Turboveg for Windows - Synbiosys.alterra.nl).

Turboveg for Windows - Synbiosys.alterra.nl).
Turboveg for Windows
© 1998-2016 Stephan Hennekens
Version 2
10-12-2016
Contents
3
Table of Contents
Foreword
0
Part I Introduction
8
Part II General
10
1 Getting
...................................................................................................................................
started
10
2 Network
...................................................................................................................................
installation
11
3 Usage...................................................................................................................................
of keyboard, mouse and toolbars
12
4 User management
................................................................................................................................... 13
5 Database
...................................................................................................................................
structure
14
6 Popup
...................................................................................................................................
lists
16
7 Linking
...................................................................................................................................
an ecological database
16
8 Trouble
...................................................................................................................................
shooting
17
Part III Database
20
1 Open................................................................................................................................... 20
2 Close................................................................................................................................... 20
3 New ................................................................................................................................... 20
4 Rename
................................................................................................................................... 21
5 Delete................................................................................................................................... 21
6 Renumber
................................................................................................................................... 21
7 Pack ...................................................................................................................................
& reindex
22
8 Combine
...................................................................................................................................
databases
22
9 Append
...................................................................................................................................
another database
23
10 Modify
...................................................................................................................................
database structure
23
11 Organise
...................................................................................................................................
header data
25
12 Modify
...................................................................................................................................
database attributes
26
13 Connecting
...................................................................................................................................
a database to another species list
26
14 Statistics
................................................................................................................................... 27
15 Hunt duplicates
................................................................................................................................... 27
16 Identification
................................................................................................................................... 28
17 Backup/Restore
................................................................................................................................... 28
18 Copy ...................................................................................................................................
from/to
29
Part IV Edit
32
1 Switch
...................................................................................................................................
edit mode
32
2 Modify
...................................................................................................................................
header data
32
3 Modify
...................................................................................................................................
species data
33
© 1998-2016 Stephan Hennekens
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4
Turboveg for Windows
4 Replace
...................................................................................................................................
species
33
5 Replace
...................................................................................................................................
all synonyms with accepted names
33
6 Geo-referencing
...................................................................................................................................
using Google Maps
33
7 Add ecological
...................................................................................................................................
indicator values
35
8 Add diversity
...................................................................................................................................
index values
36
9 Add a...................................................................................................................................
relevé
37
10 Add a...................................................................................................................................
table
37
11 Delete...................................................................................................................................
relevés
38
12 Replace
...................................................................................................................................
header data
38
13 Combine
...................................................................................................................................
relevés
39
14 Combine
...................................................................................................................................
subplots into plots
39
15 Combine
...................................................................................................................................
vegetation layers
40
16 Copy ...................................................................................................................................
current relevé
40
17 Filter ...................................................................................................................................
selected relevés
41
18 Copy ...................................................................................................................................
relevé to clipboard
41
19 Search
...................................................................................................................................
a relevé
42
Part V Import
46
1 Import
...................................................................................................................................
Turboveg XML file
46
2 Import
...................................................................................................................................
TurbovegCE XML file
49
3 Import
...................................................................................................................................
Cornell condensed species file
49
4 Import
...................................................................................................................................
Excel table
51
5 Import
...................................................................................................................................
free format species data table
52
6 Import
...................................................................................................................................
free format header data table
56
7 Import
...................................................................................................................................
SORT file ('Tabulator Tabelle')
58
8 Import
...................................................................................................................................
XY-coordinates from Shapefile
62
Part VI Select
66
1 Select...................................................................................................................................
current relevé
66
2 Select...................................................................................................................................
all relevés in current database
66
3 Deselect
...................................................................................................................................
all relevés in current database
66
4 Flip the
...................................................................................................................................
selection in current database
66
5 Select...................................................................................................................................
relevés random
66
6 Build ...................................................................................................................................
a query
67
7 Clear...................................................................................................................................
a selection
68
8 Save ...................................................................................................................................
a selection
68
9 Retrieve
...................................................................................................................................
a selection
68
Part VII Export
72
1 Export
...................................................................................................................................
to Turboveg database
72
© 1998-2016 Stephan Hennekens
Contents
5
2 Export
...................................................................................................................................
to MS ACCESS database
72
3 Export
...................................................................................................................................
to standard XML file
72
4 Export
...................................................................................................................................
to XML project file for TurbovegCE
73
5 Export
...................................................................................................................................
to ESVeg compatible XML file
74
6 Export
...................................................................................................................................
to a Cornell condensed species file
74
7 Export
...................................................................................................................................
to a user defined header data file
75
8 Export
...................................................................................................................................
to a spreadsheet table
76
9 Export
...................................................................................................................................
to a SDF formatted database
77
10 Export
...................................................................................................................................
to JUICE input files
77
11 Export
...................................................................................................................................
to ESPRESSO/TAB input file
78
12 Export
...................................................................................................................................
to MULVA input file
79
13 Export
...................................................................................................................................
to SYNTAX-5 input files
79
14 Export
...................................................................................................................................
to SYNTAXON input file
79
15 Export
...................................................................................................................................
to TAXAL input file
79
16 Export
...................................................................................................................................
to FUZPHY input files
79
17 Export
...................................................................................................................................
to species check list
79
18 Export
...................................................................................................................................
to herbarium etiquettes
79
19 Export
...................................................................................................................................
to herbarium etiquettes from template
80
20 Export
...................................................................................................................................
to Shapefile
80
21 Export
...................................................................................................................................
to mapping file
80
22 Export
...................................................................................................................................
to Google Earth
81
23 Export
...................................................................................................................................
to Darwin Core Archive
81
24 Relevé
...................................................................................................................................
data sheets
82
25 Analyze
...................................................................................................................................
header data
84
26 Analyze
...................................................................................................................................
ecological data
85
Part VIII Manage
88
1 Modify
...................................................................................................................................
popup lists
88
2 Delete...................................................................................................................................
a dictionary
88
3 Modify
...................................................................................................................................
a species list
89
4 Create
...................................................................................................................................
a new species list
89
5 Import
...................................................................................................................................
a species list
89
6 Delete...................................................................................................................................
a species list
92
7 Modify
...................................................................................................................................
an ecological database
92
8 Configuring
...................................................................................................................................
an ecological database
93
9 Format
...................................................................................................................................
longitude/latitude
93
10 Modify
...................................................................................................................................
user privileges
93
11 TurbovegCE
...................................................................................................................................
settings
94
© 1998-2016 Stephan Hennekens
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Turboveg for Windows
Index
97
© 1998-2016 Stephan Hennekens
Part
I
8
1
Turboveg for Windows
Introduction
Turboveg for Windows is a program designed for the storage, selection, and export of
vegetation data (relevés).
Data can be imported manually (separate relevés or tables) and automatically (import of data
files).
You can select relevés by choosing one or several of the header data or by choosing a
species or a combination of species.
Several filters are available to export the selected relevés to enable further analysis with
various programs (e.g. MS Access,Twinspan, Canoco, PC-ORD, Mulva, Syntax-5, Excel,
Juice, ArcView, ArcGIS, GoogleEarth).
The standard structure of the table is fixed, but you can easily extend this standard structure
by defining extra fields to fit your own needs. You can extend both the header data (e.g. a field
for soil type) and the species data (e.g. add a field for the phenology of the species). Each
database can have its own extension.
If you have never worked with Turboveg before than it is recommended to read the Getting
started 10 section of this Help first.
© 1998-2016 Stephan Hennekens
Part
II
10
Turboveg for Windows
2
General
2.1
Getting started
I you have never worked with TURBOVEG before, probably one of first things you want to do,
is to enter relevés into a database. The following steps can be taken in order to enter data,
select the data stored in the database, and to export the relevés to a relevant format for
further analysis (e.g. a classification using the software program JUICE).
Every dialog window has a Help button. Use it if you do not know what to do.
1. Create a database if no database is available or if you want to start with an empty one.
From the menu select Database | New. The only two entries to be filled in are Database
name and Range for system numbers. An empty database will be created. Two new
empty windows are opened; the window on the left site will contain the so-called header
data, the window on the right site is reserved for species data (species name, vegetation
layer and cover abundance).
2. Start entering (single) relevés by selecting Edit | Add a relevé from the menu. In two
steps a relevé can be entered. The first step will serve to put in so-called header data,
species data are entered with the second step.
If there is relevant information (e.g. measured pH values for each relevé) which can not be
stored in one of the available fields, the possibility exists to extend the database. See
Modify the database structure 23 for details.
There are more methods in Turboveg to enter relevés into a database:
Manually:
Edit | Add a table 37
To avoid entering the species for each relevé in the (printed) table a matrix of relevés and
species can be generated that can be filled. In this case the species data are first entered
into the database, in the second step the header data can be completed.
By means of computerized tables:
Import | Cornell condensed species file
Import | Free format species data file 52
Import | Free format header data file 56
49
3. Once we have stored relevés in a database, selections can be made in various ways. The
simplest method is to open the database, and to press the Spacebar on each relevé we
want to select. Make sure that the window with the header data is active. Selected relevés
will get a flag and the lines become yellow. De-selecting a relevé may also be achieved by
pressing the Spacebar.
If all relevés from the database need to be selected a one-click action can be performed
by selecting Select | Select all releves of current database 66 from the menu. The
same can be done for de-selecting all relevés by selecting Select | Deselect all releves
of current database 66 .
For sophisticated selections choose Select | Build query 67 . Selection criteria can be
© 1998-2016 Stephan Hennekens
General
11
defined on the basis of combinations of header data items and/or combinations of
species. Also the species cover abundance can be taken into account.
The selected relevés are listed in a separate window. This is the window that is first
opened (and remains opened) when a Turboveg session is started.
A selection is not restricted to one database. You may open several databases and
perform a selection in one run. The only restriction is that the relevés in the selected
databases have a unique system number. To open more database select Database |
Open 20 and mark (mouse click or press the Spacebar) the desired database names.
4. For further analyses of the data TURBOVEG offers quite a few export formats. One of
most commonly used formats is the Cornell condensed format. A Cornell condensed
formatted file can serve as an input file for e.g. TWINSPAN and CANOCO. To create a
Cornell condensed file select Export | Cornell condensedspecies file 74 from the
menu. In the export file only those relevés will be included that are listed in the window
with selected relevés. This can even be achieved when all databases are closed.
For further analyses with JUICE it is recommended to export the selection to a 'Standard
XML file' (Export | Standard XML file 72 ), instead of using the obsolete export function to
'JUICE input files'. JUICE is an excellent software program for classification; it can handle
more than 30.000 relevés in spread sheet.
To be continued…
2.2
Network installation
Use the installation program (TVSETUPxxxx.EXE) to install Turboveg for Windows on the
server. Then make a shortcut to Turboveg on each working station where the program will be
used. The program TVWIN32.EXE is by default present in the directory <network drive>:
\TURBOWIN\BIN\.
Activate the property window of the Turboveg shortcut and make sure that the working
directory is not the same as the program package-containing directory. You can set the
working directory under "Properties"->"Shortcut"->"Start in"
TVWIN32.EXE can be executed with a parameter, e.g. ‘C:\TURBOWIN’. In this case
Turboveg will be forced to store its initialisation file – TVWIN.INI – in the directory C:
\TURBOWIN. If Turboveg is executed without a parameter the Windows directory will be used
to store the initialisation file.
After the installation the following directory structure can be build on the server (the set-up
program copies all the files on to one drive, and one directory).
F:\TURBOWIN\BIN
\HELP
\IDENTIFY
\MAPS
G:\TURBOWIN\USERS
© 1998-2016 Stephan Hennekens
all
RO
RO
RO
RO
RW
manager
RO
RO
RO
RO
remarks
RW (incidentally used to administrate a new
12
Turboveg for Windows
user)
H:\TURBOWIN\POPUP
RO
RW
I:\TURBOWIN\SPECIES
properties
RO
RW (incidentally used to change the
J:\TURBOWIN\DATA
databases)
RW
of the ecological database)
RW (this directory holds the common
RO=ReadOnly
RW=ReadWrite (including Create rights)
The subdirectories HELP, IDENTIFY, and MAPS are linked to the subdirectory \BIN
(containing executables) and can therefore NOT be located on another disk or subdirectory.
If desired, all other subdirectories that are not directly linked to the subdirectory \BIN can be
moved to other disks.
In addition, on every working station the following directory structure can be build:
C:\TURBOWIN\DATA
\OLD_SELS
(the directory that holds the private databases)
Start Turboveg on the desired working station. The first time Turboveg is executed directories
have to be defined. In most cases the default directories can be accepted.
2.3
Usage of keyboard, mouse and toolbars
Menus and buttons on the dialogue windows can, in most cases, be activated by both the
mouse and the keys.
You can activate the main menu by pressing Alt+ one of the underlined characters (e.g. Alt+D
activates the menu Database). Within a menu you can choose an option by pressing the
underlined character (e.g. clicking R selects the sub-menu Rename).
In a dialogue window you can activate the desired button by pressing Alt + the underlined
character present in the text on this button.
Often used functions can also be activated by using the buttons on the toolbars. The toolbars
to the more common functions is presented below.
© 1998-2016 Stephan Hennekens
General
2.4
13
User management
User management only concerns the network version.
The following table shows an overview of the functions in Turboveg for Windows and the privileges of the
manager and users (4 types).
Manager
Users
I
II
Edit a common database
X
X
X*
Edit a private database
X
X
X
Search and replace in a common database
X
X
X*
Search and replace in a private database
X
X
X
Import data in a common database
X
X
X*
Import data in a private database
X
X
X
Add indicator values to a common database
X
X
X*
Add indicator values to a private database
X
X
Edit popup lists
X
Configure the ecological database
X
Select relevés
X
Export relevés from a common database
III IV
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
Export relevés from a private database
X
X
X
X
X
Change privileges users
X
Create a common database
X
Create a private database
X
X
X
X
X
Rename a common database
X
Rename a private database
X
X
X
X
X
Delete a common database
X
Delete a private database
X
X
X
X
X
Modify structure of a common database
X
© 1998-2016 Stephan Hennekens
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Turboveg for Windows
Modify structure of a private database
X
X
X
X
X
Renumber a common database
X
Renumber a private database
X
X
X
X
X
Organise header data
X
X
X
X
X
Re-index a common database
X
Re-index a private database
X
X
X
X
X
Change attributes of a common database
X
Change attributes of a private database
X
X
X
X
X
Backup a common database
X
X
X
Backup a private database
X
X
X
X
X
Restore a common database
X
Restore a private database
X
X
X
X
X
Edit a protected species list
Partly
Edit a non-protected species list
X
Privileges of users of common databases:
I:
Edit and export permission for all databases
II:
Edit permission for some databases, export permission for all databases
III:
No edit permission, export permission for all databases
IV:
Neither edit nor export permission for all databases
*
2.5
Edit permission for only some, manager-defined databases
Database structure
A Turboveg database is build up by three tables and three index files.
