[Traminer-users] Re : Re: longest common substring

[Matthias Studer]

Dear Hadrien,

Actually, there is no function to compute the longest common substring 
in TraMineR and, unfortunately, there is no easy way to modify the 
seqdist function (which relies on C code for performance reason). A 
custom function is thus needed. If you find a solution, please post it 
to this list, as it may interest other (or future) users.

All the best,
Matthias


Le 19.03.2012 16:30, Hadrien Commenges a écrit :
> Thank you Chris. I checked the TraMineR Extras package, but there is 
> no function to compute the longest common substring. I don't know if 
> the developers could give me an easy way to modify the seqdist 
> function in order to compute longest common substring. If not, I'm 
> very interested in the ideas you mentioned to do that, although I'm 
> not a good programmer and I don't know anything about C.
> Thanks,
> Hadrien
>
>
>
> ----- Mail d'origine -----
> De: Chris Cameron <cjc73 at cornell.edu>
> À: Users questions <traminer-users at r-forge.wu-wien.ac.at>
> Envoyé: Sun, 18 Mar 2012 18:48:56 +0100 (CET)
> Objet: Re: [Traminer-users] longest common substring
>
> Hi Hadrien -
>
> I don't see a documented way to compute the greatest common 
> substrings, so a custom function is probably necessary. (Maybe a dev 
> can tell you if there is a hidden flag to indicate substring vs 
> subsequence. The LCS code is implemented in C, so there is not an easy 
> function to modify in the TraMineR package. I have some ideas about 
> how you can make a custom function to do this if you want to talk 
> about it. Before you go that route, it would be worth checking the 
> "TraMineR Extras" package Matthias mentioned on the 16th.
>
> Good Luck
> Chris
>
>
>
>
> On Mar 17, 2012, at 3:02 PM, Hadrien Commenges wrote:
>
>     Hi,
>
>     I've a new question. I'd like to get a dissimilarity matrix based
>     on the longest common substring. The longest prefix (computed with
>     seqdist, method=LCS) doesn't work for me because I'd like to
>     compare substrings anywhere in the sequence. And the notion of
>     subsequence (computed with seqdist, method=LCS) doesn't serve my
>     purpose neither. I'd like to compute something like the LCS method
>     but with the stricter notion of substring. Is it possible?
>
>     Thanks,
>
>     Hadrien
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