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

2011-04-14 Thread Jari Oksanen
On 14/04/11 10:37 AM, Yong Zhang 2010202...@njau.edu.cn wrote:

 Dear all,
 
 I conducted the two-way indicator species analysis using TWINSPAN program, and
 following is the final result:
 
  0111
  00011011
  011000111
   01001001
 
 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

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

2011-04-14 Thread 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?

  0111
  00011011
  011000111   
   01001001 
 
 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:2010202...@njau.edu.cn
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