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 <ripley@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-owner@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.bello58@gmail.com
>>
>>
>> Message rejected by filter rule match
>>
>>
>>
>> ---------- Mensaje reenviado ----------
>> From: caro bello <caro.bello58@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,                  ripley@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]]

