[R] optimising a loop

[William Dunlap]

Try replacing your for loop with the line
   loop[cbind(as.vector(row(voisin)), match(voisin, nom.plac2))] <- as.vector(wei2)

Look help(Subscript) to see how subscripting an n-way array by
an n-column integer matrix works.

Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com 

> -----Original Message-----
> From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On Behalf Of Bastien.Ferland-
> Raymond at mrnf.gouv.qc.ca
> Sent: Thursday, November 03, 2011 10:25 AM
> To: r-help at r-project.org
> Subject: [R] optimising a loop
> 
> Dear R community,
> 
> I'm trying to remove a loop from my code but I'm stock and I can't find a good way to do it.
> Hopefully one of you will have something clever to propose.
> 
> Here is a simplified example:
> 
> I have a squared matrix:
> 
> > nom.plac2 <- c("102", "103", "301", "303","304", "403")
> > poids2 <- matrix(NA, 6,6, dimnames=list(nom.plac2,nom.plac2))
> > poids2
>     102 103 301 303 304 403
> 102  NA  NA  NA  NA  NA  NA
> 103  NA  NA  NA  NA  NA  NA
> 301  NA  NA  NA  NA  NA  NA
> 303  NA  NA  NA  NA  NA  NA
> 304  NA  NA  NA  NA  NA  NA
> 403  NA  NA  NA  NA  NA  NA
> 
> I want to replace some of the NAs following specific criterion included in 2 others matrix:
> 
> > wei2 <- matrix(c(.6,.4,.5,.5,.9,.1,.8,.2,.7,.3,.6,.4),6,2,dimnames=list(nom.plac2,
> c("p1","p2")),byrow=T)
> > wei2
>      p1  p2
> 102 0.6 0.4
> 103 0.5 0.5
> 301 0.9 0.1
> 303 0.8 0.2
> 304 0.7 0.3
> 403 0.6 0.4
> > voisin <- matrix(c("103","304", "303", "102", "103" ,"303","403","304","303","102","103" ,"303"),
>           6,2,dimnames=list(nom.plac2, c("v1","v2")),byrow=T)
> > voisin
>     v1    v2
> 102 "103" "304"
> 103 "303" "102"
> 301 "103" "303"
> 303 "403" "304"
> 304 "303" "102"
> 403 "103" "303"
> 
> So my final result is:
> 
>     102 103 301 303 304 403
> 102  NA 0.6  NA  NA 0.4  NA
> 103 0.5  NA  NA 0.5  NA  NA
> 301  NA 0.9  NA 0.1  NA  NA
> 303  NA  NA  NA  NA 0.2 0.8
> 304 0.3  NA  NA 0.7  NA  NA
> 403  NA 0.6  NA 0.4  NA  NA
> 
> 
> So, globally I want to fill for each line of "poids2" data from "wei2" associated with the good the
> good identifier found in "voisin".
> 
> This can easily be done by a loop:
> 
> > loop <- poids2
> > for(i in 1:6){
> + loop[i,voisin[i,]] <- wei2[i,]
> + }
> 
> But I expect it to be quite slow with my larger dataset.
> 
> Does any of you has an idea how I could remove the loop and speed up the operation?
> 
> Best regards,
> 
> 
> Bastien Ferland-Raymond, M.Sc. Stat., M.Sc. Biol.
> Division des orientations et projets spéciaux
> Direction des inventaires forestiers
> Ministère des Ressources naturelles et de la Faune du Québec
> 
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