R help - Aug 2015 - testing whether two character vectors contain (the same) items in the same order

> 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

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.

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



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
> <javascript:;>> wrote:
>
> >>
> >> On 6 Aug 2015, at 15:40, Bert Gunter <bgunter.4567 at gmail.com
> <javascript:;>> 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 <javascript:;>> 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 <javascript:;>
> >>
> >> ______________________________________________
> >> R-help at r-project.org <javascript:;> 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 <javascript:;>
> >
> > ______________________________________________
> > R-help at r-project.org <javascript:;> 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 <javascript:;> 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

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