On-line Manual JUICE Page Working Group for Vegetation Science

COCKTAIL classification

COCKTAIL algorithm for defining species groups

The COCKTAIL algorithm (Bruelheide 1995, 2000) was designed for statistical forming of sociological species groups. It proceeds iteratively as follows:

Step 1. The algorithm can be used either to 1a – select species differential for a vegetation unit, or 1b – define a vegetation unit characterised by a group of differential species.

Step 1a. Starting with preselected relevés (typical of a known vegetation unit) the algorithm begins by calculating all species fidelities to that vegetation unit and takes the species with the highest fidelity values as the starting species group.

Step 1b. Starting with a preselected species group which is user-defined, based on literature or previous analysis.

Step 2. The number of species of the species group is calculated in each relevé. The expected and observed cumulative distribution functions for relevés having 0 to k species are calculated. The distributions’ intersection defines the required minimum number m of species for a relevé to belong to the vegetation unit. The vegetation unit is defined by all relevés having m or more species belonging to the species group. If there is no intersection between observed and expected cumulative distribution then the algorithm aborts. This is the case when species having fewer co-occurrences than expected form the starting group.

Step 3. The occurrences of each species in the vegetation unit are counted and the fidelity is calculated.

Step 4. For all species in the species group fidelity value is tested against an (initially) fixed threshold fidelity. If fidelity exceeds the threshold the algorithm proceeds to step 5. If not there are two possibilities:

Step 4a. One of the initially selected species does not exceed the threshold. The group is rejected and the algorithm aborts.

Step 4b. The last species added has caused a previous species’ fidelity to decrease below the threshold. The previous species is removed, and the algorithm does not try to add this species again until the group has been changed by adding a further species.

Step 5. All species not belonging to the species group are sorted according to their fidelity value. If any exceed the threshold fidelity the algorithm proceeds to step 6. If not the algorithm stops. The species group is optimised when all species above the threshold are included.

Step 6. The species group is enlarged by including the (single) species with highest fidelity. Iteration continues at step 2.

Note that step 4a guarantees that the species group composition is not changed to such a degree that the initial species no longer have the highest fidelity. This restriction allows the formation of a number of species groups, some with lower maximal fidelity than others. Not every such group can be optimised. This is the case if species which do not co-occur with the vegetation type more than expected form the starting group.

When starting with preselected relevés (belonging to a known syntaxon) the vegetation unit is optimized in such a way that it is defined by differential species groups a posteriori, and the final composition of relevés in the group may be different than at the beginning. Not all syntaxa can be defined by groups of differential species – some are defined by dominance rather than by floristic composition.

Contrary to the original description of the COCKTAIL algorithm, JUICE allows the user to be more directly involved into the process of species group formation. Instead of automatical checking the species group composition in each step against the initially fixed fidelity value, it can be checked by the user if its give sense in phytosociological terms.

Co-occurring species

 This function finds species, which are most frequent in the relevés where selected species occurs. The species must be selected by mouse click in the Species table part before the running the function. The function is called from the menu ANALYSIS and CO-OCCURRING SPECIES.The selected species is shown at the top of the Co-occurring species window, with the number of relevés in which it occurs below. The list of the most frequently co-occurring species is sorted by decreasing frequency in the relevés where the selected species occurs. The value shown in the first column is the percentage of relevés of the selected species also containing the listed species. The next columns are: species name, layer, species frequency in the dataset, and frequency of joint occurrence of current and selected species.

Interspecific associations

 This procedure is the basic step of COCKTAIL method; it tests interspecific association between the selected species and each other species in the table. A fidelity measure is calculated for each pair of species, which gives information on their reciprocal affinity in the dataset. Fig. 17 shows the display form of this function, with a sorted list of species positively and negatively associated with the species previously selected by clicking in the Species part of the table. The list with positive associations can be exported to the current export *.RTF file (see Section 10).All species in the list box can be marked by shift or control button and mouse click by using the button MARK SELECTED SPECIES IN THE TABLE. The function INTERSPECIFIC ASSOCIATIONS is also used in the other parts of the program – Export of all interspecific associations (Section 10.3), Calculation of indicator values for species II (Section 7.4), Dependence sorting (Section 6) and INI groups (Section 9.5). Explanation of list columns: fidelity measure, species name, layer, species frequency in the data set, frequency of joint occurrence of current and selected species in the data set.

An example of difference between mentioned functions

The maximum value (100 %) in the function Co-occuring species has a comparison of the species A with both B and C, while the function Interspecific associations gives a maximum fidelity value only for comparison of species A with C.

Species A ++++++++++..........................
Species B ++++++++++++++++++++++++++..........
Species C ++++++++++..........................

