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st: Program bundle for sequence analysis


From   Ulrich Kohler <kohler@wz-berlin.de>
To   statalist@hsphsun2.harvard.edu
Subject   st: Program bundle for sequence analysis
Date   Tue, 8 Aug 2006 17:46:27 +0200

Dear all,

on behalf of my co-authors Christian Brzinsky-Fay and Magdalena Luniak I like 
to inform you, that a bundle of Stata programs (SQ-Ados) for performing 
sequence analysis has been uploaded to the SSC-Archive. The programs can be 
installed from within Stata with 

. ssc install sq

Sequences are entities build by a limited number of elements that are ordered 
in a specific way. A typical example is the human DNA, where the "Elements" 
Adenin, Cytosin, Guanin and Thymin (the "organic Bases") are ordered into a 
sequence. Other sequences are songs, that are build by tones that appear in a 
specific order, or careers of employers that are build by specific 
job-positions and ordered along time.

The SQ-Ados are a bundle of commands to describe, analyze and group the 
sequences of a sequence dataset. As it stands the following sq commands are 
available:

   sqset             Declare data to be sequence data
   sqdes             Describe sequences
   sqtab             Tabulate sequences
   sqegen            Generate variables reflecting entire sequences
   sqstat            Describe, summarize, and tabulate sq-egenerated variables
                            sequences
   sqindexplot       Graph sequences as sequence index plot
   sqparcoord        Graph sequences with parallel coordinates.
   sqom              Optimal matching of sequences
   sqclusterdat      Prepare a dataset to perform Cluster analyses on the
                            results of sqom
   sqclustermat      Perform one Cluster analysis on the results of sqom

All programs are fully documented with help files. In addition -help sq- 
provides a general introduction and -help sqdemo- a software demonstration. 
An article for the Stata Journal is "in the making".

Installation note
------------------

Installation of the SQ-Ados conflicts with the older SQ-package by Nick Cox. 
Users of this package need to install the SQ-Ados with

. ssc install sq, replace

and reinstall Nicks package with

. ssc install sqr

Here is Kit Baum's explanation for breaking the rule that the first claimant 
of a name has rights to the name:

> ... There was a little problem, which was not immediately  
> apparent as you do not actually have a sq.ado. The module name SQ was  
> already in use within SSC by Nick Cox for a graph7 utility. As I did  
> not detect this problem until partway through the installation, I did  
> not follow the usual rule that the first claimant of a name has  
> rights to the name. As your package is very large and complicated,  
> and has been designed for Stata 9 with Mata components, I decided to  
> exercise the discretion to rename Nick's sq routine to sqr (it makes  
> old-style graphs square). That seemed more straightforward than  
> insisting that you rename your entire suite of routines something  
> like 'seq'; 

My apologies to Nick for taking over his name, and many thanks to Kit Baum for 
not forceing me to change the SQ-Ado bundle.

Many regards

Ulrich Kohler

-- 
kohler@wz-berlin.de
+49 (030) 25491-361
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