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Re: st: Clustering with Sequence analysis/optimal matching


From   "Ed Levitas" <levitas@uwm.edu>
To   <statalist@hsphsun2.harvard.edu>
Subject   Re: st: Clustering with Sequence analysis/optimal matching
Date   Wed, 21 Mar 2012 16:32:43 +0000

Sent from my iPad

On Mar 21, 2012, at 3:25 PM, "Stefan Weih" <Stefan.Weih@wiso.stud.uni-erlangen.de> wrote:

> Uli,
> 
> thank you very much. The update works well regarding the clustering.
> 
> Please, let me ask one more question:
> 
> In determining the optimal number of clusters I tried to create a
> dendrogram using the syntax:
> 
> cluster tree wards, cutnumber(20)
> 
> Unfortunately, it returns the error message "currently can't handle
> dendrogram reversals".
> 
> Am I missing something here? Or is there are a way to make it work?
> Alternatively, is there another command which I could apply? I am thinking
> of e.g. cluster stop (however, I am  not quite sure which variables then
> to use with this command).
> 
> Highly appreciate your support.
> 
> Best regards
> Stefan
> 
> 
>> Stefan,
>> 
>> the problem that you are reporting typcially happens with the version of
>> the program that was distributed togehter with the cited SJ article.
>> There is a newer version of the program available on SSC. Please use
>> 
>> . ado uninstall st0111
>> . ssc install sq
>> 
>> to update to the most recent version of the package.
>> 
>> Note as an aside that the most recent version of the sq-package also has
>> a lot of new features, including further functions for -egen-, a way to
>> apply multidimensional scaling to the distance matrix, decreased
>> overplotting of lines in sequence index plots, and a new graphical
>> device for plotting "ideal typical" sequences (-sqmodalplot-).
>> 
>> Many regards
>> 
>> Uli
>> 
>> 
>> 
>> Am Mittwoch, den 21.03.2012, 11:38 +0100 schrieb Stefan Weih:
>>> Dear Statalist-members,
>>> 
>>> I am currently analyzing diversification strategy sequences with 16
>>> potential sequence states using the sqom (optimal matching) command.
>>> As a common next step I would like to cluster my sqom-results. For this,
>>> I
>>> am using the command sqclusterdat procedure as described in “Sequence
>>> analysis with Stata” (Brzinsky-Fay/Kohler/Luniak, 2006, The Stata
>>> Journal6(4), 435-460). The syntax I am using looks the following:
>>> 
>>> sqset Seq ID Order
>>> 
>>> sqom, subcost(matrixA) full
>>> 
>>> sqclusterdat
>>> clustermat wardslinkage SQdist, name(wards) add
>>> sqclusterdat, return
>>> 
>>> However, the clustering does not work properly. After performing
>>> sqclusterdat, return I keep receiving the following message “Group
>>> results
>>> could not be merged to sequence data. Returned to original sequence
>>> data”.
>>> 
>>> Unfortunately the cause for this message is not obvious to me. I am
>>> thankful for any guidance and hints that can help me out.
>>> 
>>> Sincerely,
>>> Stefan Weih
>>> 
>>> 
>>> The data looks like:
>>> 
>>> ID    Seq    Order
>>> 41    11    1
>>> 41    13    2
>>> 41    11    3
>>> 41    21    4
>>> 42    11    1
>>> 42    13    2
>>> 42    12    3
>>> 42    11    4
>>> 43    14    1
>>> 43    13    2
>>> 43    11    3
>>> 43    12    4
>>> 
>>> 
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>> 
>> 
>> 
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> 
> 
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