[R-sig-eco] Calculate similarity matrix for category data in R

[Yong Zhang]

Dear list,

Actually, I know how to creat the distance(similarity) matrix for quantitive data, and the "package" for doing this is summaried well by Gavin Simpson. As you can find here: http://cran.r-project.org/web/views/Environmetrics.html

Now, what I encount maybe another situation, I have a data set with 20 species, and their taxonomic units (Order, Family and Genus).  To describe my question more clearly, the data set is listed as below:

                 G                 F              O
spe1         G1              F1           O1
spe2         G1              F1           O1
spe3         G2              F2           O1
spe4         G3              F3           O2
spe5
.
.
.
.
spe20      G15             F10           O5

Note: spe1 to spe20 means the 20 species, G, F, and O are the abbreviations for Genus, Family and Order (the 3 different taxonomic units).  From above, you can find that these 20 species belong to 5 Order, 10 Family and 15 Genus (i.e., species1 and species2 are classified into the same taxonomic units, however, species2 and species3 are different at the Genus level). 

What I'd like to do is creating the similarity (distance) matrix based on the above data set.  I'm wondering if this is possible to deal with this in R, and which package is my correct choice?

Hope I make my point clear, and thanks very much for any hints in advance.

Best regards,
Yours Yong




ZHANG Yong
Lab of aquatic insects & stream ecology
Dept.of Entonology, Nanjing Agricultural University
Nanjing, 210095,China 
Phone number:  (+86) -25-84395241
E-mail:2010202035 at njau.edu.cn