Tables
Index files
TVHABITA.DBF
TVABUND.DBF
REMARKS.DBF
TVHABITA.CDX
TVABUND.CDX
REMARKS.CDX
(table with header data)
(table with species data)
(table with remarks)
The default structure of the tables is as follows.
TVHABITA.DBF
Field name
¦
Type
¦
¦
Width
© 1998-2016 Stephan Hennekens
General
¦
¦
¦
¦
¦
¦
RELEVE_NR
COUNTRY
REFERENCE
TABLE_NR
NR_IN_TAB
COVERSCALE
PROJECT
AUTHOR
DATE
SYNTAXON
SURF_AREA
UTM
ALTITUDE
EXPOSITION
INCLINATIO
COV_TOTAL
COV_TREES
COV_SHRUBS
COV_HERBS
COV_MOSSES
COV_LICHEN
COV_ALGAE
COV_LITTER
COV_WATER
COV_ROCK
TREE_HIGH
TREE_LOW
SHRUB_HIGH
SHRUB_LOW
HERB_HIGH
HERB_LOW
HERB_MAX
CRYPT_HIGH
MOSS_IDENT
LICH_IDENT
REMARKS
N
C
C
C
C
C
C
C
C
C
N
C
C
C
C
N
N
N
N
N
N
N
N
N
N
N
N
N
N
N
N
N
N
C
C
C
6
2
6
6
3
2
3
4
8
7
7
15
4
3
2
3
3
3
3
3
3
3
3
3
3
2
2
4
4
3
3
3
3
1
1
56*
15
Decimals
¦
Description
0
0
0
0
0
0
0
0
0
0
2
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
1
1
0
0
0
0
0
0
0
Relevé number (= system number)
Country code
Publication reference number
Number of table in publication
Relevé number in table
Cover scale
Project code
Author code
Date (year/month/day)
Syntaxon code
Surface area (m²)
UTM grid reference
Altitude (m)
Aspect (`NWZO')
Inclination (degrees)
Total cover (%)
Cover trees (%)
Cover shrubs (%)
Cover herb layer (%)
Cover mosses (%)
Cover lichens (%)
Cover algae (%)
Cover litter (%)
Cover open water (%)
Cover bare rock (%)
Height (high) tree layer (m)
Height low tree layer (m)
Height (high) shrub layer (m)
Height low shrub layer (m)
Mean height high herb layer (cm)
Mean height low herb layer (cm)
Maximum height herb layer (cm)
Mean height cryptogame layer (mm)
Mosses identified (Yes/No)
Lichens identified (Yes/No)
Remarks
*The total length of the remarks field covers a maximum of 1000 bytes. However, the first 56
bytes is stored in the table TVHABITA.DBF, and the remaining bytes are stored in the table
REMARKS.DBF.
TVABUND.DBF
RELEVE_NR
SPECIES_NR
COVER_CODE
LAYER
N
N
C
N
© 1998-2016 Stephan Hennekens
6
5
2
1
0
0
0
0
Relevé number (= system number)
Species number
Cover abundance code
Vegetation layer
16
Turboveg for Windows
REMARKS.DBF
RELEVE_NR
REMARKS
2.6
N
C
6 0
25 0
Relevé number (= system number)
Remarks
Popup lists
The Turboveg databases are linked to so-called popup lists (lookup tables) with a.o. authors,
literature references, cover scales, syntaxa (plant communities), and species. In the
databases an author, for example, is stored by its code; the translation to its full name is
stored in the lookup table containing authors names.
The table structure of the popup lists (as a matter a fact this counts for all the tables used by
Turboveg) is defined in a database dictionary. Therefore it is possible to (re)build all the
tables from the dictionary.
A Turboveg system can handle multiple dictionaries, each dictionary has its own set of lookup
tables.
A dictionary is indicated with a name; the standard dictionary is called 'Default dictionary'.
Dictionaries can be preselected by selecting a dictionary name from the drop down menu
which is located on the toolbar of the main window.
Also see: Modify popup lists
2.7
88
Linking an ecological database
You can link an ecological database to each and every species list. There are a few
preconditions concerning format, content, and directory of the database to be stored.
The format of the database has to be DbaseIII+.
The name of the database table has to be ECODBASE.DBF, and it must be stored in the
same directory that contains the species list. For example for South Africa the species list
is by default stored in the directory C:\TURBOWIN\SPECIES\SOUTHAFR.
It has to contain a field that holds the species numbers, since the species numbers form
the link with the species list that is present in Turboveg. If the species numbers are stored
in the first column of the database, and the field specifications are:
- Field name = ”SPECIES_NR”
- Field type = “N”
- Field length = 5
© 1998-2016 Stephan Hennekens
General
17
- Field decimals = 0
then the management of the list can be done within Turboveg. Otherwise an external
management tool that can handle dBaseIII+ formatted files is required
Do not make fields larger than necessary, and define field type as “C” (character).
Compared with a numerical field (field type = “N”) a clear distinction can be made
between missing values and ‘0’ in a character field.
An ecological database can also be created and management within Turboveg. Therefore
select Manage | Species lists | Edit | <species list concerned>. On the dialog window to
maintain the species list click the Create or Modify button.
See also: Configuring an ecological database
93
In the ecological database all kind of plant traits can be stored. These can be indicator values
(e.g. Ellenbergs indicator values) or morphological, chorological, phytosociological,
phenological, and other characteristics.
If you want to make calculations based on the values of a certain item make sure that only
numerical values are stored in the database for that particular item.
For example, if you want to know the mean altitude of all species in the relevés than do not
store the following values in the database: “0-1000”, “200-2000”, etc. Create two fields
instead, one field holding the minimal altitude, and one holding the maximal altitude. As a
result two mean values can be calculated, one for minimal altitude, and one for maximum
altitude.
Items with which we never can calculate are for example are life-form, phytosociological
status, flowering periode, etc.
Using the data from the ecological database, the mean value of an indicator value of each
relevé can be calculated (see Add ecological indicator values 35 ). In addition, if exporting
a selection to a table you can add for each species one or more parameters from the
ecological database (see Export to a spread sheet table 76 ).
2.8
Trouble shooting
The relevés do no longer contain species.
Probably the index file of the species database has been damaged. Solution: Choose
Database, Re-index to remake all indexes belonging to the damaged database.
When the indicator values are added it appears that for some relevés no
calculations have been made.
Possible solution: Choose Database, Re-index to remake all indexes belonging to the
damaged database. Then recalculate the indicator values.
It is not possible to calculate ecological indicator values per relevé.
Possibly the ecological database is present but not yet configured. See Configuring an
ecological database 93
© 1998-2016 Stephan Hennekens
18
Turboveg for Windows
The wrong species list is linked to the database.
Choose Database, Modify attributes and select the required database from the list.
Select the proper species list and click on Save attributes to store the new definition.
© 1998-2016 Stephan Hennekens
Part
III
20
Turboveg for Windows
3
Database
3.1
Open
Menu: Database | Open
In the left panel the species list(s) (blue books) and folders (if present) are presented in a tree
view.
Select the species list (and folder if present) that holds the database(s) you want to open.
Databases: You can select one or more databases by pressing SPACE or by clicking the
mouse. But, if you have selected several databases you can only select relevés. Modifying
relevés is only possible when you have selected only one database (see Selecting relevés
67 ).
Open: This is to open the selected databases.
Select all: Select all names that are present in the list Databases.
Deselect all: Deselect all names that are present in the list of Databases.
Rescan: Re-scan the hard disk for present databases.
3.2
Close
Menu: Database | Close
It is recommended to close a database when you have finished working with it, especially in
the case of the network version. If, for instance, user A wants to renumber database Z, he can
only do so in case he is the only user of that database (database Z is exclusively opened by
him). If user B is using the same database, user A will get a message that the database
cannot be exclusively opened for him and that he thus cannot renumber this database.
3.3
New
Menu: Database | New
Database name: Enter the name of the new database.
Folder: If desired you can enter or select the name of a folder. Folders are especially useful if
you have many databases that must be ordered in a meaningful way.
Species list: Choose a species list to be linked to the database.
© 1998-2016 Stephan Hennekens
Database
21
Distribution map: Choose a distribution map to be linked to the database. The usage of an
internal map is considered obsolete. For mapping it is recommended to use a GIS package.
Range for relevé numbers: Specify the range for the relevé numbers. In a system in which
several databases form a combined relevé system it is recommended to give each database
a unique range of relevé numbers.
When entering relevés this defined range serves as a check. Numbers located outside the
range of the database are not allowed.
Area: Specify whether the database is common or private. Note that only the manager can
create common databases.
Structure header database: In case an extension of the structure of the database for
header data has been defined in the database dictionary, you can create a so-called extended
database for header data.
Structure species database: If an extension of the structure of the species database has
been defined in the database dictionary, you can create a so-called extended species
database.
See also: Modify database attributes
3.4
26
Rename
Menu: Database | Rename
Choose the desired database and click on Rename. Enter the new name, and if you are
working in a network, the desired Area to store it.
3.5
Delete
Menu: Database | Delete
Choose the desired database and click on Delete.
3.6
Renumber
Menu: Database | Renumber
Renumbering a database is for example useful when relevés from other sources have to be
© 1998-2016 Stephan Hennekens
22
Turboveg for Windows
incorporated into an already existing database. All relevés, either within a database or among
databases, need to have a unique relevé number.
Starting with number: Enter the number of the first relevé in the database.
Save old number in database field: Mark if you want to save the old number. Choose a field
in the database for header data in which the old number has to be stored.
Click OK to renumber.
3.7
Pack & reindex
Menu: Database | Pack & reindex
Reindexing a database is only required in the case that index files are corrupted. This may
occur when the program is interrupted unwillingly (e.g. due to a disconnection between the
working station and server, or a power failure).
The pack function removes any record that has been marked as deleted.
3.8
Combine databases
You can combine databases in three different ways.
1. Remove the previous selection (if present) and select (Select) the relevés in the source
database (you do not have to select all relevés). Export the selected relevés to a
Turboveg database (Export | Turboveg database) and specify the name of the target
database.
Data in fields unique for the source database will not be copied to the target database. If
these data have to be copied you need to use method 2.
2. Remove the previous selection (if present) and select (Select) the relevés that have to be
combined; relevés can be selected from several databases. Export the selection to a new
Turboveg database (Export | Turboveg database). When data present in all fields
(regardless whether they are unique for a specific database or not) have to be copied you
have to choose Extended under Structure header database.
3. The most convenient option is (Database | Append another database 23 ), which will
append another database to an active (open) database.
Please note that the above mentioned options only will work if all the databases that need to
be combined are linked to the same species list.
If the databases are linked to different species lists, then a different procedure needs to be
followed:
1. Each database needs to be exported to a 'Standard XML file'. See Export | Export to
standard XML 72 file for details concerning this option.
© 1998-2016 Stephan Hennekens
Database
23
2. Create a new, and thus empty, database. You may connect this database to any species
list.
3. Import each XML file successively in the database. With the first XML to be imported you
must choose which species list will serve a the right taxon base. Instead of choosing an
existing list you may also enter a non existing taxon list name. Turboveg will then build up a
complete new species list. For more information concerning the import of XML file please
see Import | Import standard Turboveg XML file 46
.
3.9
Append another database
Menu: Database | Append another database
This option serves as an easy to use method to extend an opened database with all relevés
from another database. The additional relevés are automatically renumbered. Fields of the
selected database that are not present in the active database (target database) can optionally
be copied as well.
Choose the database you want to append and click the Append button.
Multi user-version: Only the manager has permission to append a database to a common
database.
Also see Combining databases
3.10
22
Modify database structure
Menu: Database | Modify structure
You can add fields to the database to store additional header data (select Header file) and
additional species data (select Species file).
© 1998-2016 Stephan Hennekens
24
Turboveg for Windows
It can be useful to add fields in case you have systematically collected (environmental) data
which do not fit in the standard fields (e.g. soil type, pH, management, and sociability and
phenology). By doing so you can also export these extra fields to various formats. An example
is the export of the extended header data to Cornell condensed format. When the species
data are also exported to Cornell condensed format, you can perform a Canonical
Correspondence Analysis using the program CANOCO.
You can delete or change existing fields, on the condition that these do not belong to the
standard structure. The standard structure of the database for header data contains all fields
up to and including the “remarks“ field; and that for the species data up to and including the
“layer“ field.
For the species data table there is a restriction of maximum 15 additional fields, whereas for
the header data table there is no such restrictions.
Add a field: Enter the name of the field to be added at Field Name. Enter the field type (Type),
field length (Len) and the number of decimals (Dec). Add this new information to the existing
list by clicking Add.
Field type can be “N“ (Numerical) or “C“ (Character).
If the number of decimals is greater than zero, then you have to enlarge the field length by
one, viz. the position of the decimal point.
To change a field: Select the field to be changed (Fields). Change one or more attributes
(field name, field type, field length, and number of decimals) and store the changes with
Replace.
To delete a field: Select the field to be deleted and click Delete.
© 1998-2016 Stephan Hennekens
Database
25
You store the modifications in the database structure by clicking Rebuild.
3.11
Organise header data
Menu: Database | Organise header data
This option enables the definition of both the table and the form containing header data of the
database currently open. You can control the number and the order of the fields to be present.
Available: List of available items.
Selected: List of selected items.
Add: Add items marked in the list Available to the list Selected.
Add all: Add all items marked in the list Available to the list Selected.
Remove: Remover items marked from the list Selected.
Remove all: Remove all items marked from the list Selected.
