optimising a loop

-----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 sp?ciaux
Direction des inventaires forestiers
Minist?re des Ressources naturelles et de la Faune du Qu?bec