[R-sig-eco] The final result of TWINSPAN

[Jari Oksanen]

On 14/04/11 10:37 AM, "Yong Zhang" <2010202035 at njau.edu.cn> wrote:

> Dear all,
> 
> I conducted the two-way indicator species analysis using TWINSPAN program, and
> following is the final result:
>     
>                  000000000000000000000111
>                  000000000001111111111011
>                  011111111110000000111
>                   01111111110000001001
> 
> I have to certify my analysis, I want to classify the above 24 sampling sites
> into 3 major groups based on 7 biotic metrics. The name of my 24 samples could
> be site1 to site24, from the left to the right, and I set the cut levels 0, 2,
> 5, 10, 20,  the maximum level of divisions: 6, and maximum group size for
> division:3 .  
> 
> Now, my question is whether my setting is correct? And how should I classify
> these sites into 3 groups accoding to this final result?
Dear Yong Zhang,

This is not an R issue, because there is no TWINSPAN in R. However, the
answer to your question is that strictly speaking you cannot group your data
into three major groups with TWINSPAN. TWINSPAN is a bisection method so
that first division gives you two groups, and second splits each of these
into two groups so that the next choice is to have four groups. However, in
this case one of the groups was so small (3 plots were split off from other
in the first division, and then these were split into groups of 2 plots and
1 plot) that you probably can ignore the second division of the small group.

If your goal was as vague as wanting to classify 24 sites into 3 major
groups you could do better than use TWINSPAN: what's the problem with proper
classification methods in R? Moreover, have you checked that your "biotic
metrics" suit to the pseudospecies cut level concept of TWINSPAN?

Cheers, jari oksanen