Default: Restore the natural order of fields
Sort: Sort the fields in the box with available items
Save: Save the new order of the fields
© 1998-2016 Stephan Hennekens
26
3.12
Turboveg for Windows
Modify database attributes
Menu: Database | Modify attributes
Choose the database in which one or more attributes have to be changed. Only change the
Species list when the database is empty (no relevés). If you really need to connect the
database to another species list then follow the instructions described here 26 .
Specify the lowest and highest relevé number in Range of relevés. Be sure there is no
overlap in numbering with other databases. In a stand-alone database you can, for example,
set a range from 1 to 999999.
To be able to enter relevés, the minimum and maximum should be higher than 0.
View: A list of all databases and their minimum and maximum relevé number is shown. The
databases are sorted according to relevé number.
See: Create a new database
3.13
20
Connecting a database to another species list
If you decide to connect an existing database then the followings steps need to be taken:
1. Select all relevés in the database and export these to a Standard Turboveg XML file 72 .
2. Create a new database. At this stage it is not important which species list is selected.
3. With the new database open select 'Import | Standard Turboveg XML file'. In the dialog
© 1998-2016 Stephan Hennekens
Database
27
window select the species list that needs to be connected to the data set. Further
information on how to import the XML file can be found here 46 .
3.14
Statistics
Menu: Database | Statistics
3.15
Hunt duplicates
Menu: Database | Hunt duplicates
Duplicates may occur when relevés from various sources (field books, literature, and
computerised databases) are imported into Turboveg databases. Duplicates can be detected
by calculating the floristic similarity between two relevés using the formula: i = c/(A + B - c) (=
Jacquard-index), where c is the number of species shared, A the number of species unique
to one relevé and B the total number of species of the other relevé. If i = 0 there is no floristic
similarity between the relevés, if i = 1 the relevés are identical.
This formula can be extended in such a way that the cover abundance of the species is also
taken into account: Srij = kykiykj/( kyki2+ kykj2 - kykiykj) (Similarity ratio of Ball).
© 1998-2016 Stephan Hennekens
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Turboveg for Windows
Compare with…: Select the database to compare with the already opened database. You
can also hunt duplicates in the same database.
Restrict comparison: You can speed up the comparison by specifying Year and/or Locality.
Then, only relevés with similar dates and/or locality will be compared.
Calculation: Calculation of the similarity-index can be based on the presence or absence of
species (Qualitative) or on the cover abundance of the relevés (Quantitative).
A matrix is presented where for each relevé compared the four most alike relevés are shown.
Double-click on one of the grid cells to see a comparison between two relevés.
Save: The matrix can be written to a file.
3.16
Identification
Menu: Database | Identification
The program ASSOCIA enables a syntaxonomical identification of relevés using a reference
system. Please refer to the manual of ASSOCIA for a theoretical background of the
calculations.
Synsystematic system: Choose a reference system.
Store results in database: Mark if the results of the analysis (syntaxon codes) have to be
stored in a Turboveg database. The information will be stored in separate columns, which will
be automatically added to the database.
Save analysis ASSOCIA: Mark if the export files of Associa have to be saved.
Configure ASSOCIA: Please refer to the manual of Associa for an explanation of the
settings. In most cases the default settings will do.
At Max. number of alternatives (2-10) you can specify the number of alternatives the
program has to present. Turboveg will make as many extra columns as specified.
3.17
Backup/Restore
Menu: Database | Backup/Restore
This option serves to copy relevé databases, species lists, and popup lists from the hard disk
to a diskette and reverse. Choose Backup to copy from the hard disk to a diskette or
directory and Restore to copy from a diskette or directory to the hard disk.
© 1998-2016 Stephan Hennekens
Database
29
It is possible to backup more than one database or list to a diskette.
Tab-sheet Backup
Backup a…: Select the group from which an item must be selected (relevé database,
species list, or popup list)
Backup to: Specify to which device/directory you want to back up the database.
Format: Choose TvDos if the database has to be opened with the DOS version of Turboveg.
If not, choose TvWin.
Backup: Execute the backup of the database to a diskette.
Tab-sheet Restore
Restore from: Specify from which device/directory a database has to be restored.
Copy to area: Specify whether the database has to be restored to a private or common area.
The manager is the only person authorised to restore databases to the common area.
Scan disk: The names of the Turboveg databases present on the device selected will be
listed on the screen. You can choose a database from this list.
3.18
Copy from/to
Menu: Database | Copy from/to
© 1998-2016 Stephan Hennekens
Part
IV
32
Turboveg for Windows
4
Edit
4.1
Switch edit mode
Menu: Edit | Switch edit mode
Switch edit mode allows to switch between editing of header data in forms (Form edit) or by
editing directly in the header data table (Table edit).
To switch mode you may also click the yellow region on the status bar at the bottom of
header data table.
4.2
Modify header data
Menu: Edit | Modify header data
The header data are shown on one or more pages of a form. You can select pages with the
mouse or by pressing Alt + <number of the page> (e.g. Alt+1).
Fields, which are marked with a question mark, are supported by a popup list. The popup can
be consulted by double-clicking on the question mark ?.
The cover abundance scale is the only field you are obliged to fill in.
The number of subjects (fields) and their order can be changed and modified in each
database.
See: Modify form header data 25
Confirm: When you have edited the header data and you want to close this option and/or
continue browsing (back or forwards) the program will ask whether the changes must be
saved. If you want to continue browsing you can delete the mark to ensure this question will
not longer pop-up. The data will then be automatically saved.
Next: Show the header data of the next relevé.
Previous: Show the header data of the previous relevé.
Save: Finish changing the header data and save the changing.
Close: Finish changing the header data but do not save the changing.
© 1998-2016 Stephan Hennekens
Edit
4.3
33
Modify species data
Menu: Edit | Modify species data
Choose a species (taxon) from the Species list by typing the search code. Then select a
Layer and enter the cover value and - if applicable - other species attributes. Press Add to
add the taxon to the list of selected species.
It is strongly recommended to only use the keyboard when entering the species names and
the associated attributes. Always press Enter to skip from one entry to another.
Modify: You can change a species present in the list Selected species. The data of this
species will be put again on the form. Pressing Replace after a change replaces the old
species with the new species in the list of selected species. Undo undoes the change.
You can also change species in the list Selected species by double clicking (or pressing
Enter) on the desired species.
4.4
Replace species
Menu: Edit | Replace species
This options allows to replace to replace one taxon into another. The action is
irreversible!
Range of relevés: Enter the range of relevé numbers to be changed.
Species: Specify the value to be replaced at Old and the new value at New. Species
numbers and layer designation can be entered directly, but clicking >> will popup the species
list.
4.5
Replace all synonyms with accepted names
Menu: Edit | Replace all synonyms with accepted names
This options allows to convert all taxon synonyms into accepted taxon names. The action is
irreversible!
4.6
Geo-referencing using Google Maps
Menu: Edit | Geo-referencing using Google Maps
Geo-referencing relevés with a longitude and latitude value is easy with the build-in web
© 1998-2016 Stephan Hennekens
34
Turboveg for Windows
browser addressing Google Maps. Use the zoom tool on the left site of the map to zoom in ,
zoom out and move the map to all sites. You may also use the the mouse wheel to zoom in
and out and by holding the left mouse button down the map can be dragged around.
To fix a position just double click with the mouse on the site where the relevé has been
recorded. A message box appears telling which further steps have to be taken. The longitude/
latitude-position is copied to clipboard and can then be pasted into the table with header data
(it doesn't work on the form presentation). To retrieve the values from the clipboard right click
on the header data table and choose the the appropriate option in the context menu.
Make sure that columns for longitude and latitude are available in the header data table. If this
is not the case then use the Modify structure 26 option in Turboveg to add these fields.
Because Turboveg wants to store the longitude/latitude values as decimal degrees, it is
recommended to define both both fields as Numerical, with a width of 12 tokens and 7
decimals
© 1998-2016 Stephan Hennekens
Edit
4.7
35
Add ecological indicator values
Menu: Edit | Add indicator values
This option serves to calculate the mean, standard deviation, median, and number of
observations of ecological indicator values (e.g. Ellenberg values for nitrogen, pH, etc.) of
each relevé and stores these data in separate columns in the database. If the columns are
not yet present, they will be added automatically to the database.
Range of relevés: Specify the range of relevé numbers on which you want to perform the
calculations.
Scaling cover values: Specify whether the cover values do (Ordinal or Percentage) or do
not (Boolean; only presence or absence of species) has to be taken into account.
Ecological items: Choose one or several items for which the calculations should be done.
Add columns for…: Specify which indicators have to be calculated.
Add: Execute the calculation. The extra columns will be added at the end of the table with
header data. The name of the columns consist of three parts, separated by an under score:
<alias name subject>_<calculation>_<scale> (e.g. ph_mea_b is: ph, mean and boolean).
Calculation:
© 1998-2016 Stephan Hennekens
36
Turboveg for Windows
In the case that the cover value of a species is taken into account the numerical indicator
value is multiplied with the cover (either by 1 to 9 for ordinal scale or 1-100 for percentage
scale).
ni: the numerical cover value of species i
ii: the indicator value of species i
ii * ni) /
i)
In order to know which percentage value comes with a cover abundance code select Manage,
Popup lists, Edit, Cover scales in the menu and check the table.
See Configure the ecological database
4.8
93
to define the alias names of the items.
Add diversity index values
Menu: Edit | Add diversity index values
This option servers to calculate diversity index values (Richness, Shannon diversity,
Evenness, Simpson's index of diversity) of each relevé and stores these data in separate
columns in the database. If the columns are not yet present, they will be added automatically
to the database.
Range of relevés: Specify the range of relevé numbers on which you want to perform the
calculations.
Add columns for…: Specify which index values have to be calculated.
Add: Execute the calculation. The extra columns will be added at the end of the table with
header data.
Calculations
ni: the abundance of species i
S: the number of species in a relevé (= Richness-index)
pi: the relative abundance of each species (as percentage cover), calculated as the
proportion of the total number of species (S)
Shannon-index
i * Ln(pi)
)
Eveness-index = Shannon-index / Ln(S)
Simpson-index = 1 - (pi2)
© 1998-2016 Stephan Hennekens
Edit
4.9
37
Add a relevé
Menu: Edit | Add a relevé
When entering single relevés in a database already containing data, you will be asked
whether you want to accept the header data of the currently selected relevé.
You will first need to enter the header data, followed by the species data.
4.10
Add a table
Menu: Edit | Add a table
Number of relevés in table: Specify the number of relevés you want to add.
If you have a large table (more than 20 to 30 relevés) to process, it is recommended to split
the table in two or more parts. 20 to 30 relevés will fit on the screen. This does not mean that
you have to add the species for each part of the table separately. Simply add all the species
in the first table part and mark the option Restore species list from previous table when
processing the other parts.
Cover scale: Choose the cover abundance scale. The scale chosen will be applied for all
relevés in the table. It is not possible to use different cover abundance scales in a table.
Copy species list from previous table: Mark this option to apply the species list of the
previous table (part). It is possible to delete species from this list.
Create: Create the matrix in which species and cover abundance codes can be added.
© 1998-2016 Stephan Hennekens
38
4.11
Turboveg for Windows
Delete relevés
Menu: Edit | Delete relevés
You must first mark relevés before they can be removed from the database physically. You
can mark in three ways:
In the table with header data:
By double clicking on the first column in the table with header data.
In the dialog Edit | Delete relevés:
By defining a range of relevé numbers (Define range)
By defining a list of relevé numbers (Define list)
Press Enter or click on Delete to remove the relevés physically from the database.
4.12
Replace header data
Menu: Edit | Replace header data
Item: Choose the subject (field) in which you want to search and replace.
Range of relevés: Enter the range of relevé numbers to be changed.
Automatic conversion: Check this option if an automatic conversion needs to be taken place
(Dutch version only).
Replace with data from other item: Check this option if data data needs to be replaced with
data from another column in the database.
Value: Specify the value to be replaced at Old and the new value at New.
Several exceptions occur at the ‘remarks’ field:
If Old is empty, the contents of New will be added to the remarks.
If Old is not empty, the characters written in Old will be replaced by the characters written
in New.
If “<enter>“ is present in Old all hard and soft page breaks in the remarks will be replaced
by spaces.
If “$fieldname“ (e.g. “$pqnr“) is present in New the contents of that field will be added to
the remarks.
Match: select how the new value matches the old value.
whole field: replacement takes place if Old value matches value in field
part of field: replacement takes place if Old value matches value in field, even if Old
value is only part of value in field
© 1998-2016 Stephan Hennekens
Edit
39
exact position in field: replacement takes place if Old value matches value in field from
position as indicated in Old
For all fields:
If “*“ is present in Old then all values of the selected field will be removed.
4.13
Combine relevés
Menu: Edit | Combine relevés
Using this option you can combine different relevés into a new one. Species that occur in
more than one relevé are summed up using the following formula:
C = A + (100 – A) * B / 100
where C = summed cover in percentages, A = cover in percentages of a species in relevé A
and B = the cover in percentages of the same species in relevé B. We assume that the
species have a random distribution in the plot.
The cover of each species is multiplied with the quotient of the size of the plot in which the
species exists divided by total size of all plots.
Preserve layer differentiation: indicate whether species that occur in different vegetation
layers (strata) should be combined.
For a slightly more sophisticated way of summing up relevés consider using the option
Combine subplots into plots 39 .
4.14
Combine subplots into plots
Menu: Edit | Combine subplots into plots
Use this option to combine subplots (or nested plots) in a single plot (relevé). Concerning the
species cover two methods can be applied. One is a simply summarization of values (only
used when the subplots have been recorded with the so-called Sigg-scale). The other one is
the calculation of a mean cover value for each species. It is assumed that each subplot has
the same surface area, thus the mean value is simply the summarization of the cover values
of a species in the subplots in which it occurs divided by the total number of subplots
belonging to a certain plot.
You must indicate which fields holds the identifiers for the plot number and subplot number.
Turboveg will only combine those subplots which have non-empty values for plot no. and
subplot no (in case of a numerical field the value must be greater zero).
The cover of the species in the resulting plot will always be in percentages, regardless the
cover scale method used in subplots.
