assigning and saving datasets in a loop, with names changing with "i"

Thu, Dec 20, 2007 12:57 PM

Have you looked at the SQLiteDF package?  It seems like it would do what
you want in a better way and much simpler.  Even if that does not work
then a database approach (look at the other db packages, probably RODBC
first) could be simpler, faster, and easier.  You may also want to look
at the g.data package for another approach.

Depending on what you are doing you may also want to look at the biglm
package (some similar functionality is in SQLiteDF).

Hope this helps,

Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.snow at imail.org
(801) 408-8111
 
 

> -----Original Message-----
> From: r-help-bounces at r-project.org 
> [mailto:r-help-bounces at r-project.org] On Behalf Of Marie 
> Pierre Sylvestre
> Sent: Tuesday, December 18, 2007 7:25 PM
> To: r-help at r-project.org
> Subject: [R] assigning and saving datasets in a loop,with 
> names changing with "i"
> 
> Dear R users,
> 
> I am analysing a very large data set and I need to perform 
> several data manipulations. The dataset is so big that the 
> only way I can play with it without having memory problems 
> (E.g. "cannot allocate vectors of size...") is to write a 
> batch script to:
> 
> 1. cut the data into pieces
> 2. save the pieces in seperate .RData files 3. Remove 
> everything from the environment 4. load one of the piece 5. 
> perform the manipulations on it 6. save it and remove it from 
> the environment 7. Redo 4-6 for every piece 8. Merge 
> everything together at the end
> 
> It works if coded line by line but since I'll have to perform 
> these tasks on other data sets, I am trying to automate this 
> as much as I can. 
> 
> I am using a loop in which I used 'assign' and 'get' (pseudo 
> code below).
> My problem is when I use 'get', it prints the whole object on 
> the screen.
> I am wondering whether there is a more efficient way to do 
> what I need to do. Any help would be appreciated. Please keep 
> in mind that the whole process is quite computer-intensive, 
> so I can't keep everything in the environment while R 
> performs calculations.
> 
> Say I have 1 big dataframe called data. I use 'split' to 
> divide it into a list of 12 dataframes (call this list my.list)
> 
> my.fun is a function that takes a dataframe, performs several 
> manipulations on it and returns a dataframe.
> 
> 
> for (i in 1:12){
>   assign( paste( "data", i, sep=""),  my.fun(my.list[i]))   # 
> this works
>   # now I need to save this new object as a RData. 
> 
>   # The following line does not work
>   save(paste("data", i, sep = ""),  file = paste(  
> paste("data", i, sep = ""), "RData", sep=".")) }
> 
>   # This works but it is a bit convoluted!!!
>   temp <- get(paste("data", i, sep = ""))
>   save(temp,  file = "lala.RData")
> }
> 
> 
> I am *sure* there is something more clever to do but I can't 
> find it. Any help would be appreciated.
> 
> best regards,
> 
> MP
> 
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assigning and saving datasets in a loop, with names changing with "i"

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