[R-sig-eco] The TWINSPAN program

[Gavin Simpson]

On Wed, 2011-04-13 at 15:01 +0200, Andres Mellado Diaz wrote:
> Hi,
> 
> I think that TWINSPAN and IndVal are not so different (well, it's true
> that you can use your own a-priori clustering method in IndVal,
> because its use is independent of the classification method), in fact,
> TWINSPAN is cited 38 times in Dufrene & Legendre 1997 IndVal paper.
> They largely discuss differences and limitations between both methods
> throughout their article, 

???

TWINSPAN /provides/ indicator values, but it is not its raison d'etre.
It *was* designed to *cluster* vegetation data in the two-way manner
Jari mentions and provides the indicator values as one of extra outputs.
In the past, one would have to use TWINSPAN to get indicator values
because there weren't many (any?) other options for computing them, but
if you wanted indicator values then you had to accept the TWINSPAN
clustering too - there was no either/or.

IndVal changed that so you *could* compute good indicator values along
the same lines as TWINSPAN but without having to use it esoteric
clustering algorithm. Of course Dufrene and Pierre cite the TWINSPAN
paper a lot; they were producing a new tool that at the grossest level
did something (one part) that TWINSPAN did and therefore could be
compared against.

Your entire email is focussed on one aspect of TWINSPAN and the
similarities between it and IndVal - you aren't seeing the woods for the
trees. TWINSPAN and IndVal are different beasts.

To your argument I might offer the repost: "post hoc ergo propter
hoc" (in a bastardised way: TWINSPAN and IndVal give me indicator
values, therefore TWINSPAN and IndVal are the same. ;-)

G

> cheers
> 
> Andrs
> 
> Jari Oksanen <jari.oksanen at oulu.fi> escribi:
> 
> > 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 because it has been superseded by the IndVal approach is totally
> >> incorrect.
> >>
> >> 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.
> >>
> > Howdy all,
> >
> > 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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> >
> 
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