© 1998-2016 Stephan Hennekens
40
Turboveg for Windows
Concerning the header data Turboveg will only calculate mean values for fields that are
defined as numerical (e.g. 'Total cover'). In case a certain value is equal to the defined
missing value the value is ignored. For fields that are defined as character (e.g. 'Author') the
value of the first subplot is copied into to combined plot.
4.15
Combine vegetation layers
Menu: Edit | Combine vegetation layers
With this option for each species vegetation layers can be combined into one layer with the
following formula:
C = A + (100 – A) * B / 100
where C = summed cover in percentages, A = percentages cover in of a species in layer A
and B = the percentage cover of the same species in layer B. It is assumed that the species
is randomly distributed in the plot.
By careful! As with many other functions in Turboveg this option converts the data
irreversible. It is therefore recommended to create a backup first!
4.16
Copy current relevé
Menu: Edit | Copy current relevé
© 1998-2016 Stephan Hennekens
Edit
41
With this option you can copy both header data and species data of the current selected
relevé into a new relevé.The copy becomes the last relevé in the database.
4.17
Filter selected relevés
Menu: Edit | Filter selected relevés
Selected relevés in a database (marked in column two of the table with header data) can be
filtered. This can be useful when species or header data of the selected relevés need to be
changed or edited. When the filter is active 'search and replace' actions will only take place
within the selected relevés (see Replace header data 38 and Replace species 33 )
4.18
Copy relevé to clipboard
Menu: Edit | Copy relevé to clipboard
All data from a relevé can be copied to the clipboard.
Using a word processor you can insert the text in a document.
In case an ecological database is linked to the relevé, the ecological indicator values, the
means, standard deviation, median, and the number of observations will be added for each
species.
Here below you see an example of a relevé that has been copied to the clipboard.
=> Relevé number: 7001
Country code
Biblioreference
Nr. table in publ.
Nr. relevé in table
Cover abundance scale
Author code
Date (year/month/day)
Relevé area (m2)
UTM grid system code
Altitude (m)
Aspect (degrees)
Slope (degrees)
Cover total (%)
Cover tree layer (%)
Cover shrub layer (%)
Cover herb layer (%)
Cover moss layer (%)
Cover lichen layer (%)
Cover algae layer (%)
Cover litter layer (%)
© 1998-2016 Stephan Hennekens
:
:
:
:
:
:
:
:
:
:
:
:
:
:
:
:
:
:
:
:
45
000023
2
Percentage (%)
0002
1986/08/11
0.00
- - -
0
0
0
0
0
0
0
0
42
Turboveg for Windows
Cover open water (%)
:
Cover bare rock (%)
:
Height (highest) trees (m)
:
Height lowest trees (m)
:
Height (highest) shrubs (m)
:
Height lowest shrubs (m)
:
Aver. height (high) herbs (cm):
Aver. height lowest herbs (cm):
Maximum height herbs (cm)
:
Maximum height cryptogams (mm):
Mosses identified (y/n)
:
Lichens identified (y/n)
:
Litter
:
0
0
0
0
0.0
0.0
0
0
0
0
0.0
L
T
K
F
R
N
S
-------------------------------------------------------------------------------------Alopecurus pratensis
40
6
x
5
6
6
7
0
Caltha palustris ssp. palustris
80
7
x
x
9=
x
6
0
Carex species
20
Cerastium fontanum ssp. fontanum
20
Glyceria maxima
0
Mentha aquatica
0
Persicaria amphibia
0
Phalaris arundinacea
0
Poa pratensis ssp. pratensis
99
9
5
x
10
8
9
20
7
5
3
9=
7
5
20
8
6
x
x
x
6
40
7
5
x
8~
7
7
Taraxacum species
20
Urtica dioica
0
Zostera marina
8
20
x
x
x
6
7
9
80
x
6
2
12
7
6
80
----------------------------------------Mean indicator value
1.0
Standard deviation
2.8
Median value
0.0
# of observation (n)
8.0
4.19
7.3
5.4
3.3
8.6
7.0
6.9
1.0
0.5
1.5
2.1
0.6
1.5
7.0
5.0
3.0
9.0
7.0
6.5
6.0
5.0
3.0
7.0
6.0
8.0
Search a relevé
Menu: Edit | Search a relevé
© 1998-2016 Stephan Hennekens
Edit
43
Searching a relevé in a complex database system with several databases and thousands of
relevés is no problem when you use the relevé number (= system number), provided that
each relevé in the system has a unique number.
When you enter the relevé number (= system number) Turboveg will search the number in all
available databases. If the number is present, the relevant database will be opened and the
selected relevé shown on the screen.
© 1998-2016 Stephan Hennekens
Part
V
46
Turboveg for Windows
5
Import
5.1
Import Turboveg XML file
Menu: Import | Turboveg standard XML file
The Turboveg standard XML file is an excellent format to exchange data between different
Turboveg systems. Importing data in this format enables synchronization of all popup lists
(lookup tables), as far as data from the popup lists concerned are included. If for example the
file contains taxa from species list A and the receiving database is connected to species list
B, then species list B can be extended with taxa from species list A that are new for species
list B. The same counts for all other popup lists. It is clear that the synchronization should be
handled with care, otherwise the popup lists may end up in a mess.
If you are not familiar with this import function it is recommended to first experiment a little bit
and to import a standard XML file using dummy names for the species list and the dictionary.
It is also recommended to always import the standard XML file into an empty database.
In the screen shot below the taxa are derived from the species list 'C_Europe' but redirected
to a species list called 'dummyspecieslist'. If this list does not exist than it will created and
filled with the species present in the XML file. The same counts for the popup lists as defined
in the database dictionary. In those cases do not forget to check the options Update species
list and Update popup lists.
Dummy species lists and dictionaries can easily be removed. See Delete a species list
92
© 1998-2016 Stephan Hennekens
Import
and Delete a dictionary
88
47
.
If you have become more familiar with this import function than you can start importing
species into existing species lists.
Even when the Update species list option is checked there is no danger that the species list
can get messed up, because there is an extra step in the import procedure to be taken. An
additional dialog window will open up showing all taxa - mapped or not mapped - occurring in
the XML file.
Three actions can be undertaken:
1. A taxon from the XML file can be replaced with a taxon from the Turboveg species list.
Therefore click the icon to popup the species lookup table.
2. A taxon from the XML file can be ignored
3. A taxon from the XML file can be marked as new. In that case Turboveg will add this name
as a new taxon to the list if you have explicitly allowed Turboveg to add new species in the
first dialog window.
© 1998-2016 Stephan Hennekens
48
Turboveg for Windows
Import: Continue importing the data. All species that are not mapped to a Turboveg species
number will be ignored.
Save: Save the mapping to an Excel file.
Cancel: Cancel the whole import procedure
Unfortunately a mapping facility as described here is not (yet) available for all other lookup
tables (authors, projects, syntaxa, etc.). Therefore you should handle the option Update
popup lists with care. In any case Turboveg will list all the non-mappable values in the
Message log window. Using this list you can modify the popup lists yourself, and deciding
whether or not to add certain values to the popup lists.
Also see: Export to Standard XML file
72
© 1998-2016 Stephan Hennekens
Import
5.2
49
Import TurbovegCE XML file
Menu: Import | TurbovegCE XML file
5.3
Import Cornell condensed species file
Menu: Import | Cornell condensed species file
You can import computerised vegetation tables in Cornell condensed format (input format for
e.g. TWINSPAN, CANOCO) to a database. When doing so, only the species, cover values,
and original relevé numbers will be read in. All other header data, with the exception of the
cover scale, need to be entered manually (see example below).
After the Cornell condensed file has been read the following must be checked en choices
must be made.
Check the species code translation.
Choose the cover scale (how to store the numerical cover values as cover codes in the
database) and check the transformation.
Choose a database field in which the relevé identifiers (e.g. relevé numbers) must be
stored.
The species codes that are translated ‘by hand’ will be stored in a so-called shadow list. With
each session this list will be used to translate species codes that are not in the Turboveg
species list. The shadow list is called ccshadow.dbf and by default stored in the directory ..
\TURBOWIN\DATA.
Species: In the first column of the table de species codes are stored which are extracted
from the Cornell file. The second, third, and fourth column holds respectively the species
name, the species code, and the vegetation layer. Codes that are could not be translated by
Turboveg are presented in blue colour. Double click or press Enter to popup the species list
for selecting the desired species.
Assign all species with layer code ‘0’ to…: All species without an indication for a vegetation
layer can be assigned automatically here.
Species list: Click this button to popup the species list.
Export: Click to export list of translated species to a file.
Merge: Shadow lists from different sources can be combined. Useful if you are working in a
team, and want to profit from other ones labour (importing Cornell files).
Cover values: The first column holds the numerical values found in the Cornell file. The
second column is the corresponding code according to the chosen scale. Double click or
© 1998-2016 Stephan Hennekens
50
Turboveg for Windows
press Enter to modify the code.
Store cover values in field…: Cover values are by default stored in the field “Cover
abundance”. There are however more possibilities to save the species attributes if the
species table is extended with extra fields (see Modify database structure 23 ).
Translate values using cover scale…: Choose the scale according to which the values
must be translated.
Store original relevés identifiers in…: You can store the original relevé identifiers (in most
cases these are numebers) in a field in the table with header data. This is by default the
remarks field.
However, it is recommended to store the relevé numbers in a separate field. When such a
field is not yet present, you have to add it first. See Modify database structure 23
Click Import to load the data into the database.
An example:
Selection: 15 releves
T
(I5,5(I5,F8.1))
5
1
1
3.0
2
8.0
3
8.0
2
2
2.0
4
8.0
5
18.0
6
8.0
7
2.0
2
8
2.0
9
2.0
10
38.0
11
8.0
12
38.0
2
13
3.0
14
2.0
3
1
2.0
2
2.0
5
8.0
6
8.0
7
18.0
3
8
4.0
9
8.0
10
18.0
11
8.0
12
38.0
3
15
68.0
16
3.0
17
3.0
18
3.0
19
2.0
3
20
8.0
4
2
8.0
3
18.0
21
4.0
5
1
2.0
2
8.0
9
1.0
16
2.0
6
1
3.0
9
2.0
10
8.0
11
8.0
16
3.0
6
20
38.0
7
1
3.0
2
2.0
7
3.0
9
2.0
10
38.0
7
11
4.0
15
2.0
16
8.0
19
2.0
20
8.0
7
21
8.0
22
2.0
23
2.0
24
2.0
25
2.0
8
26
38.0
9
8
1.0
26
18.0
27
18.0
28
2.0
10
7
8.0
10
2.0
14
3.0
16
2.0
24
3.0
10
26
4.0
27
1.0
28
2.0
29
2.0
30
4.0
10
31
8.0
32
2.0
33
2.0
11
1
8.0
5
2.0
11
18.0
13
2.0
14
4.0
11
28
2.0
32
8.0
12
24
68.0
29
2.0
34
3.0
13
27
38.0
14
35
3.0
36
68.0
37
8.0
15
35
2.0
36
18.0
37
68.0
0000
GAZAR;U6LIMISCA6PLAAC;C6ACACCYC7ANTSLIT6CARBDEL6CHRSM-R7CYNANAT6PASSRIG7PHYILIT6
PSORREP6RHOCDIG6SILEPRI6ZALUMAR6EUGECAP7FICILAT6HELHTER6METAMUI7PENCHEP6SYNCSOR6
DELOECK6ASPRRAC6SENELIT6SPORVIR6STEASEC6EHRHV;M6ARCOPOP6DASISUF6GLADGUE6HELHPRA6
MARI/SP6SENEELE6STOEPLU7THINDIS6DISHCRA6SAROPER6SAROPIL6
50097
50098
50099
50100
50101
50102
50103
50104
50105
50106
© 1998-2016 Stephan Hennekens
Import
50107
5.4
50108
50109
50110
51
50111
Import Excel table
For importing an Excel table with species and header data the following steps should be
taken in Excel:
1. Copy or cut the header data
2. Create or select an empty sheet
3. In the Edit menu select Past special
4. Select Transpose and click Ok
5. In Turboveg select the option 'Import free format species data' and select the sheet the
holds the species data. For next steps click here 52 .
6. For importing the header data select the option 'Import free format header data table' and
select the sheet with header data.For next steps click here 56 .
Excel table with header and species data
Table number
Releve number
Country code
Biblioreference
Year
Author code
Syntaxon code
1
2
3
4
5
6
7
8
9
10
101787101788101789101790101791101792101793101794101795101796
CZ
CZ
CZ
CZ
CZ
CZ
CZ
CZ
CZ
CZ
401824401824401824401824401824401824401824401824401824401824
1998 1998 1998 1998 1998 1998 1998 1998 1998 1998
0122 0122 0122 0122 0122 0122 0122 0122 0122 0122
35AC 35AC 35AC 35AC 35AC 35AC 35AC 35AC 35AC 35AC
RelevΘ area (m2)
Altitude (m)
Aspect (degrees)
Slope (degrees)
Cover total (%)
Cover tree layer (%)
Cover shrub layer (%)
Cover herb layer (%)
104.00 173.00 334.00 259.00 98.00 158.00 143.00 69.00 196.00 79.00
1350 1350 1350 1350 1350 1350 1350 1350 1350 1350
135
135
135
135
135
135
135
135
135
135
5
10
10
10
10
10
10
10
10
10
97
97
97
97
98
98
98
98
98
98
0
0
20
0
0
0
0
0
0
0
95
93
90
89
90
90
90
97
95
90
97
80
80
78
40
75
80
70
80
75
Anthoxanthum odoratum
Avenella flexuosa
Galium saxatile
Homogyne alpina
Molinia caerulea
Pinus mugo
Trientalis europaea
Calamagrostis villosa
Silene dioica
Vaccinium myrtillus
Picea abies
Sorbus aucuparia ssp.
glabrata
Vaccinium vitis-idaea
Athyrium distentifolium
© 1998-2016 Stephan Hennekens
hl 1
hl 3
hl 1
hl 1
hl +
s1 5
hl 1
hl .
hl .
hl .
t1 .
s1 .
.
2
.
+
.
5
+
1
+
1
.
.
.
2
+
1
.
5
1
2
.
2
+
.
.
2
+
+
.
5
+
+
.
1
.
.
.
