Hi
I have some problems with the vegdist function.I want to do a hierarchical
cluster from 138037 pixels of 1 lkm^2 from a study area of colombian Andes.
I have distributions models for 89 species so i have a matrix with the
pixels in the rows and species in the columns and is full with
absence(0)/presence(1) of each species per each pixel. I think the bigger
problem is that for agglomeration method in the hierarchical cluster i need
the hole matrix so i can´t divided it.

For doing this 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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