R appending data to rows in a loop

Question

I'm trying to run my data frame through a loop to execute a function on each row and update the columns est, ll, and ul with the results. My data frame is onch. The loop seems to be working except the results for est, ll, and ul are the same for each row (presumably the last iteration). Any thoughts would be appreciated!

for (i in 1:nrow(onch)) {
   row <- cbind(onch$c1, onch$c2, onch$c3)
   pr1 <- removal(row)
   a <- summary(pr1)
   onch$est <- a[1]
   b <- confint(pr1)
   onch$ll <- b[1]
   onch$ul <- b[2]
}

the data frame looks like this:

onch

    site    date      c1   c2  c3   est   ll   ul
1   H1     7/11/12    6     2   1   NA     NA   NA
2   H2     7/15/12    12    4   0   NA     NA   NA

Thank you for the help! I still haven't solved the nrow copy issue, but this works:

for (i in 1:nrow(onch)) {

row <- cbind(onch$c1[i], onch$c2[i], onch$c3[i])
pr1<- removal(row)
a<- summary(pr1)
    onch$est[i] <- a[1]
b <- confint(pr1)
    onch$ll[i] <- b[1]
    onch$ul[i] <- b[1,2]
 }

Can you share a sample of the data? For example using the principles explained at: meta.stackexchange.com/questions/155375/… — Jochem
– Jochem, Commented Dec 26, 2012 at 20:06
The first problem I see is that you're not referencing anything with the i. So you're doing the same process invariant of row within the for loop, as there is no i inside the loop. Secondly, because R is assign-by-copy, you are needlessly creating nrow(onch) copies of a data frame when you can probably create just one. Finally, what is the removal function? — Blue Magister
– Blue Magister, Commented Dec 26, 2012 at 20:10

Stephan Kolassa · Accepted Answer · 2012-12-26 20:37:33Z

1

Your line onch$ll <- b[1] overwrites the entire column ll of onch. To only update a specific entry, use onch$ll[ii] <- b[1] for some index ii.

answered Dec 26, 2012 at 20:37

Stephan Kolassa

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Community · Accepted Answer · 2017-05-23 11:58:40Z

0

I think you might be able to benefit from the question and answer given at: How to optimize the following code with nested while-loop? Multicore an option?

This question discusses many of the relevant principles and also indicates on how to optimise (vectorize) the code so in improves the execution.

edited May 23, 2017 at 11:58

CommunityBot

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answered Dec 26, 2012 at 20:09

Jochem

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Blue Magister · Accepted Answer · 2012-12-26 20:44:28Z

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I'll be making edits to this answer to explain it. In the meantime, give this a try. I don't have the FSA package (install.packages is squawking at me that it's not available for R 2.15.2), so I haven't tested it.

onch.removal <- lapply(1:nrow(onch),function(x) {
    pr1 <- removal(c(onch[x,"c1"],onch[x,"c2"],onch[x,"c3"]))
    return(list(est=summary(pr1)[[1]],ll=confint(pr1)[1],ul=confint(pr1)[2]))
})
onch <- data.frame(onch,onch.removal)

answered Dec 26, 2012 at 20:44

Blue Magister

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rafa.pereira · Accepted Answer · 2016-05-27 20:46:33Z

0

There is a fast solution using data.table, no need for loops.

library(data.table)
library(FSA)

setDT(onch)

onch[, v_est := summary(removal(c(c1, c2, c3)))[1] , by= site]
onch[, v_ll := confint(removal(c(c1, c2, c3)))[1] , by= site]
onch[, v_ul := confint(removal(c(c1, c2, c3)))[1,2] , by= site]

answered May 27, 2016 at 20:46

rafa.pereira

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