2
.
+
.
5
+
1
.
1
.
.
.
2
+
2
+
5
1
.
.
1
.
+
+
3
+
2
+
5
+
.
1
2
.
+
.
2
.
1
.
5
+
.
.
1
.
.
+
3
.
1
+
5
1
.
.
2
.
.
+
3
+
1
+
5
+
.
.
3
.
.
hl .
hl .
.
.
.
.
.
.
.
.
+
.
.
+
.
.
.
+
.
+
52
Turboveg for Windows
Header data separated (copy or cut) from the species data, transposed and
pasted into another sheet
Table ReleveCountrBiblior Year AuthorSynta ReleveAltitud Aspec Slope Cover
numb numb y
eferen
code xon area e (m) t
(degre total
er
er
code ce
code (m2)
(degre es)
(%)
es)
1
2
3
4
5
6
7
8
9
10
5.5
10178 CZ
7
10178 CZ
8
10178 CZ
9
10179 CZ
0
10179 CZ
1
10179 CZ
2
10179 CZ
3
10179 CZ
4
10179 CZ
5
10179 CZ
6
40182 1998
4
40182 1998
4
40182 1998
4
40182 1998
4
40182 1998
4
40182 1998
4
40182 1998
4
40182 1998
4
40182 1998
4
40182 1998
4
0122 35AC 104.0 1350
0
0122 35AC 173.0 1350
0
0122 35AC 334.0 1350
0
0122 35AC 259.0 1350
0
0122 35AC 98.0 1350
0
0122 35AC 158.0 1350
0
0122 35AC 143.0 1350
0
0122 35AC 69.0 1350
0
0122 35AC 196.0 1350
0
0122 35AC 79.0 1350
0
Cover
tree
layer
(%)
Cover Cover herb
shrub layer (%)
layer
(%)
135
5
97
0
95
97
135
10
97
0
93
80
135
10
97
20
90
80
135
10
97
0
89
78
135
10
98
0
90
40
135
10
98
0
90
75
135
10
98
0
90
80
135
10
98
0
97
70
135
10
98
0
95
80
135
10
98
0
90
75
Import free format species data table
Menu: Import | Free format species data table
By means of a wizard you can import a table containing species data into a database in four
steps.
Input formats permitted are: SDF (fixed column width), comma delimited, tab delimited,
semicolon delimited, space delimited, dBaseIII+, and MS Excel (up to version 2007).
See the two examples below. Please note that delimited formatted tables, dBaseIII+ files, and
especially Excel sheets are much easier to import than SDF formatted tables. Also note that
all the data of one relevé are organized in one column.
If you planning to import a corresponding file with header data than you must import the
species data table first followed by the import of the header data table.
It's recommended to import the species data table into an empty database. Please note that
relevés numbers are not taken from the table but are created automatically.
If you want to import a table (e.g. Excel) with header and species data, then you should
separate the header from the species part and perform two imports, one on the header data
and one on the species data. An example how to do this is explained here 51 .
© 1998-2016 Stephan Hennekens
Import
53
Before taking step 1 confirm whether each cell in the table does or does not only contains
species cover values, but also additional values. If that is the case then check the option
Table contains additional values. If additional value are taken into account then also
indicate which seperator (the dot ('.') is taken als default) has been used to distinguish
between cover value and additional value. Also select a database field in which the additional
value need to b stored. If such a field is not available then first go to Modify database
structure 23 and add an extra species parameter.
A typical example is a combination of cover value and sociability value, both separated by a
dot. However, in the example shown above species are represented by percentage values in
which the dot is used to indicate decimals and the slash ('/') to separate cover percentage
© 1998-2016 Stephan Hennekens
54
Turboveg for Windows
values from additional values.
Step 1: If the columns in the table are separated with a delimiter, e.g. a comma, a tab, or a
semicolon, you first have to choose the right format with Format table. After having selected
the right delimiter the table will be reformatted automatically.
If the format of the table is “Columns at fixed positions“ then you have to mark each new
column. You can do this by clicking the grey cell on top of the table, or by placing the blue box
on the desired column with the arrow keys and subsequently pressing the Space bar. Click
the Next button when all columns have been marked. The table will then be reformatted
automatically.
Step 2: Species column # indicates in which column the species are listed. The numbers
are present at the top of the columns. Select the correct number and click the Next button.
Turboveg for Windows will try to translate the species names found in the indicated column
into species numbers.
If the table also contains values for sociability then the option Table contains sociability
values should be switch on. If these values need to be stored in the database then the
appropriate field in the database should be selected from the drop down menu (Field to
store sociability values). Make sure that such a field is available at the time that the import
is in process. Turboveg currently only distinguishes sociability values if they are separated
from cover values with a dot (e.g. 2a.3).
Step 3: Species Turboveg could not translate are presented in blue color. Select these
species one by one, and double-click or press Enter to search the species number. A
dialogue box with the Turboveg species list appears. Choose the desired species and if
required also the layer and confirm with Enter.
The species numbers are listed in the first column of the table, the vegetation layer in the
second column.
Please note that species that could not be mapped will not be imported in the last step of the
process, unless these species are marked with value -1. Use the function key F5 to mark
these taxa in the list. In the example above two taxa have been marked as such, 'Red
pleurocarp moss' and 'Carex cf. elongata'. After the table has been imported the name of
these taxa will appear in the database between brackets. As a matter a fact Turboveg
automatically creates an additional column in which the original species names will be stored.
Mark the columns which holds the relevés and need to be imported in the same way as is
mentioned in step 1.
Next specify the cover abundance scale (Cover scale). The scale selected may differ from
the one used for the original data, giving the opportunity to switch from one scale to another
(which can result in loosing information on the cover abundance of the species).
Press Next. Turboveg for Windows checks if the cover values are in congruence with the
cover abundance scale. For each cover value found in the input file Turboveg gives the
possibility to select a cover value from a list. Select the desired value and click the Replace
all button. Empty (missing) values in the input file are represented by a dot (‘.’) and are also
presented by Turboveg as a cover value candidate. In this case click the Ignore all button.
Step 4: Press Complete to read the species table into the database.
© 1998-2016 Stephan Hennekens
Import
An example of a table in SDF format:
Table number
1 2 3 4 5 6 7 89 101112131415
Gazania rigens v. uniflora-hl
Plantago crassifolia v. crassifoli
Acacia cyclops-jl
Anthospermum littoreum-hl
Carpobrotus deliciosus-hl
Chrysanthemoides monilifera s. rot
Cynanchum natalitium-hl
Passerina rigida-jl
Phylica litoralis-hl
Psoralea repens-hl
Rhoicissus digitata-hl
Silene primuliflora v. primuliflor
Zaluzianskya maritima-hl
Eugenia capensis-jl
Ficinia lateralis-hl
Helichrysum teretifolium-hl
Metalasia muricata-jl
Pentaschistis heptamera-hl
Syncarpha sordescens-hl
Asparagus racemosus-hl
Senecio litorosus-hl
Sporobolus virginicus-hl
Stenotaphrum secundatum-hl
Ehrharta villosa v. maxima-hl
Arctotheca populifolia-hl
Dasispermum suffruticosum-hl
Gladiolus gueinzii-hl
Helichrysum praecinctum-hl
Senecio elegans-hl
Stoebe plumosa-jl
Thinopyrum distichum-hl
Disphyma crassifolium-hl
1 . + . +
2a. . 2b.
. 2a. . .
. 2b2a. .
. 2a2a. .
. + 2b. .
. + 2m. .
. + 2a. r
. 3 2b. .
. 2a2a. .
. 3 3 . .
. 1 . . .
. + . . .
. . 4 . .
. . 1 . +
. . 1 . .
. . 1 . .
. . + . .
. . 2a. .
. . . . .
. . . . .
. . . . .
. . . . .
. . . . .
. . . . .
. . . . .
. . . . .
. . . . .
. . . . .
. . . . .
. . . . .
. . . . .
1 1 .. . 2a.
. . .. . . .
. . .. . . .
. . .. . + .
. . .. . . .
. 1 .. 2a. .
. . .r . . .
+ + .. . . .
2a3 .. + . .
2a2m.. . 2b.
. . .. . . .
. . .. . + .
. . .. 1 2m.
. + .. . . .
1 2a.. + . .
. . .. . . .
. . .. . . .
. + .. . . .
3 2a.. . . .
. + .. . . .
. + .. . . .
. + .. 1 . 4
. + .. . . .
. . 32b2m. .
. . .2br . .
. . .+ + + .
. . .. + . +
. . .. 2m. .
. . .. + 2a.
. . .. + . .
. . .. . . 1
. . .. . . .
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
3
.
.
.
.
.
.
.
.
.
.
.
.
.
.
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.
.
.
.
.
.
.
.
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.
.
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.
.
.
.
.
.
.
.
.
.
.
1
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
+
An example of a table in comma delimited format:
Table number,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,
,,,,,,,,,,,,,,,,,
Gazania rigens v. uniflora-hl ,1,.,+,.,+,1,1,.,.,.,2a,.,.,.,.,
Plantago crassifolia v. crassifolia-hl ,2a,.,.,2b,.,.,.,.,.,.,.,.,.,.,.,
Acacia cyclops-jl ,.,2a,.,.,.,.,.,.,.,.,.,.,.,.,.,
Anthospermum littoreum-hl ,.,2b,2a,.,.,.,.,.,.,.,+,.,.,.,.,
Carpobrotus deliciosus-hl ,.,2a,2a,.,.,.,.,.,.,.,.,.,.,.,.,
Chrysanthemoides monilifera s. rotundata,.,+,2b,.,.,.,1,.,.,2a,.,.,.,.,.,
Cynanchum natalitium-hl ,.,+,2m,.,.,.,.,.,r,.,.,.,.,.,.,
Passerina rigida-jl ,.,+,2a,.,r,+,+,.,.,.,.,.,.,.,.,
Phylica litoralis-hl ,.,3,2b,.,.,2a,3,.,.,+,.,.,.,.,.,
Psoralea repens-hl ,.,2a,2a,.,.,2a,2m,.,.,.,2b,.,.,.,.,
Rhoicissus digitata-hl ,.,3,3,.,.,.,.,.,.,.,.,.,.,.,.,
Silene primuliflora v. primuliflora-hl ,.,1,.,.,.,.,.,.,.,.,+,.,.,.,.,
© 1998-2016 Stephan Hennekens
55
56
Turboveg for Windows
Zaluzianskya maritima-hl ,.,+,.,.,.,.,.,.,.,1,2m,.,.,.,.,
Eugenia capensis-jl ,.,.,4,.,.,.,+,.,.,.,.,.,.,.,.,
Ficinia lateralis-hl ,.,.,1,.,+,1,2a,.,.,+,.,.,.,.,.,
Helichrysum teretifolium-hl ,.,.,1,.,.,.,.,.,.,.,.,.,.,.,.,
Metalasia muricata-jl ,.,.,1,.,.,.,.,.,.,.,.,.,.,.,.,
Pentaschistis heptamera-hl ,.,.,+,.,.,.,+,.,.,.,.,.,.,.,.,
Syncarpha sordescens-hl ,.,.,2a,.,.,3,2a,.,.,.,.,.,.,.,.,
Asparagus racemosus-hl ,.,.,.,.,.,.,+,.,.,.,.,.,.,.,.,
Senecio litorosus-hl ,.,.,.,.,.,.,+,.,.,.,.,.,.,.,.,
Sporobolus virginicus-hl ,.,.,.,.,.,.,+,.,.,1,.,4,.,.,.,
Stenotaphrum secundatum-hl ,.,.,.,.,.,.,+,.,.,.,.,.,.,.,.,
Ehrharta villosa v. maxima-hl ,.,.,.,.,.,.,.,3,2b,2m,.,.,.,.,.,
Arctotheca populifolia-hl ,.,.,.,.,.,.,.,.,2b,r,.,.,3,.,.,
Dasispermum suffruticosum-hl ,.,.,.,.,.,.,.,.,+,+,+,.,.,.,.,
Gladiolus gueinzii-hl ,.,.,.,.,.,.,.,.,.,+,.,+,.,.,.,
Helichrysum praecinctum-hl ,.,.,.,.,.,.,.,.,.,2m,.,.,.,.,.,
Senecio elegans-hl ,.,.,.,.,.,.,.,.,.,+,2a,.,.,.,.,
Stoebe plumosa-jl ,.,.,.,.,.,.,.,.,.,+,.,.,.,.,.,
Thinopyrum distichum-hl ,.,.,.,.,.,.,.,.,.,.,.,1,.,.,.,
Disphyma crassifolium-hl ,.,.,.,.,.,.,.,.,.,.,.,.,.,1,+,
5.6
Import free format header data table
Menu: Import | Free format header data table
Using a wizard you can import a table containing header data into a database in two steps.
Input formats permitted are: SDF (fixed column width), comma delimited, tab delimited,
semicolon delimited, space delimited, dBase III+, and MS Excel (up to version 2007).
See the two examples below. Please note that delimited formatted tables, dBase III+ files, and
especially MS Excel sheets are much easier to import than SDF formatted tables. Also note
that all the data of one relevé should be organized in one row.
If you planning to import a corresponding file with species data than you first need to the
species data table followed by the header data table.
If you want to import a(n Excel) table with header and species data, then you should separate
the header from the species part and perform two imports, one on the header data and one
on the species data. An example how to do this explained here 51 .
Step 1: If the columns in the table are delimited with a comma, a tab, a semicolon, or a blank,
then you first have to choose the right format from Format table. After having changed the
delimiter the table will be reformatted automatically.
If the columns in the table are not delimited (“Columns at fixed positions“) then you will need
to specify where each new column in the table starts. You can do this by marking (click the
grey cell on top of the table) the first cell of each new column. Press Next when all columns
are marked. The table will then be reformatted automatically.
Field names in row indicate in which line the field descriptions are stored. Zero means that
there are no descriptions included in the file.
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57
Step 2: Specify in which fields the data of specified columns have to be incorporated. Select
a column and press the Space bar or click the column header (grey cells).
A dialogue box appears in which you have to specify in which existing or new database field
the data have to be loaded.
One of the columns has to be marked as a Key field. The key field is the link between the
source (the file to be imported) and the target (the database table with header data). It is
important that the values in the source field and target field are unique.
