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
<ddicki...@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
ddicki...@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.m...@ugent.be
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