[R] vectorized sub, gsub, grep, etc.
Adam Erickson
adam.michael.erickson at gmail.com
Fri Jul 31 01:11:07 CEST 2015
Here is a Rcpp version for exact character matching (for example) written
in C++ that is substantially faster. Hence, I think this is the way to go
where loops may be unavoidable. However, the input vector length has to
match the length of the pattern and replacement vectors, as your original
code did. That can be changed though.
#include <Rcpp.h>
using namespace Rcpp;
// [[Rcpp::export]]
CharacterVector subCPP(CharacterVector pattern, CharacterVector
replacement, CharacterVector x) {
int len = x.size();
CharacterVector y(len);
int patlen = pattern.size();
int replen = replacement.size();
if (patlen != replen)
Rcout<<"Error: Pattern and replacement length do not match";
for(int i = 0; i < patlen; ++i) {
if (*(char*)x[i] == *(char*)pattern[i])
y[x[i] == pattern[i]] = replacement[i];
}
return y;
}
"" "CD" ""
system.time(for(i in 1:50000) subCPP(patt, repl, X))
user system elapsed
0.16 0.00 0.16
Cheers,
Adam
On Wednesday, July 29, 2015 at 2:42:23 PM UTC-7, Adam Erickson wrote:
>
> Further refining the vectorized (within a loop) exact string match
> function, I get times below 0.9 seconds while maintaining error checking.
> This is accomplished by removing which() and replacing 1:length() with
> seq_along().
>
> sub2 <- function(pattern, replacement, x) {
> len <- length(x)
> y <- character(length=len)
> patlen <- length(pattern)
> replen <- length(replacement)
> if(patlen != replen) stop('Error: Pattern and replacement length do not
> match')
> for(i in seq_along(pattern)) {
> y[x==pattern[i]] <- replacement[i]
> }
> return(y)
> }
>
> system.time(for(i in 1:50000) sub2(patt, repl, X))
> user system elapsed
> 0.86 0.00 0.86
>
> Since the ordered vectors are perfectly aligned, might as well do an exact
> string match. Hence, I think this is not off-topic.
>
> Cheers,
>
> Adam
>
> On Wednesday, July 29, 2015 at 8:15:52 AM UTC-7, Bert Gunter wrote:
>>
>> There is confusion here. apply() family functions are **NOT**
>> vectorization -- they ARE loops (at the interpreter level), just done
>> in "functionalized" form. Please read background material (John
>> Chambers's books, MASS, or numerous others) to improve your
>> understanding and avoid posting erroneous comments.
>>
>> Cheers,
>> Bert
>>
>>
>> Bert Gunter
>>
>> "Data is not information. Information is not knowledge. And knowledge
>> is certainly not wisdom."
>> -- Clifford Stoll
>>
>>
>> On Tue, Jul 28, 2015 at 3:00 PM, John Thaden <jjth... at flash.net> wrote:
>> > Adam, The method you propose gives a different result than the prior
>> methods for these example vectors
>> > X <- c("ab", "cd", "ef")
>> > patt <- c("b", "cd", "a")
>> > repl <- c("B", "CD", "A")
>> >
>> > Old method 1
>> >
>> > mapply(function(p, r, x) sub(p, r, x, fixed = TRUE), p=patt, r=repl,
>> x=X)
>> > gives
>> > b cd a
>> > "aB" "CD" "ef"
>> >
>> > Old method 2
>> >
>> > 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)
>> > }
>> > sub2(patt, repl, X)
>> > gives
>> > [1] "aB" "CD" "ef"
>> >
>> > Your method (I gave it the unique name "sub3")
>> > sub3 <- function(pattern, replacement, x) { len <- length(x) y
>> <- character(length=len) patlen <- length(pattern) replen <-
>> length(replacement) if(patlen != replen) stop('Error: Pattern and
>> replacement length do not match') for(i in 1:replen) {
>> y[which(x==pattern[i])] <- replacement[i] } return(y)}sub3(patt, repl,
>> X)
>> > gives[1] "" "CD" ""
>> >
>> > Granted, whatever it does, it does it faster
>> > #Old method 1
>> > system.time(for(i in 1:50000)
>> > mapply(function(p,r,x) sub(p,r,x, fixed = TRUE),p=patt,r=repl,x=X))
>> > user system elapsed
>> > 2.53 0.00 2.52
>> >
>> > #Old method 2
>> > system.time(for(i in 1:50000)sub2(patt, repl, X)) user system
>> elapsed
>> > 2.32 0.00 2.32
>> >
>> > #Your proposed method
>> > system.time(for(i in 1:50000) sub3(patt, repl, X))
>> > user system elapsed
>> > 1.02 0.00 1.01
>> > but would it still be faster if it actually solved the same problem?
>> >
>> > -John Thaden
>> >
>> >
>> >
>> >
>> > On Monday, July 27, 2015 11:40 PM, Adam Erickson <
>> adam.micha... at gmail.com> wrote:
>> >
>> > I know this is an old thread, but I wrote a simple FOR loop with
>> vectorized pattern replacement that is much faster than either of those (it
>> can also accept outputs differing in length from the patterns):
>> > sub2 <- function(pattern, replacement, x) { len <- length(x)
>> y <- character(length=len) patlen <- length(pattern) replen <-
>> length(replacement) if(patlen != replen) stop('Error: Pattern and
>> replacement length do not match') for(i in 1:replen) {
>> y[which(x==pattern[i])] <- replacement[i] } return(y) }
>> > system.time(test <- sub2(patt, repl, XX)) user system elapsed
>> 0 0 0
>> > Cheers,
>> > Adam
>> > On Wednesday, October 8, 2008 at 9:38:01 PM UTC-7, john wrote:
>> > 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______________________________________________
>> > R-h... at r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/r-help
>> > PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> > and provide commented, minimal, self-contained, reproducible code.
>> >
>> >
>> >
>> >
>> > [[alternative HTML version deleted]]
>> >
>> > ______________________________________________
>> > R-h... at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> > https://stat.ethz.ch/mailman/listinfo/r-help
>> > PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> > and provide commented, minimal, self-contained, reproducible code.
>>
>> ______________________________________________
>> R-h... at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
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