With Multiply with… you can define a numerical factor with which the values from the input
file must be multiplied before they are written to the database.
It is not necessary to mark all fields. This enables you to skip information that can be ignored.
Press Complete to read the table into the database.
An example in SDF format:
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
50097199612
50098199612
50099199612
50100199612
50101199612
50102199612
50103199612
50104199612
50105199612
50106199612
50107199612
50108199612
50109199612
50110199612
50111199612
4 15
13100
16100
4 20
4 5
15 50
5 50
4 30
2 40
2 20
5 40
7 60
5 35
0 70
0 90
3
12
16
3
4
6
15
1
4
13
7
3
1
3
3
Column definition:
Kolomno. Description
1
6
12
16
18
22
25
29
31
Table number
Relevé number
Year
Month
Altitude (m)
Cover total (%)
Landtype
Soil_type
Number of species
An example in comma delimited format:
table_nr,releve_nr,year,month,altitude,total_cover,landtype,soiltype,nr_of_spec
1,50097,1996,12,4,15,,,3
2,50098,1996,12,13,100,,,12
3,50099,1996,12,16,100,,,16
4,50100,1996,12,4,20,,,3
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5,50101,1996,12,4,5,,,4
6,50102,1996,12,15,50,,,6
7,50103,1996,12,5,50,,,15
8,50104,1996,12,4,30,,,1
9,50105,1996,12,2,40,,,4
10,50106,1996,12,2,20,,,13
11,50107,1996,12,5,40,,,7
12,50108,1996,12,7,60,,,3
13,50109,1996,12,5,35,,,1
14,50110,1996,12,0,70,,,3
15,50111,1996,12,0,90,,,3
5.7
Import SORT file ('Tabulator Tabelle')
Menu: Import | SORT export table ('Tabulator Tabelle')
This option allows the import of a special export file from SORT, called 'Tabulator Tabelle'.
The first four lines of this file may look as follows:
D:\TODO\HENNEKENS\SORT\DATA\K_06-8.STF
01.11.07
12:52
SORT 4.0 - TABELLE: Steilkuestenvegetation bei Heiligenhafen
-------------------------------------------------------------Crucial is the presence of the word 'SORT' on the third line, and the fours line the presence of
the character string '--------'.
Upon loading the SORT file Turboveg tries to locate a line that starts with the word 'Artname'.
If this line does not occur a window will appear in which you can indicate which line holds the
first species. Continue by selecting the OK button.
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59
After having examined the SORT file Turboveg displays a window with three tab sheets.
The first sheet lists all the header data columns (fields) found in the SORT file. In the seconds
column you can map the SORT fields to Turboveg fields. By clicking a cell in the second
column a drop down list appears from which a field name can be selected. If an appropriate
field name is not available you can write down a name yourself. Always confirm changes by
pressing the ENTER key.
Values for field type, field length, and fields decimals are defined by Turboveg automatically.
These values can be changed, but should never be set to lower values.
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Turboveg for Windows
The second tab sheet lists all the species names found in the SORT file. Upon loading the file
Turboveg will try to match these names with the names from the species list which is
connected to active database. If there is no match than the number in the second column is
set to zero. Click the icon to popup the species lookup table if you want to match a species
name manually.
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61
The third column consists of two parts.
The first parts holds a table with the SORT indicators for vegetation layers in the first column.
In the second column the SORT layer can be mapped to a predefined Turboveg layer. Setting
the value in the second column to -1 all the species connected to that SORT layer will not be
imported.
The second part holds all the cover values found in the SORT table. You first need to select
the cover scale method from the drop down list on top, then map each of the SORT values
with a Turboveg cover value.
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Turboveg for Windows
Click the Import button if all values in all three sheets are set according to your wishes
5.8
Import XY-coordinates from Shapefile
Menu: Import | XY-coordinates from Shapefile
XY-coordinates can be imported from a shapefile if the records in the shapefile can be linked
to the releves in the target database. Typically that would be the releve number, but in fact any
identifier can be taken, as long as each value is unique in the database. Before you start the
import procedure make sure that appropriate fields are available in the Turboveg database to
store the XY-values. Concerning the shapefile only point data is accepted.
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Part
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Turboveg for Windows
6
Select
6.1
Select current relevé
Menu: Select | (De)select current relevé
You can manually select or deselect a relevé in several ways:
Use the menu Select, (De)select current relevé.
Press Spacebar.
Double-click in the table with header data the second column.
6.2
Select all relevés in current database
Menu: Select | Select all relevés in current database
All relevés from the active database can be added to a selection in one go (see window with
selected relevés).
6.3
Deselect all relevés in current database
Menu: Select | Deselect all relevés in current database
All relevés from the active database can be deleted from a selection in one go (see window
with selected relevés).
6.4
Flip the selection in current database
Menu: Select | Flip selection in current database
This option enables to deselect marked relevés and conversely to select (mark) not yet
selected relevés (see window with selected relevés) from the active database.
6.5
Select relevés random
Menu: Select | Random select
You have to specify the number of relevés to be selected randomly.
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67
You can execute this selection on only one database at the time; when doing so, the already
existing selection will be automatically removed.
6.6
Build a query
Menu: Select | Build query
You can select relevés from one or in more databases by defining selection criteria.
Selection criteria can be one or several items from the Header data and/or Species data.
Tab sheet Header data
First choose (Select item) the header data you want to select. Then press Define range to
define a range (e.g. 1930-1950) or Define list to enter a list of data (e.g. 1931, 1935, 1956,
…).
You perform the selection by pressing Execute. It is also possible to combine several criteria
with Combine criteria with. First choose how to combine the new criterion with the already
selected criterion. There are three possibilities.
and: restrict the selection;
or: enlarge the selection;
and not: restrict the selection.
Then select an item (Select item) and enter the data at Define range or Define list.
When combining criteria you can also add a selection on species. However, the selection on
species always restricts the selection based on the header data.
Tabsheet Species data
The selection on species is executed in the same way as the selection on header data (see
above). The items to be chosen (e.g. sociability, fertility, phenology), however, are not present
by default. These species attributes can only be entered when they are present in the
database. See: Modify database structure 23 .
Most common is a selection on species. Two ways of making species lists can be chosen:
And/Or and And Not. Choosing And/Or you make a list of which some or all species have to
be present in the relevés. You have to define which species always have to be present and
the number of the other chosen species that have to be present (Select .. out of ..). Choose
And not to make a list of species that should be absent in the relevés. In both lists you can
also specify the cover value of the chosen species.
This method to define species enables a selection of clearly delimited vegetation types in your
databases.
General tasks.
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Turboveg for Windows
Execute: Perform the selection.
Undo: Delete the latest defined criterion. It depends on the tabblad selected whether the
latest criterion of the header data or of the species will be deleted.
Save: Save the selection criteria to a file.
Retrieve: Retrieve an earlier selection from a file.
Embargo filter: Mark this option to exclude relevés, which are embargoed. Both authors and/
or projects can be placed under an embargo. See Modify popup lists 88 to change the
embargo flag of authors and/or projects.
Current selection: Specify what to do with the previous selection. Their relevé numbers are
listed in the window at the right part of the screen.
There are three possibilities which resemble Combine criteria with:
Delete: delete the previous selection (default).
Restrict: restrict the previous selection.
Extend: extend the selection.
6.7
Clear a selection
Menu: Select | Clear
This option deletes all selected relevés. You can also clear the window with selected relevés
by double clicking the icon
on the toolbar.
6.8
Save a selection
Menu: Select | Save
When saving a selection only the relevé numbers of the selected relevés will be stored. By
default this file will be stored in the directory <Turboveg installation folder>\Old_sels.
6.9
Retrieve a selection
Menu: Select | Retrieve
When you retrieve a selection only the relevé numbers will be replaced in the window with
selected relevés. You can then export the data of the selected relevés by various options.
© 1998-2016 Stephan Hennekens
Select
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Part
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Turboveg for Windows
7
Export
7.1
Export to Turboveg database
Menu: Export | TURBOVEG database
Export to a Turboveg database is for example useful when you want to copy the selected
relevés to another computer system, where Turboveg is also implemented.
It can also be used to copy all relevant relevés to be used in a specific project into one
database
Database name: Specify the name of the database. This can be an existing or a new.
Empty target database: Mark this option to empty the target database.
Area: Only the manager can create a Common database or add relevés to a common
database. It is only possible to create or change databases in the private area.
This option is only relevant for the network version.
Turboveg version: Choose TvDos (9.x) when the target database will be used in the DOS
version of Turboveg.
Structure header database: When one or more of the selected databases have an
extended structure of the header data, you have the option to copy (choose extended) or not
to copy (choose standard) the extended structure.
Structure species database: When one or more of the selected databases have an
extended structure of the species data, you have the option to copy (choose extended) or
not to copy (choose standard) the extended structure.
Please note that relevés first need to be selected before they can be exported.
Also see: Export to XML file (standard)
7.2
72
Export to MS ACCESS database
Menu: Export | MS ACCESS database
Please note that relevés first need to be selected before they can be exported.
7.3
Export to standard XML file
Menu: Export | Standard XML file
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73
Unlike the Export to Turboveg database 72 the Export to standard XML file not only exports
all the header and species data of a selected data set, but also the interpretation of all the
codes present in the data (e.g. author codes, project codes, species numbers). Even the
database dictionary used is included in the export file. The receiver of an the XML file can thus
build up a complete new Turboveg system from scratch. Therefore this export is the best
format to exchange data between Turboveg users and not the export to a Turboveg database.
The Standard XML file is also an excellent input file for JUICE.
Target directory: Specify the directory to store the output file. Click
from a list.
to select a directory
Output file: Specify the name of the output file.
Encoding: Select encoding schema if your data needs to be parsed by other software than
Turboveg
Exclude relevés that have no species: Exclude empty relevés from export.
Description: Optionally describe the selected data set
Send file as e-mail attachment: If you check this option the export file will autonomically be
compressed (zip format) and attached to an e-mail.
Submit data to EURODAT: Check this option if you want to upload the selected data to the
European Vegetation Data Bank (EURODAT). The option is temporarily disabled.
Please note that relevés first need to be selected before they can be exported.
7.4
Export to XML project file for TurbovegCE
Menu: Export | XML project file for TurbovegCE
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7.5
Turboveg for Windows
Export to ESVeg compatible XML file
Menu: Export | ESVeg compatible XML file
ESVeg compatible XML files are suitable to be imported in VegetWeb.
Please note that relevés first need to be selected before they can be exported.
7.6
Export to a Cornell condensed species file
Menu: Export | Cornell condensed species file
Export to a Cornell condensed file enables analysis with various programs, for example
CEDIT, SHAKE, TWINSPAN, CANOCO, PC-ORD, VEGRO, VEGRON, CLUTAB, DENDRO,
and ELLEN.
Target directory: Specify the directory to store the output file. Click
from a list.
to select a directory
Output file: Specify the name of the output file.
Combine/Exclude layers: Specify whether you want to combine species that are divided
over more than one vegetation layer or that you want to exclude species that are present in
one or more layers.
Exclude species: Exclude species based on their characteristics as defined in the
ecological database. See Exclude species
Format: Choose Classic if you want to apply an old version of TWINSPAN, Canoco format is
valid for most programs that need Cornell condensed file as input. Choose Vespan when you
want to analyse your data using the software package VESPAN. For VEGRO and VEGRON
Canoco format should be selected.
Transformation cover values: By default cover values are exported in percentage. Using a
transformation you can down weight cover values. Choose User defined to define your own
classes for transformation.
Standardization to site total means that each cover value of a species will be divided by the
sum of all cover values of the species in the relevé. In some cases this
standardizationenables a more reliable comparison among relevés (e.g. relevés of fishes in
open water).
Code relevés using…: In the Cornell condensed file the relevés are identified with a code,
which is by default the relevé (= system) number. However, you can also choose another
© 1998-2016 Stephan Hennekens
Export
75
identification code from the list. This code, preferably, has to be unique.
Exclude empty relevés: Exclude empty relevés (no species) in case the program that will
have the output file as import file can not handle empty relevés. An example of such a
program is TWINSPAN. In case you want to perform a numerical classification using
TWINSPAN in JUICE you also have to exclude empty relevés.
Add a dummy species in the case of an empty relevé: Add one dummy species (code
DUMMYSPE) with cover value 0.1% to an empty relevé.
Title: You can optionally specify a title.
Please note that relevés first need to be selected before they can be exported.
7.7
Export to a user defined header data file
Menu: Export | User defined header data file
Target directory: Specify the directory to store the output files. Click
from a list.
to select a directory
Output file 1: Specify the name of output file 1. This file contains the data.
Output file 2: Specify the name of output file 2. This file contains information on the structure
of output file 1.
Output file 2 is only required if you choose SDF or delimited format.
Exclude relevés that have no species: Optionally exclude relevés that have no species.
Format: Choose an export format. There are four possibilities.
SDF: Columns have a fixed width.
Delimited: Columns do not have a fixed width, but are separated by a delimiter. You have
to specify which delimiter has to be used to separate the columns and in what way
numerical values with decimals need to be formatted.
You can load the delimited format in e.g. MS Excel (up to version 2007).
DbaseIII+:
Cornell condensed: This format is required if you want to perform a Canonical
Correspondence Analysis with CANOCO. For each chosen subject you also have to
indicate whether the variables must be treated as numerical or nominal values.
Select items: Select the subjects to be present in the output file by double clicking or
pressing Ins.
Save: Save the selected subjects as pre-set.
Load: Load the pre-set selection of subjects.
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Please note that relevés first need to be selected before they can be exported.
7.8
Export to a spreadsheet table
Menu: Export | Spreadsheet table
Selected relevés can be exported to a non-ordered table. The format of the table can either
plane Ascii (with tab or semi colon separated columns) or MS EXCEL.
You have the choice to extend the table with header data and with data from the ecological
database.
© 1998-2016 Stephan Hennekens
Export
Target directory: Specify the directory to store the export file. Click
from a list.
77
to select a directory
Output file: Enter the name of the export file.
Combine/Exclude layers: Specify whether you want to combine species that are divided
over more than one vegetation layer and/or that you want to exclude species that are present
in one or more layers.
