[R] interval between specific characters in a string...

[Hervé Pagès]

On 03/12/2022 07:21, Bert Gunter wrote:
> Perhaps it is worth pointing out that looping constructs like lapply() can
> be avoided and the procedure vectorized by mimicking Martin Morgan's
> solution:
>
> ## s is the string to be searched.
> diff(c(0,grep('b',strsplit(s,'')[[1]])))
>
> However, Martin's solution is simpler and likely even faster as the regex
> engine is unneeded:
>
> diff(c(0, which(strsplit(s, "")[[1]] == "b"))) ## completely vectorized
>
> This seems much preferable to me.

Of all the proposed solutions, Andrew Hart's solution seems the most 
efficient:

   big_string <- strrep("abaaabbaaaaabaaabaaaaaaaaaaaaaaaaaaab", 500000)

   system.time(nchar(strsplit(big_string, split="b", fixed=TRUE)[[1]]) + 1)
   #    user  system elapsed
   #   0.736   0.028   0.764

   system.time(diff(c(0, which(strsplit(big_string, "", fixed=TRUE)[[1]] 
== "b"))))
   #    user  system elapsed
   #  2.100   0.356   2.455

The bigger the string, the bigger the gap in performance.

Also, the bigger the average gap between 2 successive b's, the bigger 
the gap in performance.

Finally: always use fixed=TRUE in strsplit() if you don't need to use 
the regex engine.

Cheers,

H.


> -- Bert
>
>
>
>
>
> On Sat, Dec 3, 2022 at 12:49 AM Rui Barradas <ruipbarradas using sapo.pt> wrote:
>
>> Às 17:18 de 02/12/2022, Evan Cooch escreveu:
>>> Was wondering if there is an 'efficient/elegant' way to do the following
>>> (without tidyverse). Take a string
>>>
>>> abaaabbaaaaabaaab
>>>
>>> Its easy enough to count the number of times the character 'b' shows up
>>> in the string, but...what I'm looking for is outputing the 'intervals'
>>> between occurrences of 'b' (starting the counter at the beginning of the
>>> string). So, for the preceding example, 'b' shows up in positions
>>>
>>> 2, 6, 7, 13, 17
>>>
>>> So, the interval data would be: 2, 4, 1, 6, 4
>>>
>>> My main approach has been to simply output positions (say, something
>>> like unlist(gregexpr('b', target_string))), and 'do the math' between
>>> successive positions. Can anyone suggest a more elegant approach?
>>>
>>> Thanks in advance...
>>>
>>> ______________________________________________
>>> R-help using 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.
>> Hello,
>>
>> I don't find your solution inelegant, it's even easy to write it as a
>> one-line function.
>>
>>
>> char_interval <- function(x, s) {
>>     lapply(gregexpr(x, s), \(y) c(head(y, 1), diff(y)))
>> }
>>
>> target_string <-"abaaabbaaaaabaaab"
>> char_interval('b', target_string)
>> #> [[1]]
>> #> [1] 2 4 1 6 4
>>
>>
>> Hope this helps,
>>
>> Rui Barradas
>>
>> ______________________________________________
>> R-help using 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.
>>
> 	[[alternative HTML version deleted]]
>
> ______________________________________________
> R-help using 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.

-- 
Hervé Pagès

Bioconductor Core Team
hpages.on.github using gmail.com