OptimClass: Using species-to-cluster fidelity to determine the optimal partition in classification of ecological communities

Journal of Vegetation Science

Volumn 21, Issue 2, 2010, Pages 287-299

  Tichý, Lubomír ^a   Chytrý, Milan ^a   Hájek, Michal ^a,b   Talbot, Stephen S ^c   Botta Dukát, Zoltán ^d  

^a MASARYK UNIVERSITY   (Czech Republic)

^b INSTITUTE OF BOTANY   (Czech Republic)

^c U S FISH AND WILDLIFE SERVICE   (United States)

^d INSTITUTE OF EXPERIMENTAL MEDICINE   (Hungary)

Author keywords

Cluster analysis; Cover transformation; Dendrogram; Optimal number of clusters; Ordinal clustering; Resemblance measures; Stopping rules; TWINSPAN

Indexed keywords

ABUNDANCE; ALGORITHM; CLUSTER ANALYSIS; COMMUNITY ECOLOGY; DATA SET; DENDROECOLOGY; ECOLOGICAL APPROACH; HETEROGENEITY; NUMERICAL METHOD; SPECIES RICHNESS; TWINSPAN; VEGETATION CLASSIFICATION;

EID: 77949690339     PISSN: 11009233     EISSN: 16541103     Source Type: Journal    
DOI: 10.1111/j.1654-1103.2009.01143.x     Document Type: Article

References (45)

