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

[Dave Roberts]

Dear List,

     Earlier this year on an (undoubtedly ill-advised) lark I coded up 
an R version of TWINSPAN.  It's far from a polished package at this 
point, but the code does run.  One of the interesting features is that 
you can partition a PCO or NMDS in addition to the traditional CA. To be 
clear, I am not a TWINSPAN fan either, but I wanted it for a methods 
paper I was working on.

     The problem is that I based the code on Hill, Bunch & Shaw (1975,
J of  Ecol  63:597-613) which is what I had available.  Apparently the 
algorithm in the commercial TWINSPAN is significantly modified from the 
original, but I couldn't find a description of the actual algorithm 
anywhere in the literature.  It is probably described in the User Manual 
of the software, but I was not sufficiently motivated to chase down a 
copy.  I do have a copy of the FORTRAN code, but it was apparently 
written in FORTRAN II, and is basically inscrutable, even to an old 
FORTRAN dog like me.

     So, if somebody has a clear description of the actual algorithm 
(and I think it is disturbing that I could not find one), it would be 
possible to code it up in native R.  The alternative, to write a wrapper 
for the original FORTRAN code is not a trivial task.  I gave it a couple 
of days and gave up.

-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
David W. Roberts                                     office 406-994-4548
Professor and Head                                      FAX 406-994-3190
Department of Ecology                         email droberts at montana.edu
Montana State University
Bozeman, MT 59717-3460

On 04/14/2011 01:57 AM, Jari Oksanen wrote:
> 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
>
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-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
David W. Roberts                                     office 406-994-4548
Professor and Head                                      FAX 406-994-3190
Department of Ecology                         email droberts at montana.edu
Montana State University
Bozeman, MT 59717-3460