On Wed, 2007-10-17 at 19:57 -0600, James wrote:
> On Oct 17, 2007, at 4:36 PM, James wrote:
>
> > On Oct 17, 2007, at 10:18 AM, Waterman, DG ((David)) wrote:
> >
> >> 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
On Oct 17, 2007, at 4:36 PM, James wrote:
> On Oct 17, 2007, at 10:18 AM, Waterman, DG ((David)) wrote:
>
>> 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.
>
> I'm in t
On Oct 17, 2007, at 10:18 AM, Waterman, DG ((David)) wrote:
> 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.
I'm in the process of replacing that very kind of command. In
Maybe I'm wrong, but aren't you calculating just the same as cor(data
frame,method ="spearman"), with some further parameters being monitored?
Could you please provide a commented, minimal, self-contained, reproducible
code, so that we can see what is actually going on and what is the way you
wa
PROTECTED] [mailto:[EMAIL PROTECTED] On
Behalf Of Waterman, DG (David)
Sent: Wednesday, October 17, 2007 9:18 AM
To: Dieter Best
Cc: r-help@r-project.org
Subject: Re: [R] How to speed up multiple for loop over list of data frames
I agree. Avoid the lines like:
iv = c( iv, min(i, j) )
I had co
October 2007 15:57
To: jim holtman
Cc: r-help@r-project.org; Dieter Best
Subject: Re: [R] How to speed up multiple for loop over list of data
frames
I suspect the vast majority of time is because of growing objects.
Preallocate 'iv', 'jv', 'rho_sv' and 'rho_pv
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
[EMAIL PROTECTED]
+44 (0)20 8525 0696
http://www.burns-stat.com
(home of S Poetry and "A Guide f
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 t
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 =
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