Publication details

Linking JUICE and R: New developments in visualization of unconstrained ordination analysis


ZELENÝ David TICHÝ Lubomír

Year of publication 2009
Type Article in Proceedings
Conference 18th Workshop of European Vegetation Survey in Rome
MU Faculty or unit

Faculty of Science

Field Ecology
Keywords R; JUICE; unconstrained analysis
Description JUICE program offers user friendly environment for editing, classification and analysis of vegetation data. R-project has almost unlimited possibilities of analysis and visualization of any type of data, yet its interface is not designed for user without an advanced experience. Therefore, we decided to use the benefits of these programs, using JUICE interface and R-project engine, for advanced visualization of results of unconstrained ordination analysis, such as Detrended Correspondence Analysis (DCA), Principal Components Analysis (PCA) and Non-metric Multidimensional Scaling (NMDS). In R-project, wide selection of analytical and visualization tools for multivariate ordination analysis is available in the package vegan, developed by Jari Oksanen and his colleagues. We used this package, extended its functionality for several new visualization methods and connected it with JUICE program. Beside traditional two dimensional ordination diagrams with projected environmental variables and vegetation groups, the combination of JUICE and R program offers more advanced methods such as three dimensional interactive ordination diagrams with convex hulls or spiderplots. The function such as manual update, online discussion forum, online manual and export of ordination results are also provided. We believe that this method, particularly the three dimensional visualization of ordination results, may bring new possibilities for interpretation of ordination results and their quick and effective visualization.

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