ISSN 1188-603X

No. 394 May 22, 2008 Victoria, B.C.
Dr. A. Ceska, P.O.Box 8546, Victoria, B.C. Canada V8W 3S2


Special Three-day Workshop
October 3-5, 2008
4101 University Drive, Anchorage, AK 99508

Analysis and Classification of Ecological Data Using JUICE Software: How to Use the JUICE Package in Combination with Turboveg, Twinspan, PC-ORD, MULVA, SYN-TAX, D-MAP, CANOCO and Others to Extend the Possibilities of these Programs

The workshop will be conducted by Drs. Lubomir Tichy & Milan Chytry Institute of Botany and Zoology, Masaryk University, Brno, Czech Republic

Description: This three-day course will combine lectures with hands-on application to teach the basic concepts and advanced features of the JUICE 6.5 freeware, computing package based on the Microsoft WINDOWS platform. The workshop will include:

  1. Vegetation Databanking - Basic Overview
  2. JUICE Installation, Management of Species Lists
  3. Data Import (Input from TURBOVEG and other Data Formats, Species Lists)
  4. Quality of Phytosociological Data (Plot Size, Preferential Site Selection)
  5. Manual Editing of Vegetation Tables
  6. Basic Classifications
  7. Concept of Diagnostic Species and the Theory of Phytosociological Fidelity
  8. Synoptic Tables and Automatic Editing of Vegetation Tables
  9. Stratified Data Selection from Phytosociological Databases
  10. Calculating Species Indicator Values
  11. Export Options
  12. Measuring Beta Diversity
  13. Modified TWINSPAN Classification
  14. Comparison of Classifications: OPTIMCLASS Method
  15. Formal Reproduction of Traditional Syntaxa: COCKTAIL Method
  16. Matching Relevés to Synoptic Tables
  17. Expert System for Automatic Identification of Vegetation Units
  18. Supervised Classification Methods: Neural Networks, Classification Trees
  19. Ordinations
  20. Fitting Species Response Curves
  21. Linking Phytosociological Data with Species Trait Databases
  22. Defining Species Pools: Beals Smoothing

The workshop will be held at Alaska Pacific University and be limited to 20 participants. Cost of workshop: $325 (a special price is available for fulltime students). Checks, Visa, or purchase order should be made payable to "Alaska Pacific University" and sent to: JUICE Workshop, Environmental Science, Alaska Pacific University, 4101 University Drive, Anchorage, Alaska 99508; telephone contact for payment is Jeannine Fitzgeralds, Environmental Science Office @ (907) 564-8207; FAX (907) 562- 4276; email: . Classes from 9:00 -12:00 and 1:00 - 4:00 pm.

Participants should bring their own laptop computers. Further information concerning the JUICE package may be found on the Web homepage ( ); a JUICE Manual will be available for distribution two weeks prior to the workshop.

Questions concerning the workshop should be addressed to: Stephen Talbot, U.S. Fish and Wildlife Service, 1011 East Tudor Road, Anchorage, AK 99503; phone (907) 786-3381, fax (907) 786- 3905, email:


From: Raj Prasad (2003) Management and control of gorse and Scotch broom in British Columbia. Technology Transfer Note Number 30, Pacific Forestry Centre, Victoria, British Columbia.


The following control strategies for broom and gorse are recommended based on information and experience gained from the literature, operational trials and research.


A. Cutting:

If the adult plants have stem larger than 2 cm in diameter they should be cut off low to the ground. If the plants are cut when the carbohydrate food reserves are lowest in the root (after flowering) or at the start of the drought season, the incidence of resprouting should be low. Any sprouts that occur may not survive the drought period in the summer.

If the stems are less than 2 cm in diameter they should be pulled out, either by hand or with a broom puller, and not cut. Seedlings and smaller plants have a greater tendency to sprout after cutting than adult plants.

The initial treatment, including chipping, may cost about $ 1000/ha; the first follow-up treatment will cost about $ 300/ha; the cost of subsequent follow-up treatments will continue to decline.

B. Cut the plant and treat the stump:

Cutting the adult plants and treating the stumps with a herbicide (Release) immediately after cutting appears to be an effective way of killing broom.

A follow-up treatment should be carried out to control emerging seedlings before they reach 50 cm in height. Since broom seedlings grow much faster , this follow-up treatment may be needed before the second year after the initial treatment, and repeated every few years until the broom plants are totally eradicated from the site. The seedlings should be pulled out by hand and not cut, as cutting promote sprouting.

