Simple shade plots aid better long-term choices of data pre-treatment in multivariate assemblage studies

Journal of the Marine Biological Association of the United Kingdom

Volumn 94, Issue 1, 2014, Pages 1-16

  Clarke, K Robert ^a,b   Tweedley, James R ^b   Valesini, Fiona J ^b  

^a PLYMOUTH MARINE LABORATORY   (United Kingdom)

^b MURDOCH UNIVERSITY   (Australia)

Author keywords

community ecology; dispersion weighting; estuaries; fish assemblages; macrobenthos; multivariate statistics; shade plots; transformation choice; Western Australia

Indexed keywords

ABUNDANCE; COMMUNITY ECOLOGY; DISPERSION; ESTUARINE ECOSYSTEM; FISH; MACROBENTHOS; MATRIX; MULTIVARIATE ANALYSIS; PRECIPITATION (CLIMATOLOGY); WATER QUALITY;

AUSTRALIA; PERTH [WESTERN AUSTRALIA]; SWAN ESTUARY; WESTERN AUSTRALIA;

EID: 84892707521     PISSN: 00253154     EISSN: 14697769     Source Type: Journal    
DOI: 10.1017/S0025315413001227     Document Type: Article

References (43)

1. Anderson M.J. (2001) A new method for non-parametric multivariate analysis of variance. Austral Ecology 26, 32-46.
2. Box G.E.P. and Cox D.R. (1964) An analysis of transformations. Journal of the Royal Statistical Society, Series B 26, 211-252.
3. Bray J.R. and Curtis J.T. (1957) An ordination of the upland forest communities of Southern Wisconsin. Ecological Monographs 27, 325-349.
4. Brearley A. (2005) Ernest Hodgkin's Swanland. Perth: University of Western Australia Press.
5. Buckley B.W., Sullivan W., Chan P. and Leplastrier M. (2010) Two record breaking Australian hail storms: storm environments, damage characteristics and rarity. In 25th Conference on Severe Local Storms. 11-14 October 2010 Denver: American Meteorological Society.
6. Available at: https://ams.confex.com/ams/pdfpapers/175723.pdf (accessed 16 August 2013). Chatfield C. and Collins A.J. (1980) Introduction to multivariate analysis. London: Chapman & Hall.
7. Clarke K.R. (1993) Non-parametric multivariate analyses of changes in community structure. Australian Journal of Ecology 18, 117-143.
8. Clarke K.R. and Ainsworth M. (1993) A method of linking multivariate community structure to environmental variables. Marine Ecology Progress Series 92, 205-219.
9. Clarke K.R. and Gorley R.N. (2006) PRIMER v.6: user manual/tutorial. Plymouth: PRIMER-E.
10. Clarke K.R. and Green R.H. (1988) Statistical design and analysis for a 'biological effects' study. Marine Ecology Progress Series 46, 213-226.
11. Clarke K.R. and Warwick R.M. (1998) Quantifying structural redundancy in ecological communities. Oecologia 113, 278-289.
12. Clarke K.R. and Warwick R.M. (2001) Change in marine communities: an approach to statistical analysis and interpretation, 2nd edition. Plymouth: PRIMER-E.
13. Clarke K.R., Chapman M.G., Somerfield P.J. and Needham H.R. (2006a) Dispersion-based weighting of species counts in assemblage analyses. Marine Ecology Progress Series 320, 11-27.
14. Clarke K.R., Somerfield P.J. and Chapman M.G. (2006b) On resemblance measures for ecological studies, including taxonomic dissimilarities and a zero-adjusted Bray-Curtis coefficient for denuded assemblages. Journal of Experimental Marine Biology and Ecology 330, 55-80.
15. Clarke K.R., Warwick R.M. and Brown B.E. (1993) An index showing breakdown of seriation, related to disturbance, in a coral-reef assemblage. Marine Ecology Progress Series 102, 153-160.
16. Clifford H.T. and Stephenson W. (1975) An introduction to numerical classification. New York: Academic Press.
17. Faith D.P., Minchin P.R. and Belbin L. (1987) Compositional dissimilarity as a robust measure of ecological distance. Vegetatio 69, 57-68.
18. Field J.G., Clarke K.R. and Warwick R.M. (1982) A practical strategy for analysing multispecies distribution patterns. Marine Ecology Progress Series 8, 37-52.
19. Gower J.C. (1971) A general coefficient of similarity and some of its properties. Biometrics 27, 857-872.