1. Aho, K., Roberts, D.W. & Weaver, T. 2008. Using geometric and non-geometric internal evaluators to compare eight vegetation classification methods. Journal of Vegetation Science 19: 549-562.
2. Barkman, J.J. 1989. Fidelity and character-species, a critical evaluation. Vegetatio 85: 105-116.
3. Belbin, L. & McDonald, C. 1993. Comparing three classification strategies for use in ecology. Journal of Vegetation Science 4: 341-348.
4. Botta-Dukát, Z., Chytrý, M., Hájková, P. & Havlová, M. 2005. Vegetation of lowland wet meadows along a climatic continentality gradient in Central Europe. Preslia 77: 89-111.
5. Bruelheide, H. 2000. A new measure of fidelity and its application to defining species groups. Journal of Vegetation Science 11: 167-178.
6. Chytrý, M., Tichý, L., Holt, J. & Botta-Dukát, Z. 2002. Determination of diagnostic species with statistical fidelity measures. Journal of Vegetation Science 13: 79-90.
7. Chytrý, M., Danihelka, J., Ermakov, N., Hájek, M., Hájková, P., Kočí, M., Kubešová, S., Lustyk, P., Otýpková, Z., Popov, D., Roleček, J., Řezníčková, M., Šmarda, P. & Valachovič, M. 2007. Plant species richness in continental southern Siberia: effects of pH and climate in the context of the species pool hypothesis. Global Ecology and Biogeography 16: 668-678.
8. Dale, M.B. 1988. Knowing when to stop: cluster concept - concept cluster. Coenoses 3: 11-32.
9. Dubes, R.C. 1987. How many clusters are best? - an experiment. Pattern Recognition 20: 645-663.
10. Dufrêne, M. & Legendre, P. 1997. Species assemblages and indicator species: the need for a flexible asymmetrical approach. Ecological Monographs 67: 345-366.
11. Feoli, E., Lagonegro, M. & Biondani, F. 1981. Strategies in syntaxonomy: a discussion of two classifications of grasslands of Friuli (Italy). In: Dierschke, H. (ed.) Syntaxonomie. pp. 95-107. J. Cramer, Vaduz, LI.
12. Gerdol, R., Ferrari, C. & Piccoli, F. 1985. Correlation between soil characters and forest types: a study in multiple discriminant analysis. Vegetatio 60: 49-56.
13. Hájek, M., Horsák, M., Hájková, P. & Dítě, D. 2006. Habitat diversity of central European fens in relation to environmental gradients and an effort to standardise fen terminology in ecological studies. Perspectives in Plant Ecology, Evolution and Systematics 8: 97-114.
14. Hájek, M., Tichý, L., Schamp, B.S., Zelený, D., Roleček, J., Hájková, P., Apostolova, I. & Dítě, D. 2007. Testing the species pool hypothesis for mire vegetation: exploring the influence of pH specialists and habitat history. Oikos 116: 1311-1322.
15. Hakes, W. 1994. On the predictive power of numerical and Braun-Blanquet classification: an example from beechwoods. Journal of Vegetation Science 5: 153-160.
16. Hill, M.O. 1979. TWINSPAN - A FORTRAN program for arranging multivariate data in an ordered two-way table by classification of the individuals and attributes. Cornell University, Ithaca, NJ, US.
17. Illyés, E., Chytrý, M., Botta-Dukát, Z., Jandt, U., Škodová, I., Janišová, M., Willner, W. & Hájek, O. 2007. Semi-dry grasslands along a climatic gradient across Central Europe: vegetation classification with validation. Journal of Vegetation Science 18: 835-846.
18. Jennings,M.D., Faber-Langendoen, D., Loucks, O.L., Peet, R.K. & Roberts, D. 2009. Standards for associations and alliances of the U.S. National Vegetation Classification. Ecological Monographs 79: 173-199.
19. Lance, G.N. & Williams, W.T. 1967. A general theory of classificatory sorting strategies: I. Hierarchical systems. Computer Journal 9: 373-380.
20. Legendre, P. & Legendre, L. 1998. Numerical ecology. 2nd ed. Elsevier, Amsterdam, NL.
21. McCune, B. & Allen, T.F.H. 1985. Will similar forests develop on similar sites? Canadian Journal of Botany 63: 367-376.
22. McCune, B., Grace, J.B. & Urban, D.L. 2002. Analysis of ecological communities. MjM Software Design, Gleneden Beach, OR, US.
23. Milligan, G.W. & Cooper, M.C. 1985. An examination of procedures for determining the number of clusters in a data set. Psychometrika 50: 159-179.
24. Mucina, L. 1997. Classification of vegetation: past, present and future. Journal of Vegetation Science 8: 751-760.
25. Mucina, L. & Hauser, M. 1993. A new method for determining optimal number of clusters in vegetation data. Abstracta Botanica 17: 147-153.
26. Neumann, D.A. & Norton, V.T. 1986. Clustering and isolation in the consensus problem for partitions. Journal of Classification 3: 281-297.
27. Noest, V. & van der Maarel, E. 1989. A new dissimilarity measure and a new optimality criterion in phytosociological classification. Vegetatio 83: 157-165.
28. Podani, J. 1998. Explanatory variables in classifications and the detection of the optimum number of clusters. In: Hayashi, C., Ohsumi, N., Yajima, K., Tanaka, Y., Bock, H.-H. & Baba, Y. (eds.) Data science, classification and related methods. pp. 125-132. Springer, Tokyo, JP.
29. Podani, J. 1999. Extending Gower's general coefficient of similarity to ordinal characters. Taxon 48: 331-340.
30. Podani, J. 2000. Introduction to the exploration of multivariate biological data. Backhuys Publishers, Leiden, NL.
31. Podani, J. 2005. Multivariate exploratory analysis of ordinal data in ecology: pitfalls, problems and solutions. Journal of Vegetation Science 16: 497-510.
32. Podani, J. 2006. Braun-Blanquet's legacy and data analysis in vegetation science. Journal of Vegetation Science 17: 113-117.
33. Popma, J., Mucina, L., van Tongeren, O. & van der Maarel, E. 1983. On the determination of optimal levels in phytosociological classification. Vegetatio 52: 65-75.
34. Ratliff, D. & Pieper, R.D. 1981. Deciding final clusters: an approach using intra- and intercluster distances. Vegetatio 48: 83-86.
35. Rohlf, F.J. 1963. Classification of Aedes by numerical taxonomic methods (Diptera: Culicidae). Annals of the Entomological Society of America 56: 798-804.
36. Roleček, J., Tichý, L., Zelený, D. & Chytrý, M. 2009. Modified TWINSPAN classification in which the hierarchy respects cluster heterogeneity. Journal of Vegetation Science 20: 596-602.
37. Sneath, P.H.A. & Sokal, R.R. 1973. Numerical taxonomy. W.H. Freeman, New York, NY, US.
38. Sokal, R.R. & Rohlf, F.J. 1995. Biometry. 3rd edition. W.H. Freeman, New York, NY, US.
39. Szafer, W. & Pawłowski, B. 1927. Die Pflanzenassoziationen des Tatra-Gebirges. A. Bemerkungen über die angewandte Arbeitstechnik. In: Szafer, W., Kulczynski, B., Pawzowski, B., Stecki, K. & Sokozowski, A.W. (eds.) Die Pflanzenassoziationen des Tatra-Gebirges. III., IV. und V. Teil. Bulletin International de l'Academie Polonaise des Sciences et des Lettres B 3 (Suppl. 2): 1-12.
40. Tichý, L. & Chytrý, M. 2006. Statistical determination of diagnostic species for site groups of unequal size. Journal of Vegetation Science 17: 809-818.
41. van Groenewoud, H. 1992. The robustness of correspondence, detrended correspondence, and TWINSPAN analysis. Journal of Vegetation Science 3: 239-246.
42. Ward, J.H. 1963. Hierarchical grouping to optimize an objective function. Journal of the American Statistical Association 58: 236-244.
43. Westhoff, V. & van der Maarel, E. 1973. The Braun-Blanquet approach. In: Whittaker, R.H. (ed.) Ordination and classification of plant communities. pp. 617-737. W. Junk, The Hague, NL.
44. Whittaker, R.H. 1960. Vegetation of the Siskiyou Mountains, Oregon and California. Ecological Monographs 30: 279-338.
45. Whittaker, R.H. 1962. Classification of natural communities. Botanical Review 28: 1-239.