The cut plant material should be disposed of by burning, chipping or removed from the site, to avoid creating a fire hazard.


A. Remove the entire adult plant:

Since gorse is capable of resprouting from cut stems, ideally the entire adult plant should be removed, roots and all.

Where practical, adult plants should be uprooted, by pulling or with a brush rake, with the roots left to dry.

This method is not appropriate for sensitive sites or sites with species at risk.

This should be only done on heavily disturbed site, as much soil will be exposed and gorse seeds in the soil will grow as a result.

Due to the high level of ground disturbance, a large number of seedlings can be expected to emerge and should be pulled out before they become too large.

B. Cut the plant below ground level:

Since adult gorse plants do tend to resprout from roots, the plant can be killed if the stem is cut at least 5 cm below ground level. However, care must be taken because prolific resprouting will result if the stem is cut anywhere above the root.

This method is applicable to small areas because it is extremely difficult and labour intensive.

C. Cut the plant and treat the stump:

Cutting the plant and painting the stumps with a herbicide (Release) immediately after cutting appears to be the most effective way of killing gorse on most sites.

D. Mulching:

Mulching a large area with uneven terrain is not economical, but mulching might have some limited application on small, selected areas where other methods cannot be employed.

The uprooted or cut plant material should be disposed of by chipping or removed from the site to avoid creating a fire hazard. Burning gorse may not be desirable due to the high content of volatile oils in the branches which creates an oily, black smoke.

Follow-up treatments will be necessary to control the seedlings that emerge from the seed bank. The seedlings should be pulled out by hand before they reach 50 cm in height, and not cut as cutting promotes sprouting. Since gorse seedlings are fairly slow growing, this follow-up treatment will likely not be required until the second year after the initial treatment. It should be repeated every few years until the gorse plants are totally eradicated from the site.

The initial treatment will be the most expensive due to the size of the adult plants, but follow-up treatment will be considerably less costly and will become less expensive for each successive treatment.

New infestation of gorse should be treated before older infestations. Younger plants are smaller and therefore easier and less costly to remove. Early eradication also prevents the build up of a large seed bank on the site.

Priority should be given to removal of gorse within 10 m of roads to prevent spread of seeds by vehicles. Roads should be surveyed once a year for new gorse infestations. These infestations should be removed by pulling the plants before they seed and create a seed bank.


Chytrý, M. (ed.) (2007):
Vegetace Ceské republiky: 1. Travinná a kerícková vegetace (Vegetation of the Czech Republic: 1. Grassland and heathland vegetation). Academia, Praha, 525 p. ISBN 978-80-200-1462-7 [hard cover] Price: 550.00 Kc
Orders can be placed at:

This is the first volume of the four-volume compendium on the Vegetation of the Czech Republic. The first volume deals with 12 classes, 41 alliances and 111 plant associations. These vegetation units were established based on 21,794 releves using the computer techniques in the JUICE computer program package (see above).

The project aims at creating vegetation classification of the Czech Republic, based on the analysis of data from the Czech National Phytosociological Database and associated with a computer expert system for automatic identification of vegetation units. The results will be published in a four-volume monograph, which will contain descriptions of phytosociological associations, alliances and classes, comparative tables of species composition, distribution maps and photographs of representative stands.

Individual volumes will contain:

  1. Grassland and heathland vegetation (2007)
  2. Ruderal, weed, rock and scree vegetation (2009)
  3. Aquatic and wetland vegetation (2009)
  4. Forest and scrub vegetation (2010)

For more information on this project go to the Vegetation Science Group web site

If you click on the link "Text", you will get a .doc file that contains the unformatted text of this volume. If you do not read Czech, skip the first 27 pages and starting with page 28, you will get an excellent English translation of the introductory chapters.

The "Distribution Maps" will be of little interest to the foreign readers,


The "Tables" contain vegetation tables of all the syntaxonomical units covered in this volume.


The demand by environment protection agencies for consistent and well-documented systems of vegetation classification led in the 1990s to the implementation of modern national projects of vegetation classification in some European countries, e.g., Great Britain (Rodwell 1990-2000), Austria (Mucina et al. 1993), the Netherlands (Schaminée et al. 1995-1999), Slovakia (Valachovi? et al. 1995, Jarolímek et al. 1997, Valachovi? 2001), Germany (Dierschke 1996) and the German federal state of Mecklenburg-Vorpommern (Berg et al. 2004).

