[R] vectorized sub, gsub, grep, etc.
Christos Hatzis
christos at nuverabio.com
Thu Oct 9 06:11:25 CEST 2008
Hi John,
As I mentioned in our private exchange, this is well known in R, i.e.
vectorized versions are not always faster or more efficient than straight
loops. It is a misconception that loops should be avoided at any cost. See
John Fox's illuminating article on Rnews (p. 46) on this subject.
http://cran.r-project.org/doc/Rnews/Rnews_2008-1.pdf
To me, unless the application is way too demanding, I take the vectorized
version over the loop any day, as it is much simpler to write, usually a
one-liner, and therefore much easier to maintain in the long run.
-Christos
> -----Original Message-----
> From: r-help-bounces at r-project.org
> [mailto:r-help-bounces at r-project.org] On Behalf Of john
> Sent: Thursday, October 09, 2008 12:38 AM
> To: r-help
> Subject: Re: [R] vectorized sub, gsub, grep, etc.
>
> Hello Christos,
> To my surprise, vectorization actually hurt processing speed!
>
> #Example
> X <- c("ab", "cd", "ef")
> patt <- c("b", "cd", "a")
> repl <- c("B", "CD", "A")
>
> sub2 <- function(pattern, replacement, x) {
> len <- length(x)
> if (length(pattern) == 1)
> pattern <- rep(pattern, len)
> if (length(replacement) == 1)
> replacement <- rep(replacement, len)
> FUN <- function(i, ...) {
> sub(pattern[i], replacement[i], x[i], fixed = TRUE)
> }
> idx <- 1:length(x)
> sapply(idx, FUN)
> }
>
> system.time( for(i in 1:10000) sub2(patt, repl, X) )
> user system elapsed
> 1.18 0.07 1.26
>
> system.time( for(i in 1:10000) mapply(function(p, r, x)
> sub(p, r, x, fixed = TRUE), p=patt, r=repl, x=X) )
> user system elapsed
> 1.42 0.05 1.47
>
> So much for avoiding loops.
> John Thaden
>
> ======= At 2008-10-07, 14:58:10 Christos wrote: =======
>
> >John,
> >Try the following:
> >
> > mapply(function(p, r, x) sub(p, r, x, fixed = TRUE),
> p=patt, r=repl, x=X)
> > b cd a
> >"aB" "CD" "ef"
> >
> >-Christos
>
> >> -----My Original Message-----
> >> R pattern-matching and replacement functions are
> >> vectorized: they can operate on vectors of targets.
> >> However, they can only use one pattern and replacement.
> >> Here is code to apply a different pattern and replacement
> for every
> >> target. My question: can it be done better?
> >>
> >> sub2 <- function(pattern, replacement, x) {
> >> len <- length(x)
> >> if (length(pattern) == 1)
> >> pattern <- rep(pattern, len)
> >> if (length(replacement) == 1)
> >> replacement <- rep(replacement, len)
> >> FUN <- function(i, ...) {
> >> sub(pattern[i], replacement[i], x[i], fixed = TRUE)
> >> }
> >> idx <- 1:length(x)
> >> sapply(idx, FUN)
> >> }
> >>
> >> #Example
> >> X <- c("ab", "cd", "ef")
> >> patt <- c("b", "cd", "a")
> >> repl <- c("B", "CD", "A")
> >> sub2(patt, repl, X)
> >>
> >> -John
>
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