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 drobe...@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"<2010202...@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 drobe...@montana.edu
Montana State University
Bozeman, MT 59717-3460

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