On Aug 7, 2015, at 12:22 AM, Federico Calboli wrote: > >> On 7 Aug 2015, at 01:59, Bert Gunter <bgunter.4...@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.ste...@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.calb...@helsinki.fi> >> wrote: >> >>>> >>>> On 6 Aug 2015, at 15:40, Bert Gunter <bgunter.4...@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.calb...@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.calb...@helsinki.fi >>>> >>>> ______________________________________________ >>>> R-help@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.calb...@helsinki.fi >>> >>> ______________________________________________ >>> R-help@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@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.calb...@helsinki.fi > > ______________________________________________ > R-help@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 ______________________________________________ R-help@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.