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The TWINSPAN program
6 messages · Diogo B. Provete, Gavin Simpson, Jari Oksanen +1 more
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 but to claim TWINSPAN is not used because it has been superseded by the IndVal approach is totally incorrect.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. G
Good Luck, Diogo 2011/4/13 <r-sig-ecology-request at r-project.org>
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https://stat.ethz.ch/mailman/listinfo/r-sig-ecology or, via email, send a message with subject or body 'help' to r-sig-ecology-request at r-project.org You can reach the person managing the list at r-sig-ecology-owner at r-project.org When replying, please edit your Subject line so it is more specific than "Re: Contents of R-sig-ecology digest..." Today's Topics: 1. The TWINSPAN program (Yong Zhang) ---------- Mensagem encaminhada ---------- From: "Yong Zhang" <2010202035 at njau.edu.cn> To: "r-sig-ecology" <r-sig-ecology at r-project.org> Date: Wed, 13 Apr 2011 17:06:24 +0800 Subject: [R-sig-eco] The TWINSPAN program Helo all, These days, when I looked into the multivariate analysis of community data, I noticed that there is a very useful classification approach named "TWINSPAN", maybe most of you already know that its full name is "Two-way indicator species analysis", and the program has the same name---TWINSPAN. Could any one tell me whether this program is for free? And when and how could get one? Any hint or suggestion from you will be greatly appreciated. Thanks very much for your time and answer. All the best, Yong 2011-04-13 ZHANG Yong Lab of aquatic insects & stream ecology Dept.of Entonology, Nanjing Agricultural University Nanjing, 210095,China Phone number: (+86) -25-84395241 E-mail:2010202035 at njau.edu.cn _______________________________________________ R-sig-ecology mailing list R-sig-ecology at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
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%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
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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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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