20. Gray J.S., Aschan M., Carr M.R., Clarke K.R., Green R.H., Pearson T.H., Rosenberg R. and Warwick R.M. (1988) Analysis of community attributes of the benthic macrofauna of Frierfjord/Langesundfjord and in a mesocosm experiment. Marine Ecology Progress Series 46, 151-165.
21. Hallett C.S., Valesini F.J. and Clarke K.R. (2012) A method for selecting health index metrics in the absence of independent measures of ecological condition. Ecological Indicators 19, 240-252.
22. Kruskal J.B. (1964) Multidimensional scaling by optimizing goodness of fit to a nonmetric hypothesis. Psychometrika 29, 1-27.
23. Legendre P. and Legendre L. (1998) Numerical ecology. 2nd English edition. Amsterdam: Elsevier.
24. Mantel N. (1967) The detection of disease clustering and a generalized regression approach. Cancer Research 27, 209-220.
25. McArdle B.H. and Anderson M.J. (2001) Fitting multivariate models to community data: a comment on distance-based redundancy analysis. Ecology 82, 290-297.
26. Mumby P.J., Clarke K.R. and Harborne A.R. (1996) Weighting species abundance estimates for marine resources assessment. Aquatic Conservation: Marine and Freshwater Ecosystems 6, 115-120.
27. Olsgard F. and Somerfield P.J. (2000) Surrogates in marine benthic investigations-which taxonomic unit to target? Journal of Aquatic Ecosystem Stress and Recovery 7, 25-42.
28. Olsgard F., Somerfield P.J. and Carr M.R. (1997) Relationships between taxonomic resolution and data transformations in analyses of a macrobenthic community along an established pollution gradient. Marine Ecology Progress Series 149, 173-181.
29. Olsgard F., Somerfield P.J. and Carr M.R. (1998) Relationships between taxonomic resolution, macrobenthic community patterns and disturbance. Marine Ecology Progress Series 172, 25-36.
30. Pearson K. (1901) On lines and planes of closest fit to systems of points in space. Philosophical Magazine 2, 559-572.
31. R Core Team (2013) R: a language and environment for statistical computing. Vienna: R Foundation for Statistical Computing.
32. Sneath P. (1957) The application of computers to taxonomy. Journal of General Microbiology 17, 201-226.
33. Somerfield P.J. and Clarke K.R. (1995) Taxonomic levels, in marine community studies, revisited. Marine Ecology Progress Series 127, 113-119.
34. Tweedley J.R. and Hallett C.S. (2013) Monitoring the effects of artificial oxygenation on biota. Perth: Swan River Trust, Perth, 62 pp.
35. Tweedley J.R., Warwick R.M., Valesini F.J., Platell M.E. and Potter I.C. (2012) The use of benthic macroinvertebrates to establish a benchmark for evaluating the environmental quality of microtidal, temperate southern hemisphere estuaries. Marine Pollution Bulletin 64, 1210-1221.
36. Valesini F.J., Potter I.C. and Clarke K.R. (2004) To what extent are the fish compositions at nearshore sites along a heterogeneous coast related to habitat type? Estuarine, Coastal and Shelf Science 60, 737-754.
37. Valesini F.J., Hourston M., Wildsmith M.D., Coen N.J. and Potter I.C. (2010) New quantitative approaches for classifying and predicting local-scale habitats in estuaries. Estuarine, Coastal and Shelf Science 86, 645-664.
38. Valesini F.J., Tweedley J.R., Clarke K.R. and Potter I.C. (in press) The importance of local, system-wide and regional spatial scales in structuring temperate estuarine fish communities. Estuaries and Coasts.
39. Warton D.I., Wright S.T. and Wang Y. (2012) Distance-based multivariate analyses confound location and dispersion effects. Methods in Ecology and Evolution 3, 89-101.
40. Whittaker R.H. (1952) A study of summer foliage insect communities in the Great Smoky Mountains. Ecological Monographs 22, 1-44.
41. Wildsmith M.D., Rose T.H., Potter I.C., Warwick R.M. and Clarke K.R. (2011) Benthic macroinvertebrates as indicators of environmental deterioration in a large microtidal estuary. Marine Pollution Bulletin 62, 525-538.
42. Wilkinson L. (1994) Advanced Applications: Systat for DOS version 6. Chicago, IL: SYSTAT Inc.
43. Wilkinson L. and Friendly M. (2009) The history of the cluster heat map. The American Statistician 63, 179-184.