Add species numbers: Do you want to add an extra column with species numbers?
Species data: By default cover abundance codes are exported. If available however, you may
also select another species parameter. If cover abundance is selected then you may also
decide to export cover values as percentage values or ordinal values (1 up to 9). If sociability
values are also stored in the database then you can export these values as well. Cover
abundance values will be the be combined with sociability values, separated with a dot (e.eg
2a.3) .
Orientation header data: Choose Vertical if each relevé may contain only one character
per column. The values will be written over several rows (thus vertically).
Choose Horizontal if the column width may be more than one character.
Cover: Choose the way the cover values must be presented, either by the original codes, in
ordinals (1-9) or in percentage (0-100).
Select header data: Select one or more header data that have to be present at the top of the
table.
Using Load and Save you can retrieve previous and save current selected header items.
Select ecological data: If available you can select one or more ecological parameters which
will be added to the table as extra columns. See Linking an ecological database 16 .
Using Load and Save you can retrieve current and save previous selected items.
Please note that relevés first need to be selected before they can be exported.
7.9
Export to a SDF formatted database
Menu: Export | SDF formatted database
7.10
Export to JUICE input files
Menu: Export | JUICE input files
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JUICE (Tichý 2001) is an excellent program designed for editing and classifying large
phytosociological tables. The maximum capacity is 30.000 relevés in one table, and many
functions are included for easy manipulation of phytosociological tables, including header
data. Various options include calculation of average Ellenberg values for relevés, export of
table data into other programs, mapping of species occurrence from actual data sets, etc.
JUICE includes TWINSPAN for classification, which is implemented as an external service. It
is recommended for smaller datasets.
The most important feature of JUICE however, is the classification of relevés using the
Cocktail classification method (Bruelheide 1995, 2000). This method tests the statistical
coincidence of species occurrence in order to find reasonable groups of diagnostic species,
as they are traditionally used in phytosociology. Vegetation classification is subsequently
created by combination of different species groups.
Export to JUICE input files is a combination of a Cornell condensed species file and a user
defined header data file. The latter is optional.
Target directory: Specify the directory to store the export file. Click
from a list.
to select a directory
Name for all export files (.cc!, .exp, .str): Enter the name for all the possible export files.
The extensions are added automatically. In order to apply header data in JUICE, the prefix for
all file names must be the same.
Combine/Exclude layers: Specify whether you want to combine species that are divided
over more than one vegetation layer and/or that you want to exclude species that are present
in one or more layers.
Include header data: Mark this options if you want header data to be included in the JUICE
table.
Select header data: Select at least one header item to be exported.
Using Load and Save you can retrieve previously and save currently selected header items.
For a more convenient input file for JUICE see: Export to XML file (standard)
72
Please note that relevés first need to be selected before they can be exported.
7.11
Export to ESPRESSO/TAB input file
Menu: Export | ESPRESSO/TAB input file
Please note that relevés first need to be selected before they can be exported.
© 1998-2016 Stephan Hennekens
Export
7.12
Export to MULVA input file
Menu: Export | MULVA input file
Please note that relevés first need to be selected before they can be exported.
7.13
Export to SYNTAX-5 input files
Menu: Export | SYNTAX-5 input files
Please note that relevés first need to be selected before they can be exported.
7.14
Export to SYNTAXON input file
Menu: Export | SYNTAXON input file
Please note that relevés first need to be selected before they can be exported.
7.15
Export to TAXAL input file
Menu: Export | TAXAL input file
Please note that relevés first need to be selected before they can be exported.
7.16
Export to FUZPHY input files
Menu: Export | FUZPHY input files
Please note that relevés first need to be selected before they can be exported.
7.17
Export to species check list
Menu: Export | Species check list
Please note that relevés first need to be selected before they can be exported.
7.18
Export to herbarium etiquettes
Menu: Export | Herbarium etiquettes
Please note that relevés first need to be selected before they can be exported.
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7.19
Turboveg for Windows
Export to herbarium etiquettes from template
Menu: Export | Herbarium etiquettes from template
When a selection is based on one or a number of species Turboveg can create herbarium
etiquettes for the selected species (and only those species). The export to etiquettes can only
be done directly after the selection has been made.
A sample template as MS Excel document is located in the folder '<installation folder>
\Herbarium'. This sample can modified to fit your own needs.
Important is that each etiquette consumes a fixed number of rows (x) and columns (y). Also
the number of etiquettes on a row (z) is fixed.
The very first line of the Excel sheet contains three parameters indicating the above
mentioned dimensions:
1. RowBlockCount=x (located in row1, column 1)
2. ColBlockCount=y (located in row 1, column 2)
3. BlockCount=z (located in row 1, column 3)
The number of etiquettes that can be created is only limited by the number of rows that Excel can handle
in a sheet.
In each etiquettes the character string placed between square brackets (e.g. '[RELEVE_NR]') refers to a
field name in the Turboveg database (so called placeholders) . When creating the etiquettes Turboveg will
replace the placeholders with values derived from the selected relevés.
An exception is the placeholder [SPECIES_NAME]. There is no equivalent field name in a Turboveg
database, but Turboveg will replace this placeholder with a species name.
Please note that relevés first need to be selected before they can be exported.
7.20
Export to Shapefile
Menu: Export | Shapefile
If meant for ESRI ArcGIS then it is recommended to after importing the Shapefile in a project
to export it and rename it. This procedure will avoid corruption of the attribute table when
removing or adding columns.
Please note that relevés first need to be selected before they can be exported.
7.21
Export to mapping file
Menu: Export | Mapping file
Please note that relevés first need to be selected before they can be exported.
© 1998-2016 Stephan Hennekens
Export
7.22
81
Export to Google Earth
Menu: Export | Google Earth
Please note that relevés first need to be selected before they can be exported.
7.23
Export to Darwin Core Archive
Menu: Export | Darwin Core Archive
This option is currently in beta stage!
The export to Darwin Core Archive in Turboveg is developed to facilitate the publication of species
information derived from vegetation relevés to GBIF (Global Biodiversity Information Facility). Read more
about Darwin Core Archive here.
A Darwin Core Archive consists of an eml file and a zip file. The eml file (also included in the zip file)
contains meta information of the database, the zip file contains the actual data and the xml file
describing the columns in the data file. The data file is a simple straight forward TAB delimited text file.
Both eml and zip file should be sent to - most likely - the contact person of the national GBIF node.
To explain how to fill in the extensive export form in Turboveg, an example is presented below of how it is
done for data from the Dutch National Vegetation Database. Please note that the institution name and
code should somehow be standardized, at least at national level. Therefore it is recommended to consult
the national GBIF node before creating and uploading Darwin Core Archives.
After the export has been created the selection of relevés is automatically saved to a file, which name is
composed by 'DWCA', the name of institute and the date. By retrieving a selection of a previously made
export, a data set can be uploaded once more. This is useful if in course of time the data has been
improved. A previously made selection can be easily be retrieved by choosing 'Select', 'Retrieve' in the
Turboveg menu.
Please note that GBIF also has developed the IPT (Integrated Publishing Tool), a software platform to
facilitate the efficient publishing of biodiversity data on the Internet, using the GBIF network. Read more
about the IPT here.
In case the precision of the geographical extent is unknown it recommended to enter a negative number
in the Turboveg database. Negative numbers will interpreted as missing values.
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Turboveg for Windows
Please note that relevés first need to be selected before they can be exported.
7.24
Relevé data sheets
Menu: Export | Relevé data sheets
The header data and species data of the selected relevés can be copied to a file. An example
of a relevé is showed below.
Header data: Header data can, optionally, be written to a file.
Remarks: Remarks can, optionally, be written to a file.
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83
Ecological data: Ecological data (e.g. mean Ellenberg nitrogen indication values per relevé),
can optionally, be written to a file, provided that the database with ecological data is linked
(see Linking an ecological database 16 ).
Empty entries: Empty header data can, optionally, be inserted in the list.
An example:
=> Relevé number: 7002
Country code
:
Biblioreference
:
Nr. table in publ.
:
Nr. relevé in table
:
Cover abundance scale
:
Project code
:
Author code
:
Date (year/month/day)
:
Syntaxon code
:
Relevé area (m2)
:
UTM grid system code
:
Altitude (m)
:
Aspect (degrees)
:
Slope (degrees)
:
Cover total (%)
:
Cover tree layer (%)
:
Cover shrub layer (%)
:
Cover herb layer (%)
:
Cover moss layer (%)
:
Cover lichen layer (%)
:
Cover algae layer (%)
:
Cover litter layer (%)
:
Cover open water (%)
:
Cover bare rock (%)
:
Height (highest) trees (m)
:
Height lowest trees (m)
:
Height (highest) shrubs (m)
:
Height lowest shrubs (m)
:
Aver. height (high) herbs (cm):
Aver. height lowest herbs (cm):
Maximum height herbs (cm)
:
Maximum height cryptogams (mm):
Mosses identified (y/n)
:
Lichens identified (y/n)
:
Litter
:
Peatlayer
:
Ph
:
Conductiv
:
Grazing
:
Haymaking
:
Sand
:
Sandwclay
:
Claywsand
:
Clay
:
© 1998-2016 Stephan Hennekens
45
000023
3
Percentage (%)
0002
1986/08/08
0.00
- -
0
0
0
0
0
0
0
0
0
0
0
0
0.0
0.0
0
0
0
0
0.0
0.0
0.00
0.00
-
-
84
Turboveg for Windows
Silt
Peat
Soildescr
:
:
:
Community
:
Stevns +
L
T
K
F
R
N
S
------------------------------------------------------------------------Agrostis stolonifera
70
8
x
5
7~
x
5
0
Alopecurus geniculatus
45
9
6
3
8=
7
7
2
Alopecurus pratensis
80
6
x
5
6
6
7
0
Anthriscus sylvestris
5
7
x
5
5
x
8
0
Caltha palust s. palus
50
7
x
x
9=
x
6
0
Cardam praten s. prate
75
4
x
x
6
x
x
0
Cerast fontan s. fonta
45
Deschampsia cespitosa
20
6
x
x
7~
x
3
0
Elymus repens
10
7
6
7
x~
x
7
0
Festuca pratensis
65
8
x
3
6
x
6
0
Festuca rubra
15
Filipendula ulmaria
30
7
5
x
8
x
5
0
Glyceria fluitans
20
7
x
3
9=
x
7
0
Holcus lanatus
60
7
6
3
6
x
5
1
Juncus compressus
5
8
5
3
8=
7
5
1
Juncus effusus
10
8
5
3
7
3
4
0
Lolium perenne
20
8
6
3
5
7
7
0
Myosotis scorpioides
1
7
x
5
8~
x
5
0
Persicaria amphibia
25
8
6
x
x
x
6
0
Phalaris arundinacea
35
7
5
x
8~
7
7
0
Poa praten s. praten
99
Ranunculus repens
99
6
x
x
7~
x
7
1
Rumex acetosa
30
8
x
x
x
x
6
0b
Taraxacum species
45
Trifolium repens
40
8
x
x
5
6
6
1
Triglochin palustre
5
8
x
x
9=
x
1
3
Urtica dioica
10
x
x
x
6
7
9
0
-----------------------------------------Mean indicator value
7.2
5.6
4.0
7.0
6.3
5.9
0.4
Standard deviation
1.1
0.5
1.3
1.3
1.4
1.7
0.8
Median value
7.0
6.0
3.0
7.0
7.0
6.0
0.0
# of observation (n)
22.0
9.0 12.0 20.0
8.0 22.0 23.0
Please note that relevés first need to be selected before they can be exported.
7.25
Analyze header data
Menu: Export | Analyze header data
This option enables to visualize the relation between two header data items (including species
number and excluding remarks) in a graph. The graph is presented by a Visual Basic
Component which gives you the possibility to manipulate the graph. The screen shot below is
© 1998-2016 Stephan Hennekens
Export
85
meant to clarify this option. However, this help does not contain a full explanation of this
option.
X-axis: Select an item to represent the X-axis (double-click or press on Ins). Basically you
can choose each desired item.
Y-axis: Select an item to represent Y-axis (double-click or press on Ins). If you select the
same item as was selected for the X-axis, the frequency of the chosen item will be calculated
( e.g. the number of times each syntaxon is present in the selection). In all other cases you
have to choose a numerical item (e.g. number of species per relevé), since the data have to
be reduced to means per unit of the X-axis.
Interval: State the difference between two values on the X-axis (e.g. year: 1930-1995, 19351940, etc.). You can only choose intervals higher than 0 if the subject is numerical (e.g. year,
and thus not syntaxon).
The following is applied at the calculations: >= lower limit and < upper limit.
Sort labels: Mark this option if the labels on the X-axis have to be sorted.
Exclude empty entries: Mark this option if missing values have to be omitted from the
calculations.
If you have finished the settings, click Draw to visualize the graph.
A screen shot showing a graphic is given below. Click on the icons of the toolbar for
elucidating their function.
Please note that relevés first need to be selected before they can be exported.
7.26
Analyze ecological data
Menu: Export | Analyze ecological data
Please note that relevés first need to be selected before they can be exported.
© 1998-2016 Stephan Hennekens
Part
VIII
88
Turboveg for Windows
8
Manage
8.1
Modify popup lists
Menu: Manage | Popup lists | Edit | <select a list to edit>
Before you start modifying a popup lust make sure that you have selected the right dictionary
(see also Popup lists 16 ). A dictionary van be selected from the drop down menu located on
the toolbar of the main window.
Only the manager is authorized to change the popup lists.
In a popup list you can modify, delete or add a record. Hereto you have to activate a cell by
pressing Enter or by double clicking.
The lookup table for Authors and Projects contain an “Embargo“ field, which you can set on
“T“ (True) or “F“ (False). Setting the value on True, means that the relevés concerned can
only be selected and/or exported under strict conditions.
Add: Add a record.
Delete: Delete a record.
Export: Save the list to a file.
8.2
Delete a dictionary
Menu: Manage | Popup lists | Delete
You can delete a dictionary by selecting a name from the list.
This option deletes all the popup lists belonging to the selected dictionary.
