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

[Gavin Simpson]

Dear Yong,

This *is* a list about R. Your question has *nothing* to do with R.
Please ask such questions elsewhere, like the ORDNEWS list.

On Thu, 2011-04-14 at 15:37 +0800, Yong Zhang wrote:
<snip />
> I conducted the two-way indicator species analysis using TWINSPAN
> program, and following is the final result:

Being painfully aware of the output TWINSPAN generates, I'm certain this
isn't all that TWINSPAN output, but I presume it is the binary indicator
for the groups/splits from the output?

>                  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 .  

Then you are out of luck, without using some other means of pruning back
divisions. TWINSPAN implements a binary split process, and without other
intervention you get 0, 2, 4, 8, 16 groups etc. You /can/ post-process
the results of TWINSPAN using another DOS application to merge lower
nodes of certain, specific branches into higher nodes to get different
numbers of groups than 2, 4, 8, ..., but I forget the name of this DOS
application at the moment - I used to teach a computer class using this
so I have the details somewhere so will see if I can hunt those old
notes out.

My interpretation of the above would be that you could just ignore the
split that cuts the 3 extreme right samples into two groups so you have
groups consisting of the first 11 samples, the next 10 in another group,
and the final 3 samples in a group. But that is without seeing any of
the other output, so I don't know if the CA clustering technique used is
doing silly things splitting your main group of samples - i.e. are there
samples close to the origin but on opposite sides that are similar to
one another but which have been pushed into separate groups?

Hopefully the above helps, but please direct further and future requests
for help with non-R applications to more appropriate lists.

G

> Now, my question is whether my setting is correct? And how should I
> classify these sites into 3 groups accoding to this final result?
> 
> Thanks in advance for your time and suggestion.
> 
> Kind wishes,
> 
> Yong 
> 
> 
> 2011-04-14 
> 
> 
> 
> 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
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