Canoco 5: a new version of an ecological multivariate data ordination program

doi:10.3724/SP.J.1003.2013.04133

Abstract

Abstract:

Ordination of multidimensional data on community composition is one of the most important multivariate statistical methods used in biodiversity research. The aim of ordination is to visualize multidimensional data structure at a low-dimensional ordination space. Canoco is one of the most popular programs for ordination analysis and Canoco 4.5 was widely used for such analysis after its release in 2002, because of its simple user interface and powerful graphic tools. A new version of Cannoco, Canoco 5 was released in October 2012. This new version simplifies data entry, provides a better help system and graphics tools, simplifies steps of variation partitioning and significance tests, adds some new methods (e.g. PCNM, NMDS, association analysis of functional traits, etc.). This paper provides an overview of the major improvements to ??Canoco 5, and addresses important steps required for particular analyses.

Key words: variation partitioning, PCNM, NMDS, functional traits, phylogenetic

Jiangshan Lai. Canoco 5: a new version of an ecological multivariate data ordination program[J]. Biodiv Sci, 2013, 21(6): 765-768.

Figures/Tables 10

References 9

1	Borcard D, Legendre P (2002) All-scale spatial analysis of ecological data by means of principal coordinates of neighbour matrices.Ecological Modelling, 153, 51-68.
2	Legendre P, Borcard D, Peres-Neto PR (2005) Analyzing beta diversity: partitioning the spatial variation of community composition data.Ecological Monographs, 75, 435-450.
3	Legendre P, Borcard D, Peres-Neto PR (2008) Analyzing or explaining beta diversity? Comment.Ecology, 89, 3238-3244.
4	Lepx J, Smilauer P (2003) Multivariate Analysis of Ecological Data Using CANOCO. Cambridge University Press, Cambridge.
5	Petchey OL, Gaston KJ (2006) Functional diversity: back to basics and looking forward.Ecology Letters, 9, 741-758.
6	ter Braak CJF, Smilauer P (2002) CANOCO Reference Manual and CanoDraw for Windows User's Guide: Software for Canonical Community Ordination. Version 4.5. Microcomputer Power, Ithaca, New York.
7	ter Braak CJF, Smilauer P (2012) CANOCO Reference Manual and User's Guide: Software for Ordination. Version 5. Microcomputer Power Ithaca, New York.
8	von Wehrden H, Hanspach J, Bruelheide H, Wesche K (2009) Pluralism and diversity: trends in the use and application of ordination methods 1990-2007.Journal of Vegetation Science, 20, 695-705.
9	Zhang JT (张金屯) (2004) Quantitative Ecology (数量生态学). Science Press, Beijing. (in Chinese)

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