I'm not sure I understand your question. Both functions return ""
"CD" "" because they perform exact string matching. The
first demonstrates how string or character replacements can be vectorized, while
the second merely demonstrates how Rcpp can accelerate this type of operation.
Cheers,
Adam
> On Jul 30, 2015, at 21:09, John Thaden <jjthaden at flash.net> wrote:
>
>
> Can you show what is its solution for the original sample data? Why that
discrepancy for you original sub2() function?
>
> From:"Adam Erickson" <adam.michael.erickson at gmail.com>
> Date:Thu, Jul 30, 2015 at 6:11 pm
> Subject:Re: [R] vectorized sub, gsub, grep, etc.
>
> 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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