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en:hier-divisive [2019/05/22 10:25]
David Zelený
en:hier-divisive [2019/05/23 09:59] (current)
David Zelený
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 [[{|width: 7em; background-color:​ white; color: navy}hier-divisive_exercise|Exercise {{::​lock-icon.png?​nolink|}}]] [[{|width: 7em; background-color:​ white; color: navy}hier-divisive_exercise|Exercise {{::​lock-icon.png?​nolink|}}]]
  
-<​imgcaption twinspan-orig-modif|>​{{ :​obrazky:​twinspan-original-modified.jpg?​direct|}}</​imgcaption>​+<​imgcaption twinspan-orig-modif|Dendrogram of the original (a) and modified (b) TWINSPAN algorithm. While in the original TWINSPAN, at each level of the division each cluster is divided into two clusters (unless the cluster contains too few samples), in the modified TWINSPAN only the most compositionally heterogeneous cluster is divided into two clusters.>{{ :​obrazky:​twinspan-original-modified.jpg?​direct|}}</​imgcaption>​
  
 **TWINSPAN** (abbreviation standing for __T__wo-__w__ay __in__dicator __sp__ecies __an__alysis) is hierarchical and divisive method of numerical classification,​ which uses the results of ordination (namely CA) to divide the whole dataset into subdivisions. The method has been introduced by Mark O. Hill in 1979. It is not the only divisive algorithm in hand (others like DIANA or COINSPAN exist), but it is with no doubt far the most commonly used one.  **TWINSPAN** (abbreviation standing for __T__wo-__w__ay __in__dicator __sp__ecies __an__alysis) is hierarchical and divisive method of numerical classification,​ which uses the results of ordination (namely CA) to divide the whole dataset into subdivisions. The method has been introduced by Mark O. Hill in 1979. It is not the only divisive algorithm in hand (others like DIANA or COINSPAN exist), but it is with no doubt far the most commonly used one. 
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 TWINSPAN is often criticized by statisticians for being a not-elegant sequence of arbitrary and not fully documented steps but is favoured by ecologists for often returning ecologically intuitive results. Especially vegetation ecologists have a long tradition in using TWINSPAN, which is justified by the fact that the author (M. O. Hill) is himself a vegetation ecologist and he designed the method to closely resemble the traditional Braun-Blanquet approach of classifying vegetation (e.g. because it produces the two-way ordered table and emphasized the use of indicator species with high fidelity to individual groups, <imgref twinspan-table>​). TWINSPAN is often criticized by statisticians for being a not-elegant sequence of arbitrary and not fully documented steps but is favoured by ecologists for often returning ecologically intuitive results. Especially vegetation ecologists have a long tradition in using TWINSPAN, which is justified by the fact that the author (M. O. Hill) is himself a vegetation ecologist and he designed the method to closely resemble the traditional Braun-Blanquet approach of classifying vegetation (e.g. because it produces the two-way ordered table and emphasized the use of indicator species with high fidelity to individual groups, <imgref twinspan-table>​).
  
-<​imgcaption twinspan-table|>​{{:​obrazky:​twinspan-table-vltava.jpg?​direct|}}</​imgcaption>​+<​imgcaption twinspan-table|Two-way ordered table resulting from TWINSPAN algorithm (this example is based on Vltava dataset, which has been reduced to contain only species occurring in at least 30 samples (out of 97) to contain fewer species; the calculation was done in twinspanR library.>​{{:​obrazky:​twinspan-table-vltava.jpg?​direct|}}</​imgcaption>​
  
 The true algorithm is actually much more complex, and even the original description by Hill (1979) does not contain all details (some changes have been introduced later by other authors directly in the FORTRAN code of the TWINSPAN program). Perhaps the most detailed description of the algorithm with attention to some of the details is given in Kent (2012). Some software offers TWINSPAN (note that the implementation in each of them actually slightly differs, since some are using a different version of the FORTRAN code): TWINSPAN for Windows, PC-ORD, CAP and JUICE. In R, I created a simple experimental package ''​twinspanR'',​ which is an R-wrapper around the twinspan.exe program and works only on Windows platform (this implementation includes both original and modified TWINSPAN algorithm). The true algorithm is actually much more complex, and even the original description by Hill (1979) does not contain all details (some changes have been introduced later by other authors directly in the FORTRAN code of the TWINSPAN program). Perhaps the most detailed description of the algorithm with attention to some of the details is given in Kent (2012). Some software offers TWINSPAN (note that the implementation in each of them actually slightly differs, since some are using a different version of the FORTRAN code): TWINSPAN for Windows, PC-ORD, CAP and JUICE. In R, I created a simple experimental package ''​twinspanR'',​ which is an R-wrapper around the twinspan.exe program and works only on Windows platform (this implementation includes both original and modified TWINSPAN algorithm).
en/hier-divisive.txt · Last modified: 2019/05/23 09:59 by David Zelený