How to import table data from TURBOVEG

Open, Save, Imports and Exports

The program uses a special format for data storage. JUICE files have the same name and three different suffixes (WCT - table data, colours, ecological informations about species etc.; EXP - header data; STR - header structure).

Open
Save
Import
    Table from
        TURBOVEG
        EXCEL
        Cornell condensed file
        Text file
    Short headers
    Species data
    Species groups

Export
    Select RTF file
    Table
    S ynoptic table
    CC! file
    DMAP file
    MULVA input file
    MATLAB input file
    Export HEAD for (colour) relevés
    Short headers
    Species data
    All interspec. associations

Open file

Displayed dialog box allows to select WCT files available in selected directory. Header data are only optional and needn't be imported and opened together with WCT file. They may be attached to WCT file additionally (see Import header data).

Save file

The table with all additional informations as colours, structure, species names, ecological values, separators etc. is saved through dialog box. The program will ask you to save current file before its end or selection of the function Open file.

Table and header data imports

The program is designed as an extension of the TURBOVEG database program. However, I have prepared some other import filters for users who have no possibility to use TURBOVEG. We have small experiences with these import gates and I will be pleasured if you will inform me about your success with them.

Import from TURBOVEG

Export table and header data from TURBOVEG:

Open TURBOVEG for WINDOWS.
Select database.
Make a new selection of relevés using the menu SELECT.
Export selected relevés by using the function EXPORT and JUICE INPUT FILES. The program will generate three files with the same name - Cornell condensed file with table data and EXP and STR files with headers. An example of these files is available for download.
Select fields of header data which will be used in JUICE.

Import table to the JUICE program

Open the menu FILE and IMPORT and TABLE FROM and TURBOVEG.
Press button OPEN CHECK LIST FILE and find the file with actual check list. If the string lenght is stored correctly, current check list will be listed in the bottom part of the form. The path and file name will be stored into INI file and recognised automatically during the next import.

Warrning! Numbers 5, 7, 38 are an example of character numbers which delimite string lenghts reserved for SPECIES NO., CODE and SPECIES in the text file. They are correct only for NEWFLORA.TXT file, parameters for other check list files will depend on the real string lenght of lines and can be stored into the first line of the text file (see KUBAT.TXT file as an example).
Warrning! The Central European version of the checklist in downloaded installation package (NEWFLORA.TXT) is valid only for Austria, Czech Republic, and Slovakia for TURBOVEG exports). If you are the user from other country or use other phytosociological database program, please, create check list yourself. It is recommended to export this check list from TURBOVEG before the first data import :-). The check list export function can be found in the program the menu MANAGE and SPECIES LIST and <any TURBOVEG in checklist> and EXPORT and LIMITED LIST FOR JUICE.
Press the button OPEN CC! FILE and select Cornell condensed file with TURBOVEG format to be imported (analyse carefuly training data file structure). Files with header data will be attached and displayed together with basic information about header fields and table size.

Warrning! The table should be saved immidiately after import in JUICE format.

Connection of new relevés with an existing table

This function was created for an additional storage of new relevés into previously managed table. It is possible to connect only WCT table with some Cornell condensed file - the connection of two JUICE tables (WCT files) is not possible.

Open WCT table
Select FILE IMPORT TABLE FROM TURBOVEG
Open CC! file and select option Append table (without head) into old table

Warrning! Header data should be imported through HEADER DATA IMPORT.

The program will compare actual and new list of species and connect same species in the same layer. The user can modify this selection in this window. Upper part of this form is reserved for species which were not connected automatically. You can select appropriate species and press the button CONNECT SELECTED SPECIES. All unidentified species from the new CC! file will be imported down the table as new species.

Header data import

The structure of header data is selected in TURBOVEG and exported before the first import to JUICE. It may happen that some necessary information needed for the table analysis will miss after table preparation. This function allows to connect newly exported header data to an existing WCT file with new header informations.

Select FILE IMPORT TABLE FROM TURBOVEG
Open CC! file with exported header data

Warrning! The table data must contain TURBOVEG relevé number. The selection of relevés must be the same or larger than the selection of relevés in current WCT file.
Select option REPLACE ONLY HEADER DATA
Press CONTINUE >>> - all headers will be replaced by new values.

Import from spreadsheed file (e. g. Microsoft EXCEL)

This table format is useful only for smaller tables. Please, for large tables use TURBOVEG database system or convert your table into Cornell condensed file. Study the table import format carefully!!!

Download an example and open the file in any text editor. See the format. The same format is generated e. g. by Microsoft EXCEL, when the table is saved as CSV file. The same format is also generated during table export from JUICE to Microsoft EXCEL.
Select menu FILE IMPORT TABLE FROM EXCEL.
Press the OPEN FILE button and setect character which separate columns, store line number with relevé numbers, line number with the first species and check, if the second column contains layer numbers.
Import table.

Import from CC! file

This possibility allows to import data only with short cut species names. The structure of CC! file must be similar as in FILE IMPORT TABLE FROM TURBOVEG. Please, in problems contact author of the program.

Import from text file

It is the easiest import format for users without TURBOVEG. The table consists of four files with the same name and different suffixes: TXT, TAB, EXP, STR. There is an example of such table. These files can be also exported through EXPORT and TABLE as a text files.

TXT file consists of three columns (SPECIES NAME, LAYER, TABLE DATA) with the same number of characters which are separated by 5 spaces.

TAB file is optional. Each line contains a special identification number of relevé (a range from 1 to 999.999) as a TURBOVEG relevé number. The file can be omitted.

