---------- 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
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