Re: st: Clustering with Sequence analysis/optimal matching

["Stefan Weih" <Stefan.Weih@wiso.stud.uni-erlangen.de>]

Thanks for your comments, Brendan.

However, as indicated in the correspondance earlier, I did use Ward's
method. Also no typo involved. For the complete syntax on my clustering
procedure, please see below:

sqclusterdat
clustermat wardslinkage SQdist, name(wards) add
cluster tree wards, cutnumber(20)
sqclusterdat, return

Thanks in advance for any further feedback.

Best regards
Stefan
_____________________

> According to my limited understanding of cluster analysis, reversals
> shouldn't occur with Ward's method. They are expected with some other
> methods.

> Did you actually use Ward's method?

> Is your distance matrix actually called wards or is that a typo in your
-cluster tree- command?

> Brendan
-- 
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> Ireland
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________________________

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 There is a newer version of the program available on SSC.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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