INI groups

 This function searches for an appropriate species combination as a starting group for the function COCKTAIL groups, i. e. a group of two or more species which frequently occur together. Select one or a few species and add them into the form. State the number of species to be added to the group (1-10 can be added at a time) and press the Run button. The function calculates interspecific associations of the first species from the list with all the other species, sorts them by decreasing values, and selects the one or more most associated species. These most associated species are added to the list. The procedure is repeated with the second species and with all subsequent species now in the list, and is terminated after testing all listed species. Mark backwards in the table marks the listed species with the specified colour.Warning! High number of species to be added in larger tables can cause a very long cycle, so the program will have to be manually interrupted.

COCKTAIL groups

 The function COCKTAIL GROUPS searches for optimal combinations of species, which have similar distributions in the data set and can be used as sociological species groups in vegetation classification. The reciprocal test of species associations is based on the fidelity calculation. A relevé is considered to contain the species group if more than half of species of the group occur in it. How to create a species group: Select a starting group of species (one or more species, which were selected by the functions Interspecific associations or INI groups); all the selected species should have the same colour. Open the form and add starting group into the list box. Calculate the minimum number of selected species which must be present in a relevé if the group is to be considered present in it. The minimum is calculated statistically so that observed frequency of joint occurrence of several species exceeds the expected frequency in case of random and independent distribution of these species in the dataset. However, using half of the selected species as the minimum value is better in many cases. The desired minimum value can be specified manually after the calculation of statistical minimum value is done. Recolour relevés where at least the minimum number of species is present (i.e. where the group is present). Calculate fidelity for the coloured group of relevés – a new form displays. Select any new species, which has similar distribution. Recolour this species and add it into the COCKTAIL groups form. Continue from point 3. Terminate the process when the group seems to be optimal for syntaxonomic classification. This may be when it is similar to a group of diagnostic species traditionally recognized in the syntaxonomic literature.

An optimized group with relatively high fidelity values (see bellow) can be saved by writing its name into the combo box and using the function ADD GROUP INTO THE TABLE. If you wish to see the percentage synoptic column only for coloured relevés, select the SYNOPTIC COL button.

Species groups can be added directly into the table as a pseudospecies (with ### before the group name). Such groups can be treated and analysed in the same way as proper species and can be combined with other species in the function Group aggregation. The column defined by selected species group can be tested for constants and dominants displayed after setting of cover threshold parameter (Header data analysis).

Group aggregation

The group aggregation function selects relevé groups by combining presence of species groups and dominance of individual species. It uses species groups loaded in the table and dominant species which are defined by cover values exceeding a selected threshold. Species groups and dominant species are combined by the logical operators AND, OR, AND NOT, with the hierarchy defined by parentheses.

The query contains logical operators AND, OR and NOT (= AND NOT). Species group names consist of the characters ### followed by the species group name. Names of dominant species are not preceded by characters ###, but they have suffixes such as UP05 or UP25. For example, UP05 means that species is considered if its cover in the given relevé is higher than 5 % (UP25 means higher than 25 %).

Before running the query it can be checked by Show definition.

Warning: All pairs of logical variables associated by one operator must be put in parentheses!

For details of the procedures described in Sections 9.6 and 9.7, see Bruelheide (1995, 1997, 2000) or Bruelheide & Jandt (1995).

Expert system

Expert system can automatically assign a relevé to a vegetation type, if there is already a classification based on species groups. The classification algorithm must be included in *.ESY file. This file should preferably be created as a product of the classification in a large dataset and must include all required information on aggregated species, species groups and their combinations into vegetation types. A result of the expert system run is shown in Fig. 21. The *.ESY file has a text structure and can be created manually.

In the first part of this file aggregated species are defined:
(example – species name; species number; number of species aggregated; Turboveg numbers of aggregated species)

(S) Allium senescens ssp. m;47972;2;456;457;
(S) Artemisia campestris;47981;2;860;861;
(S) Avenula pratensis;47985;2;1183;1184;
-1
(the end of this section is marked by -1)

The next section defines species groups:
(example – group name; minimum number of species in one relevé; Turboveg numbers of species included.......)

Agrimonia eupatoria;4;210;1096;2954;11496;
Asplenium cuneifolium;3;1038;11236;838;
Astragalus austriacus;4;1088;2645;12080;1101;
-1
(the end of this section is also marked by -1)

The last section contains logical formulas with community definitions:
(First line – community name, second line – logical formula)

Asplenium cuneifolium-Sesleria albicans community
<### Asplenium cuneifolium>AND(<### Sesleria albicans>OR<Sesleria albicansUP25>)
Cirsium pannonicum-Sesleria albicans community
[<Sesleria albicansUP05>AND<### Cirsium acaule>]NOT[(<### Sesleria albicans>OR<Sesleria albicansUP50>)OR<### Festuca pallens>]