[R] Large database help

[Uwe Ligges]

Rogerio Porto wrote:

> Hello all.
> 
> I have a large .txt file whose variables are fixed-columns, 
> ie, variable V1 goes from columns 1 to 7, V2 from 8 to 23 etc.
> This is a 60GB file with 90 variables and 60 million observations.
> 
> I'm working with a Pentium 4, 1GB RAM, Windows XP Pro.
> I tried the following code just to see if I could work with 2 variables
> but it seems not possible: 
> R : Copyright 2005, The R Foundation for Statistical Computing
> Version 2.2.1  (2005-12-20 r36812)
> ISBN 3-900051-07-0
> 
>>gc()
> 
>          used (Mb) gc trigger (Mb) max used (Mb)
> Ncells 169011  4.6     350000  9.4   350000  9.4
> Vcells  62418  0.5     786432  6.0   289957  2.3
> 
>>memory.limit(size=4090)
> 
> NULL
> 
>>memory.limit()
> 
> [1] 4288675840
> 
>>system.time(a<-matrix(runif(1e6),nrow=1))
> 
> [1] 0.28 0.02 2.42   NA   NA
> 
>>gc()
> 
>           used (Mb) gc trigger (Mb) max used (Mb)
> Ncells  171344  4.6     350000  9.4   350000  9.4
> Vcells 1063212  8.2    3454398 26.4  4063230 31.0
> 
>>rm(a)
>>ls()
> 
> character(0)
> 
>>system.time(a<-matrix(runif(60e6),nrow=1))
> 
> Error: not possible to alocate vector of size 468750 Kb
> Timing stopped at: 7.32 1.95 83.55 NA NA 
> 
>>memory.limit(size=5000)
> 
> Erro em memory.size(size) : .....4GB
> 
> So my questions are:
> 1) (newbie) how can I read fixed-columns text files like this?
> 2) is there a way I can analyze (statistics like correlations, cluster etc)
>     such a large database neither increasing RAM nor changing to 64bit
>     machine but still using R and not using a sample? How? 


Use what you are already suggesting in your subject: a database.
Then you can access the variables separately and you have no problems 
reading the file.

Even with a real database, if you want to calculate on 60 million 
observations (~500Mb) at once, you are near the limit, but only works if 
you do not need several variables at once and depends on the methods you 
are going to apply.

Uwe Ligges


> Thanks in advance.
> 
> Rogerio.
> 
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