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

[Dave Roberts]

Dear Zoltan,

    Thanks for the note.  The R function I wrote does in fact follow the 
Roleček et al protocol, and that's partly what motivated the idea to 
write it up. Lubomír Tichý, Petr Smilauer, and Laco Mucina have all 
contributed information in the development, but I've still been stymied 
by the lack of solid information on the actual algorithm.

    I think it is quite possible to write a function that operates on 
the principle of TWINSPAN, following Roleček et al, but writing a 
function that exactly matches the output from the commercial package may 
prove to be too much trouble.

Thanks, Dave

Zoltan Botta-Dukat wrote:
> Dear Dave,
> 
> This modified version of TWINSPAN may be interesting for you when you 
> compare methods:
> 
> Modified TWINSPAN classification in which the hierarchy respects cluster 
> heterogeneity
> 
> Jan Roleček, Lubomír Tichý, David Zelený, Milan Chytrý 2009 Modified 
> TWINSPAN classification in which the hierarchy respects cluster 
> heterogeneity Journal of Vegetation Science 20(4): 596–602
> http://onlinelibrary.wiley.com/doi/10.1111/j.1654-1103.2009.01062.x/abstract 
> 
> 
> Zoltan
> 
> 2011.04.26. 23:40 keltezéssel, Dave Roberts írta:
>> 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.
>>
> 
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