From jorismeys at gmail.com  Wed Nov 17 17:47:51 2010
From: jorismeys at gmail.com (Joris Meys)
Date: Wed, 17 Nov 2010 17:47:51 +0100
Subject: [Rd] Bug in agrep computing edit distance?
In-Reply-To: <C90963B4.2B00%ddickison@carnegielearning.com>
References: <C90963B4.2B00%ddickison@carnegielearning.com>
Message-ID: <AANLkTi=mUOWUPD=7PWkKMHarcHW6rb58TvWnsjEKMUho@mail.gmail.com>

It might have to do something with spaces and the interpretation of
insertions, as far as I understand the following examples :

> agrep("x",c("x","xy","xyz","xyza"),max=list(all=1))
[1] 1 2 3 4
> agrep("x    ",c("x    ","xy  ","xyz ","xyza"),max=list(all=1))
[1] 1
> agrep("xx",c("xx","xyx","xyzx","xyzax",max=list(all=1)))
[1] 1 2 3 4
> agrep("xx",c("xx","xyx","xyzx","xyzax",max=list(ins=1)))
[1] 1 2 3 4
> agrep("xx   ",c("xx   ","xyx  ","xyzx ","xyzax",max=list(all=2)))
[1] 1
> agrep("xx   ",c("xx   ","xyx  ","xyzx ","xyzax",max=list(all=3)))
[1] 1

If the sequences are made the same length in spaces, this function
gives the expected result in the second example, but it definitely
doesn't do that any more when you start playing around with
insertions. If not a bug, it definitely behaves pretty weird...

Cheers
Joris

On Wed, Nov 17, 2010 at 4:49 PM, Dickison, Daniel
<ddickison at carnegielearning.com> wrote:
> I posted this yesterday to r-help and Ben Bolker suggested reposting it
> here...
>
> Dickison, Daniel <ddickison <at> carnegielearning.com> writes:
>
>>
>> The documentation for agrep says it uses the Levenshtein edit distance,
>> but it seems to get this wrong in certain cases when there is a
>> combination of deletions and substitutions. ?For example:
>>
>> > agrep("abcd", "abcxyz", max.distance=1)
>> [1] 1
>>
>> That should've been a no-match. ?The edit distance between those strings
>> is 3 (1 substitution, 2 deletions), but agrep matches with max.distance
>>>=
>> 1.
>>
>> I didn't find anything in the bug database, so I was wondering if somehow
>> I'm misinterpreting how agrep works. ?If not, should I file this in
>> Bugzilla?
>>
>
> ?Could you re-post this on r-devel? ?It definitely sounds like
> this is worth following up. ?Based on a little bit of playing around,
> it's quite clear that I don't understand what's going on. ?The examples
> show things like
>
> agrep("lasy","lazy",max=list(sub=0))
>
> ?which makes sense, but
>
> agrep("lasy","lazybc",max=1)
> agrep("lasy","lazybc",max=0.001)
> agrep("lasy","layt",max=list(all=1))
>
> and
>
> agrep("x",c("x","xy","xyz","xyza"),max=list(insertions=2))
> agrep("x",c("x","xy","xyz","xyza"),max=list(deletions=2))
> agrep("x",c("x","xy","xyz","xyza"),max=list(all=2))
>
> ?all give "1 2 3 4" ??
>
> ?this makes it clear that I really don't understand what's going on
> based on the documentation. ?I tried to trace into the C code
> (which calls functions from the TRE regexp library) but that didn't
> help much ...
>
>
>
> Daniel ?Dickison
> Research Programmer
> ddickison at carnegielearning.com
> Toll Free: (888) 851-7094 x103
> FAX: (412) 690-2444
>
> Revolutionary Math Curricula. Revolutionary Results.
>
> Carnegie Learning, Inc. | 437 Grant St. 20th Floor | Pittsburgh, PA 15219
> www.carnegielearning.com
>
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>



-- 
Joris Meys
Statistical consultant

Ghent University
Faculty of Bioscience Engineering
Department of Applied mathematics, biometrics and process control

tel : +32 9 264 59 87
Joris.Meys at Ugent.be
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[Rd] Bug in agrep computing edit distance?
Joris Meys