Software

Stand-alone programs

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 in ecology and systematics. Most are equally applicable to other fields when reduction of dimensionality and exploration of data structure are desired.

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).

URL: http://cran.r-project.org/web/packages/mclust/index.html

Package 'vegan'

R package vegan was started by Jari Oksanen, but it currently includes contributions from many other authors (Oksanen et al. 2008). It is the biggest R package for community ecologists and vegetation ecologists. It contains ordination methods, diversity analysis and many other functions.

URL: http://cran.r-project.org/web/packages/vegan/index.html.

Package 'vegclust'

R package vegclust was created by Miquel De Cáceres, and provides functions for fuzzy or hard clustering of vegetation data (De Cáceres et al. 2010). At least four tasks are necessary in the management of vegetation classifications: (1) Assigning a meaningful vegetation type to the plant community observed in a sampled site; (2) Updating the current definition of vegetation types according to the new vegetation information collected; (3) Defining new vegetation types with those relevés that are considered to be very different to any of the available types; (4) Reviewing classifications generated by other means. The vegclust package provides functions for maintaining plot-based community classifications using fuzzy clustering methods. Three models are available: Fuzzy C-means, Noise Clustering and Possibilistic C-means.

URL: http://cran.r-project.org/web/packages/vegclust/index.html

Package 'vegdata'

R package vegdata was created by Florian Jansen (Jansen & Dengler 2010). It is designed to solve problems related to taxon names that arise when analyzing vegetation data sets. The package provides a set of functions to load data from (at present: Turboveg) databases.

URL: http://cran.r-project.org/web/packages/vegdata/index.html

Package 'Taxonstand'

R package Taxonstand was created by Luis Cayuela (Cayuela et al. 2012). It allows to automatically standardise plant names using The Plant List (http://www.theplantlist.org). The scripts included in this package allow connection to the online search engine of the Plant List and retrieve information from each species about its current taxonomic status.

URL: http://cran.r-project.org/web/packages/Taxonstand/index.html

Bibliography

    • Dengler, J., Jansen, F., Glöckler, F., Peet, R.K., De Cáceres, M., Chytrý, M., et al. (2011). The Global Index of Vegetation-Plot Databases (GIVD): a new resource for vegetation science. Journal of Vegetation Science, 22, 582–597.
  • Cayuela, L., Granzow-de la Cerda, Í., Albuquerque, F. S., & Golicher, D. J. (2012). taxonstand: An r package for species names standardisation in vegetation databases. Methods in Ecology and Evolution, 3(6), 1078–1083.
    • De Cáceres, M. & Legendre, L. (2009) Associations between species and groups of sites: indices and statistical inference. Ecology, 90, 3566-3574.
    • De Cáceres, M., Legendre, P. & Moretti, M. (2010) Improving indicator species analysis by combining groups of sites. Oikos, 119, 1674-1684.
    • De Cáceres, M., Font, X., García, R. & Oliva, F. (2003) VEGANA, un paquete de programas para la gestión y análisis de datos ecológicos. VII Congreso Nacional de la Asociación Española de Ecología Terrestre, pp. 1484-1497. Barcelona.
    • De Cáceres, M., Font, X. & Oliva, F. (2010) The management of vegetation classifications with fuzzy clustering. Journal of Vegetation Science, 21, 1138-1151.
    • Dufrêne, M. & Legendre, P. (1997) Species assemblages and indicator species: The need for a flexible asymetrical approach. Ecological Monographs, 67, 345-366.
    • Hennekens, S. M. & Schaminée, J. H. J. (2001) TURBOVEG, a comprehensive data base management system for vegetation data. Journal of Vegetation Science, 12, 589-591.
    • Jansen, F. & Dengler, J. (2010) Plant names in vegetation databases – a neglected source of bias. Journal of Vegetation Science, 21, 1179-1186.
    • Kaufman, L. & Rousseuw, P. J. (1990) Finding Groups in Data: An Introduction to Cluster Analysis. New York: Willey & Sons Inc.
    • Oksanen, J., Kindt, R., Legendre, P., O’Hara, R. B., Simpson, G. L. & Stevens, M. H. H. (2008) vegan: Community Ecology Package. R package version 1.11-0. http://cran.r-project.org/, http://vegan.r-forge.r-project.org/.
    • Podani, J. (1993) SYN-TAX-5.0: Computer programs for multivariate data analysis in ecology and systematics. Abstracta Botanica, 17, 289-302.
    • Roberts, D. W. (2006) Labdsv: laboratory for dynamic synthetic vegephenomenology. Version 1.2–2. URL http://ecology.msu.montana.edu/labdsv/R.
    • Rodwell, J. S., Pignatti, S., Mucina, L. & Schaminée, J. H. J. (1995) European Vegetation Survey: update on progress. Journal of Vegetation Science, 6, 759-762.
    • Schmidtlein, S., Tichý, L., Feilhauer, H. & Faude, U. (2010) A brute-force approach to vegetation classification. Journal of Vegetation Science, 21, 1162-1171.
    • Schaminée, J. H. J., Hennekens, S. M., Chytry, M. & Rodwell, J. S. (2009) Vegetation-plot data and databases in Europe: an overview Preslia, Praha, 81, 173-185.
    • Tichý, L. (2002) JUICE, software for vegetation classification. Journal of Vegetation Science, 13, 451-453.
    • Wildi, O. & Orlóci, L. (1996) Numerical Exploration of Community Patterns. A guide to the use of MULVA-5. 2nd edition. SPB Academic Publishing b.v., Amsterdam, 171 pp.
    • Wiser, S, Spencer, N., De Cáceres, M., Kleikamp, M., Boyle, B., Peet, R.K. (2011) Veg-X – An exchange standard for plot-based vegetation data. Journal of Vegetation Science, 22, 598-609.