These projects have the following features in common: thorough revision of previously described vegetation units on the basis of a critical reassessment of large relevé data sets; documentation of accepted associations using species composition tables; the detailed revision of the nomenclature of vegetation units; and the compilation of the distribution maps of phytosociological associations within the area in question. Research teams have shared their experiences from these projects with vegetation scientists from other European countries at the annual meetings of the European Vegetation Survey working group that have been held every year since 1992 (Mucina et al. 1993c, Rodwell et al. 1995). This working group has also produced the European synopsis of vegetation units at levels ranging from classes to alliances (Mucina 1997, Rodwell et al. 2002).

Despite a long tradition of phytosociological research and a good level of documentation of vegetation, the Czech Republic did not possess the modern classification of vegetation. In 1995 a decision was made to start to work on a new monograph entitled Vegetation of the Czech Republic. The initial, partial goal was to generate the Czech National Phytosociological Database which would contain the representative sample of relevés from different habitats and regions of the Czech Republic in an easily accessible electronic format (Chytrý & Rafajová 2003). Such relevés existed but were scattered in a number of scientific books, articles, theses, unpublished research reports, inventory surveys of protected areas, field books and other written materials maintained by different botanists.

Thanks to Professor John S. Rodwell from Lancaster University (UK) and Stephan M. Hennekens from Alterra - Green World Research in Wageningen (The Netherlands), we were able to use know-how from the British and Dutch vegetation classification projects from the very beginning of our work on the database. In 1995-1997, John Rodwell arranged a series of courses to acquaint with the principles of phytosociological database management and particularly with the computer program TURBOVEG (Hennekens 1995, Hennekens & Schaminée 2001). The author of this program Stephan M. Hennekens kindly provided it to Czech users free of charge.

TURBOVEG was prepared for use in Central Europe in cooperation with colleagues from Austria (Ladislav Mucina, Harald Niklfeld, Walter Gutermann) and Slovakia (Milan Valachovi?, Ivan Jarolímek) and in 1996 it was made accessible to all vegetation scientists in the Czech Republic (Chytrý 1996). In February 1997 Masaryk University in cooperation with John Rodwell organized a TURBOVEG training course in Brno for colleagues and students from the Czech Republic and Slovakia. Subsequently, a network of local TURBOVEG coordinators was established, which covered all major botanical institutions in the Czech Republic.

Besides the creation of the relevé database, the preparation of the monograph Vegetation of the Czech Republic also necessitated the development and testing of methods for vegetation classification using large data sets. In the case of data sets with tens of thousands of relevés, standard methods developed for classification of smaller data sets are not suitable or do not allow the potential of these data to be fully exploited. In addition, there has been only very limited experience with how various shortcomings in data quality affect the analysis of large relevé data sets. It was therefore necessary to perform various methodological studies.

One of the challenges was to establish a method of selection of relevés from the database which would prevent the negative impact on the resultant classification caused by the uneven distribution of relevés within the Czech Republic (Knollová et al. 2005). For vegetation classification on the basis of a phytosociological database, we selected the Cocktail method (Bruelheide 1995, 2000). This method creates explicit definitions of vegetation units which allow an unambiguous assignment of every relevé to these units. It thus allows matching of newly obtained relevés to the units of established classification. The Cocktail method underwent comprehensive testing and modifications and was extended with a procedure that enabled the assignment of relevés to vegetation units based on similarity (Ko?í et al. 2003, Tichý 2005).

Attention was also devoted to the testing and development of statistical methods to determine species fidelity to vegetation units (Chytrý et al. 2002, Tichý & Chytrý 2006), an important criterion in the determination of diagnostic species and the presentation of vegetation classification in tables. Chytrý & Tichý (2003) calculated species fidelities to vegetation classes and alliances of the current standard vegetation classification of the Czech Republic (Moravec et al. 1995), using data from the Czech National Phytosociological Database. Based on this analysis, they were able to evaluate the quality of delimitation of vegetation units. This work was used as a guideline for identification of (1) which vegetation units from the current classification should be adopted in the new classification system and (2) which should be eliminated or modified. Since 1998 all methods of analysis of phytosociological data used in the project have been included in the computer program JUICE (Tichý 2002), which has become a tool for the comprehensive analysis of phytosociological data and is currently being used by a number of individuals and institutions in many countries worldwide.


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