linking juice and - david zelený (澤大衛) · linking juice and : new developments in...

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

European Vegetation Survey, 18th International Workshop, Roma, Italy, March 25-28 2009

e de e op e s sua a o o u co s a ed o d a o a a ys sDavid Zelený & Lubomír Tichý

Institute of Botany and Zoology, Masaryk UniversityKotlářská 2, CZ-61137 Brno, Czech Republic

e-mail: zeleny@sci.muni.cz, tichy@sci.muni.cz

JUICE 7.0

is a Windows application forediting, classification and analysis oflarge phytosociological tables andother ecological data. It has beendeveloped by Lubomír Tichý(Masaryk University Brno) since1998, written in Visual Basic and

R-project

is a free software environmentfor statistical computing andgraphics, running on a wide varietyof platforms. Following R packagesare used by JUICE:• vegan (Oksanen, Kindt, Legendre,O’Hara et al.) - number of tools for

optimized for Windows OS (butoperating also under Linux via Wineemulator). JUICE can also auto-matically or semi-automaticallyoperate other commercial or free-ware software, such as PC-ORD,CANOCO, SYNTAX or Mulva.For more information about JUICEand free program download, visithttp://www.sci.muni.cz/botany/juice/or http://tinyurl.com/cwtrf9.

)analysis of ecological communities,diversity and multivariate analysis;• ordijuice (Zelený) - connectingJUICE and R and offering someadditional visualization tools;• rgl (Adler & Murdoch) - threedimensional interactive ordinationdiagrams;• geometry (Grasman & Gramacy) -calculation of convex hulls;• tcltk and tkrgl (Murdoch & Chen)

Linking JUICE and R offers quick and effective availability ofselected R analytical and visualization functions: JUICE offers userfriendly environment of vegetation data handling and import, R worksas an engine for analysis and visualization.Recently implemented unconstrained ordination analyses arep y • tcltk and tkrgl (Murdoch & Chen) -

user interface for interaction withfigures.

Recently implemented unconstrained ordination analyses areDetrended Correspondence Analysis, Principal Component Analysisand Non-metric Multidimensional Scaling, all available in veganlibrary written by Oksanen et al.

Technical solutionsLi k b t JUICE d R i di t d b h i th fil i t d Thi d i ll l R i t

This study was supported by long-term research plan MSM 0021622416 and grant project G759 (Masaryk University Brno, Czech Republic). The background image originates from http://www.wallpaperpimper.com

Link between JUICE and R is mediated by sharing the files viaR/bin directory and using libraries ordijuice. JUICE offerswizard for selection of appropriate analysis parameters andtype of graphical output. Data are saved into R/bin file, and Ris initialized to run in a batch mode by sending the script withselected parameters into Windows command line. R draws thefigure onto graphical device (X11 or rgl) and opens Tcl/Tkpanel; after either the device or Tcl/Tk bar is closed, R is termi-

nated. This design allows several R sessions to runsimultaneously using the same data, but different parameters.

Updates of ordijuice library are available from R repository inhttp://www.sci.muni.cz/botany/zeleny/R. If ordinations are inuse, once per day is checked for new updates and user isnoticed about the option to update.