013/2/8 >> Subject: vegdist Error en double(N * (N - 1)/2) : tama?o del vector >> especificado es muy grande >> To: caro.bell...@gmail.com >> >> >> Message rejected by filter rule match >> >> >> >> ---------- Mensaje reenviado ---------- >> From: caro bello <caro.bell...@gmail.com> >> To: r-help@r-project.org >> Cc: >> Date: Fri, 8 Feb 2013 15:18:40 -0800 (PST) >> Subject: vegdist Error en double(N * (N - 1)/2) : tamaño del vector >> especificado es muy grande >> Hi >> I have some problems with the vegdist function. I want to calculate a >> distance matrix with jaccard. I have binary data. >> >> The problem is that i have a matrix of 138037 rows (sites) and 89 columns >> (species). my script is: >> >> rm(list=ls(all=T)) >> >> gc() ##para borrar todo lo que quede oculto en memoria >> >> memory.limit(size = 100000) # it gives 1 Tera from HDD in case ram >> memory is over >> >> DF=as.data.frame(MODELOS) >> >> DF=na.omit(DF) >> >> DISTAN=vegdist(DF[,2:ncol(DF)]**,"jaccard") >> >> Almost immediately IT produces the error: Error en double(N * (N - 1)/2) : >> tamaño del vector especificado es muy grande >> >> I think this a memory error, but i don´t know why if i have a pc with 32GB >> of ram and 1 Tera of HDD. >> >> I also try to do a dist matrix whit the function dist from package proxy, >> i >> did: >> >> library(proxy) >> >> vector=dist(DF, method = "Jaccard") >> >> it starts to run but when it gets to 10 GB of ram, a window announces >> that R >> committed an error and it will close, so it closes and start a new >> section. >> >> I really don't know what is going on and less how to solve this, can >> anybody >> help me? >> >> thanks >> >> Carolina Bello IAVH-COLOMBIA >> >> >> >> >> -- >> View this message in context: >> http://r.789695.n4.nabble.com/**vegdist-Error-en-double-N-N-1-** >> 2-tama-o-del-vector-**especificado-es-muy-grande-**tp4658010.html<http://r.789695.n4.nabble.com/vegdist-Error-en-double-N-N-1-2-tama-o-del-vector-especificado-es-muy-grande-tp4658010.html> >> Sent from the R help mailing list archive at Nabble.com. >> >> [[alternative HTML version deleted]] >> >> >> >> ______________________________**________________ >> R-help@r-project.org mailing list >> https://stat.ethz.ch/mailman/**listinfo/r-help<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. >> >> > > -- > Brian D. Ripley, rip...@stats.ox.ac.uk > Professor of Applied Statistics, > http://www.stats.ox.ac.uk/~**ripley/<http://www.stats.ox.ac.uk/~ripley/> > University of Oxford, Tel: +44 1865 272861 (self) > 1 South Parks Road, +44 1865 272866 (PA) > Oxford OX1 3TG, UK Fax: +44 1865 272595 > > ______________________________**________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/**listinfo/r-help<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. > [[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.
