Outer loop variable in nested R foreach loop

Question

I'm trying to use the foreach package in a nested loop, but my inner loop don't recognizes the outer's counter, what m I missing?

v3 <- search.compounds.by.mass(100.05,0.5)
foreach(j=2:length(v2)) %:% {
    foreach(i=1:length(v3), .combine=rbind) %dopar% {
        write.table(paste(v3[i], paste(get.reactions.by.compound(v3[i]), collapse=" "), sep=" "), "file1",quote=FALSE, row.names=FALSE, col.names=FALSE, append=TRUE)
        write.table(paste(v3[i], paste(get.pathways.by.compounds(v3[i]), collapse=" "), sep=" "), "file2",quote=FALSE, row.names=FALSE, col.names=FALSE, append=TRUE)
        v3 <- search.compounds.by.mass(v2[j],0.5)
    }
}

Agnew

What is the error message? Also, what is in the variable v2 (you can use dput(v2) so we can reproduce it) – Rosary

Answer 1

The problem is that you are incorrectly applying the %:% operator. It is designed to merge two foreach objects, resulting in a single foreach object that can be used to repeatedly evaluate whatever expression you supply to it. So, if you want to use %:%, you need to first merge the two foreach() statements, and then use the resulting object to drive a single call to %do% (or in your case, %dopar%). See (1) below for an example.

Alternatively, if you want to nest the two foreach() objects, use %do% twice, as in (2) below.

Either way works, although for parallel jobs I might prefer the one using %:%. Your code, though, like (3) below, combines elements of the two strategies to produce a hybrid that can't do anything.

X <- c("A", "B")
Y <- 1:3

## (1) EITHER merge two 'foreach' objects using '%:%' ...
foreach (j = X, .combine = c) %:% foreach(i = Y, .combine = c) %do% {
    paste(j, i, sep = "")
}
# [1] "A1" "A2" "A3" "B1" "B2" "B3"


## (2) ... OR Nest two 'foreach' objects using a pair of '%do%' operators ...
foreach(j = X, .combine = c) %do% {
    foreach(i = Y, .combine = c) %do% {
        paste(j, i, sep = "")
    }
}
# [1] "A1" "A2" "A3" "B1" "B2" "B3"


## (3) ... BUT DON'T use a hybrid of the approaches.
foreach(j = X, .combine = c) %:% {
    foreach(i = Y, .combine = c) %do% {
        paste(j, i, sep = "")
    }
}
# Error in foreach(j = X, .combine = c) %:% { : 
#   "%:%" was passed an illegal right operand

Hecht

Good to hear. By the way, if you want to read more about some of the decisions involved in how to structure nested loops, type vignette("nested") at the R command line. – Loidaloin

It's painful to note that the vignette shows the right way to do it, and explicitly states it's a binary operator, but it's so easy to make this mistake. – Skulduggery