Nomenclature of plants follows Dobolyi (2002). Syntaxonomical nomenclature follows Borhidi & Sánta (1999) and Borhidi (2003). For databasing the authors used TurboVeg for Windows. Up to now, CoenoDatRef contains some 9,000 relevés of app. 400 natural and/or semi-natural associations.
JUICE
The program JUICE (Tichý 2002) was designed as a Microsoft Windows application for editing, classification and analysis of large phytosociological tables and databases. This software includes many functions for easy manipulation of table and header data. Various options include classification using COCKTAIL, ISOPAM and TWINSPAN methods, calculation of interspecific associations, fidelity measures, average Ellenberg indicator values, preparation of synoptic tables, automatic sorting of relevé tables, and export of table data into other applications (word processors, spreadsheet programs or mapping packages). JUICE is optimized for use in association with TURBOVEG. URL: http://www.sci.muni.cz/botany/juice/
MULVA-5
MULVA-5 (Wildi & Orloci 1996) is a program package designed to apply multivariate statistical methods to vegetation and site data as a means of investigation in plant ecology. The individual programs of MULVA-5 allow you to analyse relevés by correlating vegetation and site factors and by investigating vegetation patterns. Lists of species (relevé data) can be analysed for similarity to find groups (Classification) or establish a meaningful order (Ordination). You can investigate the floristic and ecological composition of relevés as well as similar occurrence of species. MULVA-5 can also be used to derive simple models from the relevé and site data. URL: http://www.wsl.ch/land/products/mulva/
SYN-TAX
The package SYN-TAX was developed by Janos Podani (Podani 1993), and runs as a Microsoft Windows application. It contains programs for data analysis with emphasis on applications inecology and systematics. Most are equally applicable to other fieldswhen reduction of dimensionality and exploration of data structure aredesired. URL: http://www.exetersoftware.com/cat/syntax/syntax.html
TURBOVEG
The computer software package TURBOVEG (for Microsoft Windows) was developed in The Netherlands for the processing of phytosociological data (Hennekens & Schaminée 2001). This package comprises an easy-to-use data base management system. The data bank to be managed can be divided into several data bases. The program provides methods for input, import, selection, and export of relevés. URL: http://www.synbiosys.alterra.nl/turboveg/
VEGANA
VEGANA (VEGetation edition ANAlysis tools) is a set of programs, written in Java language (therefore multiplatform), that provides a framework for editing and analyzing community data (De Cáceres et al. 2003). It is maintained at the Plant Biology Department of the Universitat de Barcelona. URL:http://biodiver.bio.ub.es/vegana
R packages
The R statistical environment has become the standard for statistical analysis in many scientific domains. We strongly encourage vegetation scientists and community ecologists dealing with vegetation classification to learn R. Developers of new methodological approaches are also encouraged to present them to the vegetation community as R packages. Here we report an (incomplete) list of packages that can be useful to carry out numerical analyses for classification of vegetation.
Package 'BiodiversityR'
The BiodiversityR package offers a graphical user interface to methods of community ecology and biodiversity analysis available from the ‘vegan’ package (Oksanen et al. 2008) and described in the freely available Tree Diversity Analysis manual (Kindt and Coe 2005). URL: https://CRAN.R-project.org/package=BiodiversityR
Package 'cluster'
R package cluster was developed by Martin Maechler, among others. It implements the clustering methods described in Kaufman & Rousseuw (1990). URL: http://cran.r-project.org/web/packages/cluster/index.html
Package 'ecodist'
R package ecodist was developed by Sarah Goslee and Dean Urban. It implements dissimilarity-based analysis functions (i.e. Mantel test, non-metric multidimensional scaling, principal coordinates analysis,...) intended for use with spatial and community data. URL: http://cran.r-project.org/web/packages/ecodist/index.html
Package 'indicspecies'
Indicspecies is an R package created and maintained by Miquel De Cáceres and Florian Jansen. It contains a set of functions to assess the strength of relationship between species and a classification of sites. As such, it includes the well-known IndVal method (Dufrêne & Legendre 1997) and extends it by allowing the user to study combinations of site groups (De Cáceres et al. 2010). Apart from the IndVal index, the package allows computing many other indices suitable for this kind of associations (De Cáceres & Legendre 2009), such as the phi coefficient of association. It is also possible to check the statistical significance of such associations. URL: http://cran.r-project.org/web/packages/indicspecies/index.html
Package 'isopam'
R package isopam is maintained by Sebastian Schmidtlein and contains the isopam algorithm itself (Schmidtlein et al. 2010) and some auxiliary functions. URL: http://cran.r-project.org/web/packages/isopam/index.html
Package 'labdsv'
R package labdsv was created by David W. Roberts (Roberts 2006). It contains a wide variety of ordination and vegetation analyses useful in analysis of datasets in community ecology. Includes many of the common ordination methods, with graphical routines to facilitate their interpretation, as well as several novel analyses. Tutorials to use labdsv functions can be found at: http://ecology.msu.montana.edu/labdsv/R/. URL: http://cran.r-project.org/web/packages/labdsv/index.html
Package 'mclust'
R package mclust was not designed for vegetation analysis, but contains functions for model-based clustering and normal mixture modeling. We cite it here because this package contains useful functions for the comparison of classifications. For example, it provides functions for finding the best correspondence between classifications and calculating the adjusted Rand index (see Comparison and Validation of vegetation classifications).