[R] testing whether two character vectors contain (the same) items in the same order

[David Winsemius]

On Aug 7, 2015, at 12:22 AM, Federico Calboli wrote:

> 
>> On 7 Aug 2015, at 01:59, Bert Gunter <bgunter.4567 at gmail.com> wrote:
>> 
>> Boris:
>> 
>> You may be right, but it seems like esp to me based on the op's non-description of likelihood of coming from the same noisy process. My response would be: seek local statistical help, as your replies indicate a good deal of statistical confusion.
>> 
>> Cheers,
>> Bert
> 
> Bert,
> 
> as this is R-help and not cross-validated I am looking for a precanned function that would test whether the order of characters in two character vectors comes from the same (noisy) process.  I would thus expect you to say something on the lines of:
> 
> function X uses method Y to do something like that
> function W uses method Z to do something like that
> …
> 
> look into those, figure out exactly what you are testing and use the most appropiate function.  
> 
> The whys and wherefores are for me to deal with, I just want to know whether someone has built a function that does, or seems to do, what I asked for.  As I said, this is R-help, and I seek help for R use.

> findFn("levenshtein")
found 57 matches;  retrieving 3 pages
2 3 
Downloaded 44 links in 17 packages.


 stringdist::stringdist( paste0(x, collapse=""), paste0(letters[y], collapse="") )
[1] 30

-- 
HTH;
David.

> 
> I do concede that my original question might have left many wondering, but I guess my reply to Boris would have cleared any doubts.  I am therefore puzzled by the great deal of confusion on your part in understanding the purpose of my question and, in general, of this list.
> 
> Best wishes
> 
> F
> 
> 
>> 
>> 
>> 
>> On Thursday, August 6, 2015, Boris Steipe <boris.steipe at utoronto.ca> wrote:
>> You are looking for what is known as the "Cayley distance" between vectors - an edit distance that allows only transpositions. RSeek mentions PerMallows (https://cran.r-project.org/web/packages/PerMallows/PerMallows.pdf) and Rankluster (https://cran.r-project.org/web/packages/Rankcluster/Rankcluster.pdf) as packages that support work with Cayley distances. It seems to me that distCayley() in Rankcluster does what you want. From the examples:
>> 
>> x=1:5
>> y=c(2,3,1,4,5)
>> distCayley(x,y)
>> 8
>> 
>> 
>> Cheers,
>> Boris
>> 
>> 
>> 
>> 
>> 
>> On Aug 6, 2015, at 9:51 AM, Federico Calboli <federico.calboli at helsinki.fi> wrote:
>> 
>>>> 
>>>> On 6 Aug 2015, at 15:40, Bert Gunter <bgunter.4567 at gmail.com> wrote:
>>>> 
>>>> Define "goodness of match" .  For exact matches, see ?"==" , all.equal, etc.
>>> 
>>> Fair point.  I would define it as a number that tells me how likely it is that the same (noisy) process produced both lists.
>>> 
>>> BW
>>> 
>>> F
>>> 
>>> 
>>> 
>>> 
>>>> 
>>>> Bert
>>>> 
>>>> On Thursday, August 6, 2015, Federico Calboli <federico.calboli at helsinki.fi> wrote:
>>>> Hi All,
>>>> 
>>>> let’s assume I have a vector of letters drawn only once from the alphabet:
>>>> 
>>>> x = sample(letters, 15, replace = F)
>>>> x
>>>> [1] "z" "t" "g" "l" "u" "d" "w" "x" "a" "q" "k" "j" "f" "n" “v"
>>>> 
>>>> y = x[c(1:7,9:8, 10:12, 14, 15, 13)]
>>>> 
>>>> I would now like to test how good a match y is for x.  Obviously I can transform the letters in numbers and use a rank test, but I was left wondering whether this is the only solution and whether there are more appropriate solutions that are already implemented in R (I am not going to reinvent the wheel if I can avoid it).
>>>> 
>>>> BW
>>>> 
>>>> F
>>>> 
>>>> 
>>>> --
>>>> Federico Calboli
>>>> Ecological Genetics Research Unit
>>>> Department of Biosciences
>>>> PO Box 65 (Biocenter 3, Viikinkaari 1)
>>>> FIN-00014 University of Helsinki
>>>> Finland
>>>> 
>>>> federico.calboli at helsinki.fi
>>>> 
>>>> ______________________________________________
>>>> R-help 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.
>>>> 
>>>> 
>>>> --
>>>> Bert Gunter
>>>> 
>>>> "Data is not information. Information is not knowledge. And knowledge is certainly not wisdom."
>>>>  -- Clifford Stoll
>>>> 
>>> 
>>> 
>>> --
>>> Federico Calboli
>>> Ecological Genetics Research Unit
>>> Department of Biosciences
>>> PO Box 65 (Biocenter 3, Viikinkaari 1)
>>> FIN-00014 University of Helsinki
>>> Finland
>>> 
>>> federico.calboli at helsinki.fi
>>> 
>>> ______________________________________________
>>> R-help 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-help 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.
>> 
>> 
>> -- 
>> Bert Gunter
>> 
>> "Data is not information. Information is not knowledge. And knowledge is certainly not wisdom."
>>   -- Clifford Stoll
>> 
> 
> 
> --
> Federico Calboli
> Ecological Genetics Research Unit
> Department of Biosciences
> PO Box 65 (Biocenter 3, Viikinkaari 1)
> FIN-00014 University of Helsinki
> Finland
> 
> federico.calboli at helsinki.fi
> 
> ______________________________________________
> R-help 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.

David Winsemius
Alameda, CA, USA