[R] How to speed up multiple for loop over list of data frames

Waterman, DG (David) david.waterman at diamond.ac.uk
Wed Oct 17 18:18:10 CEST 2007

I agree. Avoid the lines like:
iv     = c( iv, min(i, j) )

I had code that was sped up by 70 times after fixing the size of my
output object before entering a loop.


-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org]
On Behalf Of Patrick Burns
Sent: 17 October 2007 15:57
To: jim holtman
Cc: r-help at r-project.org; Dieter Best
Subject: Re: [R] How to speed up multiple for loop over list of data

I suspect the vast majority of time is because of growing objects.

Preallocate 'iv', 'jv', 'rho_sv' and 'rho_pv' to be their final length
and then subscript into them with their values.

Patrick Burns
patrick at burns-stat.com
+44 (0)20 8525 0696
(home of S Poetry and "A Guide for the Unwilling S User")

jim holtman wrote:

>First thing to do is to use Rprof (?Rprof) on a subset of your data to 
>see where time is being spent.  My guess is that most of it is in the 
>calls to 'cor' and if this is the case, they you have to figure out 
>some other algorithm.
>Also if these dataframes all contain numeric information, convert them 
>to matrices intially because the subsetting that you are doing on the 
>dataframe (e.g., alist[[p]][i,"v"]) can be very expensive.  The output 
>from Rprof will help determine what course of action you should take.
>On 10/16/07, Dieter Best <dieterbest_2000 at yahoo.com> wrote:
>>Hi there,
>> I have a multiple for loop over a list of data frames
>> for ( i in 1:(N-1) ) {
>>   for ( j in (i+1):N ) {
>>       for ( p in 1:M ) {
>>           v_i[p]    = alist[[p]][i,"v"]
>>           v_j[p]    = alist[[p]][j,"v"]
>>       }
>>       rho_s = cor(v_i, v_j, method = "spearman")
>>       rho_p = cor(v_i, v_j, method = "pearson" )
>>       iv     = c( iv, min(i, j) )
>>       jv     = c( jv, max(i, j) )
>>       rho_sv = c( rho_sv, rho_s)
>>       rho_pv = c( rho_pv, rho_p)
>>   }
>> N is of the order of 400, M about 800.
>> This takes me an entire day basically. Is there anything I could do
to speed things up or is cor really that slow?
>> -- D
>>       [[alternative HTML version deleted]]
>>R-help at r-project.org mailing list
>>PLEASE do read the posting guide 
>>and provide commented, minimal, self-contained, reproducible code.

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PLEASE do read the posting guide
and provide commented, minimal, self-contained, reproducible code.
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