[R-sig-eco] The TWINSPAN program
jari.oksanen at oulu.fi
Wed Apr 13 14:47:37 CEST 2011
On 13/04/11 15:34 PM, "Gavin Simpson" <gavin.simpson at ucl.ac.uk> wrote:
> On Wed, 2011-04-13 at 09:25 -0300, Diogo B. Provete wrote:
>> Dear Zang,
>> this procedure is not currently used, since Pierre Legendre and coleagues
>> developed a new metric called IndVal, which is available in the labdsv
>> package in R.
> I'm sorry, (I don't like TWINSPAN...) but to claim TWINSPAN is not used
> because it has been superseded by the IndVal approach is totally
> TWINSPAN and IndVal do **very** different things; the former produces a
> cluster analysis that happens to churn out [a form of] indicator species
> values, whilst the latter **only** computes [a form of] indicator values
> - you have to supply the clustering.
Gavin is absolutely correct here (and I am not a TWINSPAN fan either).
Various clustering methods are the closest thing to Twinspan in base R.
However, they don't provide you species clustering which makes Twinspan
unique. Twinspan works on the original community matrix and produces a
simultaneous classification for plots and species. I don't use
classification but casually, and I don't know if there are such simultaneous
two-way classification problems in R. Indval and friends for quite a
different problem, like Gavin wrote (twice).
As far as I know, Twinspan is not available in R. Two persons have contacted
me and proposed to port Twinspan to R, and I have provided them the basic
files and promised to help them in the work, but I haven't heard anything of
the project after the initial contact.
I do think that Twinspan is a suboptimal choice for classification problems,
but I won't go into details. I urge you to study its behaviour yourself if
get your hands on Twinspan.
Cheers, Jari Oksanen
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