STR file defines table data (variable names) and their starting possition in EXP file.

EXP file contains relevé information about the site and environmental factors. It must be created in accordance with STR file.

Select menu FILE IMPORT TABLE FROM TEXT FILE. Find a path of your table and select TXT file.
The computer will detect different cover characters and will try to find cover values for them. You can change these values by double click on any line in the list window.
Press CONTINUE >>> and import a table.

Import short headers

Short headers can contain only six characters per one relevé. They are displayed on the top ot the table and may contain Relevé number, Turboveg number, Sequence number, Group number, different counts or calculations (e. g. Equitability), part of header data (e. g. Year or Syntaxon code) or some other external information loaded through import of short headers.

The import allows to combine several informations into one header (For example it is possible to reserve first two characters for vegetation class and next four characters for a year of relevé sampling). The file have to contain Relevé number and short header value. The value can be copied only partly (define source range of copied characters) and can also replace only part of actual short head.

Warrning!!! Please, before import of your data try to create exporting file with short headers and study its structure.

Species data import

Species data are stored near to species name in slightly grey field of the table. Species data can contain e. g. layer, some ecological or biological information about the species. This field can be used for species sorting and making separators among species groups. The import uses all text files with fixed lenght of lines, which contain a species name and species data information(s).

Exports

The JUICE program allows to export selected parts of tables, header data, latitude and longitude coordinates for the mapping program DMAP (Morton 2001), fidelity values for Interspecific associations of COCKTAIL group functions, Cornell condensed files, synoptic tables and average Ellenberg values. Generally, there are two export types. The first type uses ad hoc defined files, usually in *.TXT format. The second type uses *.RTF format into which you can make several exports of data of different type. This file remains open until you end your session or make a new selection under FILE and EXPORT and CURRENT FILE: <path and file name>.

Table export

The table is exported into an *.RTF file to facilitate editing and presentation.
Select relevé colour and mark the relevés to be exported
Check the *.RTF file setting (menu FILE EXPORT CURRENT FILE: <any path and file name>)
Press FILE EXPORT TABLE
Choose colour of relevés to be exported and frequency threshold for species to be placed below the table.
If you want to change the cover scale used in the output file, double-click in the list box on any percentage value which needs a new character value and change the output character.

Synoptic table export

The full synoptic table can be exported into the *.RTF file for editing and presentation.

Select relevé colour and mark the relevés to be exported
Check the *.RTF file setting (menu FILE and EXPORT and CURRENT FILE: <any path and file name>)
Display the table in the form of synoptic table (menu SYNOPTIC TABLE PERCENTAGE or CATEGORIES)
Press FILE EXPORT SYNOPTIC TABLE

Export of fidelity values

Synoptic tables PERCENTAGE, CATEGORIAL and FIDELITY VALUE can be saved into the selected RTF file and replaced into some text editor for final editing. Before export display the synoptic table in required form and then select FILE EXPORT SYNOPTIC TABLE. The synoptic table will be added into the current file (menu FILE EXPORT CURRENT FILE: <file name>).

Table export in Cornell condensed format

A table modified by JUICE can be exported into a Cornell condensed file which is an input file for several other applications.

Select relevé colour and mark relevés to be exported
Press FILE EXPORT CC! FILE FOR (colour) RELEVÉS and save the file.

MATLAB input file export

The MATLAB export was developed for neural network data analysis. Please, try to study the structure of exported file or contact author of the program.

MULVA input file export

MULVA software is DOS classification package which is freely available on internet. The program JUICE supports export and it is possible to sort table according to program results.

Header data export

This function creates a text file with selected items. For example, latitude/longitude export can be used for authomatic distribution mapping of relevés belonging to the same group.

Select relevé colour and mark relevés to be exported
Press FILE EXPORT HEADER DATA FOR (colour) RELEVÉS
Select header items to be exported (use mouse and CTRL or Shift button) and save the file.

Export of DMAP coordinates

The JUICE program can create the *.DIS and *.NAM files necessary for mapping with DMAP- (Morton 2001). There are three ways how to do this: (1) export species (and also saved species groups) of a selected colour, (2) relevés of a selected colour or (3) export the entire table. All variants of DMAP export are available in the menu FILE EXPORT DMAP FILE.

Warrning! The program is possible to run DMAP automatically in the case you have DMAP installed in the directory C:\DMAPW.

Export short headers

Species data export

Species data are stored near to species name in slightly grey field of the table. Species data can contain e. g. layer, some ecological or biological information about the species. This field can be used for species sorting and making separators among species groups. The export cleate a text file with defined fixed lenght of each line. The file contains species name and species data. Each exported file with species data can be imported through function Species data import.

Export of all interspecific associations

Interspecific association (expressed as species-to-species fidelity value) can be calculated for all pairs of species present in the data set. Selected species and a list of the most associated species, sorted by decreasing fidelity, can be exported into *.RTF file. This procedure is repeated for all species in the data set whose frequency is higher than selected threshold. An example is stored at the web page: http://www.sci.muni.cz/botany/assoc_a.htm.

Select relevé colour and mark relevés to be exported
Check the *.RTF file setting (menu FILE EXPORT CURRENT FILE: <path and file name >)
Press FILE EXPORT ALL INTERSPECIFIC ASSOCIATIONS
Select the number of associated species to be exported and the frequency threshold for species to be considered. If you want to export all values set the first column to the maximum and second to the minimum value possible. The program will calculate interspecific associations for all species and export the species meeting the selected criteria, along with their fidelity values.