"missing" and just "does not apply"

[Derek Sikes]

Dear taxacomers,

I'm sure there are some good references about this issue (which, if any of you could provide for the list, we would all be grateful, I'm sure) but I ran some simple tests to confirm and demonstrate that one should not distinguish between missings and innaplicables.  I made a simple web page to display the results to those interested:

http://viceroy.eeb.uconn.edu/sikesff/inapplicable/inapplicable.htm

If I understand Dr.  Boeger's problem correctly- but perhaps he is dealing with a different issue...

Yours,

Derek Sikes



you wrote:

Hi all,

I am sure a lot of you, that deal with PAUP* (and other computer phylogeny software), already ran into this same question.  How to distinguish between really "missing" and just "does not apply" characters?   Was anyone sucessful in doing that???  I have tried to use a distinct code (say, a "x") for these "does not apply" states and built a usertype stepmatrix to indicate that the "cost" of going from any other state to "x" would be "0" (hoping that this means "do not consider the "x" " for the software), but was not successfull since PAUP did not accept the stepmatrix below:

begin assumptions;
 usertype unav (stepmatrix)=6 01234x

 - 1 2 3 4 0
 1 - 1 2 3 0
 2 1 - 1 2 0
 3 2 1 - 1 0
 4 3 2 1 - 0
 0 0 0 0 0 -;



Well....I would reaaaallly appreciate if anyone of you has some ï   
suggestion on how to handle with this problem...

***********************************
Walter A. Boeger, Ph.D.
Dept Zoologia, UFPR
Caixa Postal 19073
Curitiba, PR 81531-990
Brasil
phone: 55413663144 ext. 206
fax: 55412662042
wboeger at bio.ufpr.br
http://zoo.bio.ufpr.br/departamento
ICQ:  36546488
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So many worms...so little time
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Derek Sikes
Dept. of Ecology and Evol. Biology U-43
University of Connecticut
Storrs, CT 06269  USA

FAX: 860-486-6364

dss95002 at uconnvm.uconn.edu
http://viceroy.eeb.uconn.edu/sikes

"Remember that Truth alone is the matter you are in Search after; and if you have been mistaken, let no Vanity reduce you to persist in your mistake." Henry Baker, London, 1785
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