Also see Popup lists
16
© 1998-2016 Stephan Hennekens
Manage
8.3
89
Modify a species list
Menu: Manage | Species lists | Edit | <choose the list you want to modify>
Species lists can be changed or extended with new species or synonyms. There are
protected and unprotected species lists. The Dutch version of Turboveg for Windows is by
default linked to the Dutch species list (higher plants and cryptogams), which is a protected
list. This means that the user is not allowed to and cannot make changes in species numbers
lower than 90.000. You can only add species by using a species number higher than 90.000.
Edit: Change the species selected (see Modify or add species)
Add new: Add a species.
Add synonym: Add a synonym of the selected species.
Delete: Remove the selected species.
Export: Save the species list to a file.
Modify (eco database): If present, this option can be used to modify the ecological database.
See Linking an ecological database 16 and Modifying an ecological database 92
Configure (eco database): If present, this option can be used to configure the ecological
database. See Linking an ecological database 16 and Configure the ecological
database 93
8.4
Create a new species list
Menu: Manage | Species lists | New | Create empty species list
You can create a new species list by entering a unique name in the Name field, followed by
pressing Enter. See Modify species list 89
to learn more on how to add species to the list.
8.5
Import a species list
Menu: Manage | Species lists| New | Import from file
Use this option if you have a computerised species list ready. In order to import this file the
format be dBaseIII. If your list is not in a dbaseIII format then use for example MS-Excel to
save the list as a dBaseIII file. Make sure that on the very first line of the Excel table the
column names are defined. The column names will be used the define the field names in the
© 1998-2016 Stephan Hennekens
90
Turboveg for Windows
dBase file. If you do not define the column names, and the first line holds the first species in
the list, than that species will get lost.
See below for some examples of species lists that will be accepted.
After selecting the input file, Turboveg will come up with a dialog window. In this window a
snapshot is given of a few records of the input file. The snapshot shows what field holds what
kind of information.
Target
Name species list: Enter the name of the species list you want to create. This name might
not conflict with others names species list. (Turboveg can handle multiple species list;
however, a relevé database is connected to only one species list).
Source
Synonyms included: Confirm if the input file has a separate field with information on the
status of the species (synonym or valid). You can select the field on the right side of the
checkbox.
In general an empty field indicates a valid species, whereas a non-empty field indicates a
synonym. If the field type is logical (or boolean) than FALSE indicates a valid species, and
TRUE a synonym. Is the field type numerical than 0 indicates a valid species, and any other
number > 0 a synonym. In case of a character field, a blank (empty, or space) indicates a
valid species, and any other character a synonym.
If synonyms are included then there are two options of how the synonyms are related
to there valid counter parts.
1. A synonym follows directly after its valid counter part.
2. The row position of the synonym in the list is trivial, but then a species number
must be included to set the relation to the valid counter part.
Species numbers included: Confirm if the input file has a separate field with species
numbers. You can select the field on the right side of the checkbox.
If you do not confirm this option than Turboveg will generate numbers for you, from 1 up to as
many valid species there are in the list.
If you confirm, Turboveg will check whether the numbers are unique, as far as it concerns
valid species. If it turns out that the numbers are not unique that redo the import and do not
confirm this option.
7 character abbreviation included: Confirm if the input file has a separate field with species
codes. You can select the field on the right side of the checkbox.
If you do not confirm this option than Turboveg will generate species codes for you. In general
Turboveg will generate codes where the first 4 characters are derived from the genus name,
and other 3 characters are derived from the epitheton.
If you confirm, Turboveg will check whether the codes are unique, as far as it concerns valid
species. If it turns out that the codes are not unique that redo the import and do not confirm
this option.
Common names included: Confirm if the input file has a separate field with information on
common names. Common names are also known as non-scientific, or trivial names. You can
select the field on the right side of the checkbox.
© 1998-2016 Stephan Hennekens
Manage
91
Genus names included: Confirm if in the input file genera are included as separate taxa.
For example Abies species, or Zostara species. If you do not confirm, Turboveg will
automatically add a record for each genus present in the list.
Author citation included: Confirm if the species names are made up with author citation.
Create protected list: Create a protected species list if you want to share the list with other
users, and want to avoid that changes can be made (in order to keep species data from
different users compatible). The exception applies for species with numbers 90.000 or higher.
Species names: Select the name of the field (column) in the input file that holds the species
names.
Examples of species lists
- A very basic list (indication for subspecies or variant left out):
Cladonia
Cladonia
Cladonia
Cladonia
Cladonia
Cladonia
Cladonia
Cladonia
Cladonia
glauca
gracilis
gracilis gracilis
gracilis elongata
gracilis turbinata
grayi
humilis
incrassata
macilenta
- A basic list:
Cladonia
Cladonia
Cladonia
Cladonia
Cladonia
Cladonia
Cladonia
Cladonia
Cladonia
glauca
gracilis
gracilis ssp. gracilis
gracilis ssp. elongata
gracilis ssp. turbinata
grayi
humilis
incrassata
macilenta
- A more sophisticated list (author citation included):
Cladonia
Cladonia
Cladonia
Cladonia
Cladonia
Cladonia
Cladonia
Cladonia
glauca Floerke
gracilis (L.) Willd.
gracilis (L.) Willd. ssp. gracilis
gracilis (L.) Willd. ssp. elongata (Ach.) Ahti
gracilis (L.) Willd. ssp. turbinata (Ach.) Ahti
grayi G. Merr. ex Sandst.
humilis (With.) J.R. Laundon
incrassata Floerke
© 1998-2016 Stephan Hennekens
92
Turboveg for Windows
Cladonia macilenta Hoffm.
-
S
S
S
S
List with valid species and synonyms (indicated with ’S’)
Cladonia
Cladonia
Cladonia
Cladonia
Cladonia
Cladonia
Cladonia
Cladonia
Cladonia
Cladonia
Cladonia
Cladonia
Cladonia
glauca Floerke
gracilis (L.) Willd.
gracilis (L.) Willd. ssp. gracilis
gracilis (L.) Willd. ssp. elongata (Ach.) Ahti
elongata (Wulfen.) Hoffm.
nigripes (Nyl.) Trass
gracilis (L.) Willd. var. nigripes (Nyl.) Ahti
gracilis (L.) Willd. ssp. turbinata (Ach.) Ahti
gracilis (L.) Willd. var. dilatata auct.
grayi G. Merr. ex Sandst.
humilis (With.) J.R. Laundon
incrassata Floerke
macilenta Hoffm.
- list with valid species, synonyms, species numbers, and species codes
S
S
S
S
8.6
176
177
178
179
179
179
179
180
180
181
182
183
184
CLAOGLA
CLAOGRC
CLAOG-G
CLAOG-E
CLAOG-E
CLAOG-E
CLAOG-E
CLAOG-T
CLAOG-T
CLAOGRA
CLAOHUM
CLAOINC
CLAOMAI
Cladonia
Cladonia
Cladonia
Cladonia
Cladonia
Cladonia
Cladonia
Cladonia
Cladonia
Cladonia
Cladonia
Cladonia
Cladonia
glauca Floerke
gracilis (L.) Willd.
gracilis (L.) Willd. ssp. gracilis
gracilis (L.) Willd. ssp. elongata (Ach.) Ahti
elongata (Wulfen.) Hoffm.
nigripes (Nyl.) Trass
gracilis (L.) Willd. var. nigripes (Nyl.) Ahti
gracilis (L.) Willd. ssp. turbinata (Ach.) Ahti
gracilis (L.) Willd. var. dilatata auct.
grayi G. Merr. ex Sandst.
humilis (With.) J.R. Laundon
incrassata Floerke
macilenta Hoffm.
Delete a species list
Menu: Manage | Species lists | Delete
You can delete a species list by selecting a name from the list.
8.7
Modify an ecological database
Menu: Manage | Species list | Edit | <choose the list you want to modify> | <click
© 1998-2016 Stephan Hennekens
Manage
93
Modify>
Add column: Add a new column to store species information.
Delete column: Remove a column (the current one) from the database.
Search: Search a species. You can also pop-up the search-dialog by pressing the Spacebar.
Synchronize: Extend the database with species that are present in the species list, but are
not present in the ecological database. This means that you never have to add species by
hand.
To edit data press Enter or double-click on a cell
8.8
Configuring an ecological database
Menu: Manage | Species lists | Edit | <choose a species list> | <click on Configure >
All fields present in the ecological database are shown in a table.
Specify for each item an alias name in the column Long alias.
Choose an item that serves as the key field when linking to the species list (species
number). Click or press Enter on the column Key field to set the value to .T. (True).
Specify with which items the calculations have to be made. These have to be items that
are represented by numerical values, such as the Ellenberg indicator values. Click or
press Enter on the column Calculate field to set the value to .T. (True). Specify a fourcharacter abbreviation in the column Short alias.
To save the settings after completing, press Save.
8.9
Format longitude/latitude
Menu: Manage | Format longitude/latitude
Make a choice here how you have stored (if any) longitude/latitude values; as 'Decimal
values', or as 'Degrees, Minutes, Seconds'. In the latter case the format should be defined.
8.10
Modify user privileges
Menu: Manage | Users
© 1998-2016 Stephan Hennekens
94
Turboveg for Windows
This option only concerns the network version.
Edit: Change the rights of a user.
New: Add a new user.
Delete: Remove a user from the list.
8.11
TurbovegCE settings
Menu: Manage | TurbovegCE settings
This options enables the definition of settings for TurbovegCE (Turboveg Compact Edition) on
a PocketPC (PDA) using a management tool. This tool will not appear if a proper
communication between desktopPC and PDA is not established. For communication
between the two devices ActiveSync needs to be installed.
User: enter the name of the person who is going to work with the PDA concerned. The user
name will be included in names of export files.
Memory card: It is very important to indicate the proper name for the memory card (if
present). To find out what the exact name of the card on PDA is use the Windows Explorer to
browse the directory structure. If properly indicated TurbovegCE will store most information
on this card (backups, export and import files, maps, etc), not only saving main memory
space, but also ensuring the safest storage of data.
Backup and Backup interval: It is recommended to switch on the automatic creation of
backups.
Grid system: To be able to work with GIS maps (only Shapefiles are currently supported by
TurbovegCE) a grid system should be selected. However, if your study area is outside the
Netherlands, Germany or Ireland than ‘NO GRID’ should be selected.
Baud rate and COM port: Information on Baud rate and COM port concern the GPS
receiver and should be obtained from its documentation.
Operating System: Select the Operating System running on the PDA concerned.
© 1998-2016 Stephan Hennekens
Manage
© 1998-2016 Stephan Hennekens
95
Index
Index
-D-
-AAdd a relevé
37
Add a vegetation table
37
Add diversity index values
36
Add indicator values
35
Analyze ecological data
85
Analyze header data
84
Append another database
23
ASSOCIA - identification software
28
-BBackup databases
28
Backup popup lists
28
Backup species lists
28
Build a query
67
-CCANOCO export header data to input file
75
CANOCO export species data to
74
Clear selection
68
Clipboard - copy a relevé to
41
Close database
20
Combine relevés
39
Combine vegetation layers
40
Combining databases
22
combining nested plots
39
combining subplots
39
Configuring ecological database
93
Connecting a database to another species list
26
Co-ordinates
33
Copy a relevé into a new relevé
40
Copy a relevé to clipboard
41
Copy databases from one folder to another
29
Cornell condensed file export of species data to
74
Cornell condensed file - import
49
Create new database
20
Create new species list
89
© 1998-2016 Stephan Hennekens
Darwin Core Archive - export to
81
Darwin Core Archive export
81
Data exchange format
72
Database append another
23
Database delete
21
Database modify attributes
26
Database modify structure
23
Database - new
20
Database - re-index
22
Database - rename
21
Database - renumber relevés
21
Database close
20
Database dictionary
16
Database open
20
Database structure
14
Databases - backup/restore
28
Databases - combining
22
DcA
81
Define form header data
25
Delete database
21
Delete dictionary
88
Delete relevés
38
Delete species list
92
Deselect all relevés
66
Deselect current relevé
66
Dictionary
16
Dictionary - delete
88
Diversity index values - add
36
Duplicated relevés - hunt for
27
-EEcological database - modify
92
Ecological database - configuring
93
Ecological database link to a species list
16
Edit header data
32
Edit mode - switch
32
Edit species data
33
ESPRESSO export to input file
78
ESVeg compatible XML file - export to
74
Evenness
36
Excel - export to
76
Excel header data table - import
56
Excel species data table - import
52
97
98
Export
Export
Export
Export
Export
Export
Export
Export
Export
Export
Export
Export
Export
Export
Export
Export
Export
Export
Export
Export
Export
Export
Export
Export
Export
Export
Turboveg for Windows
- Darwin Core Archive
81
species data to JUICE input file
74
to a header data file
75
to a SDF table
77
to a spread sheet table
76
to check list species
79
to Cornell condensed species file
74
to Darwin Core Archive
81
to ESPRESSO/TAB input file
78
to ESVeg compatible XML file
74
to FUZPHY input files
79
to graphics
84
to herbarium etiquettes
79
to herbarium etiquettes from template
80
to JUICE input files
77
to mapping file
80
to MS Access database
72
to MULVA input file
79
to relevé data sheets
82
to Shapefile
80
to SYNTAX-5 input files
79
to SYNTAXON input file
79
to TAXAL input file
79
to Turboveg database
72
to XML file (standard)
72
to XML project file for TurbovegCE
73
-F-
Header data export to Cornell condensed file
75
Header data export to MEGATAB header data file
75
Header data export to Spreadsheet file
75
Header data - import
56
Header data - modify
32
Herbarium etiquettes - export to
79
Herbarium etiquettes from template - export to
80
Hunt duplicates relevés
27
-IIdentification - synsystematic
28
Import a TurbovegCE XML file
49
Import Cornell condensed species file
49
Import Excel header data table
56
Import Excel species data table
52
Import Excel table with species and header data
Import header data
56
Import SORT export table
58
Import species data
52
Import species list
89
Import Turboveg standard XML file
46
Import XY-coordinates from Shapefile
62
Indicator values - add
35
Installation
11
Introduction
8
-J-
Filter selected relevés
41
Flip selection in a database
66
Format longitude/latitude
93
FUZPHY input files - export to
79
JUICE export species data to input file
JUICE export to input files
77
JUICE input file
72
-G-
-K-
GBIF
81
Geo-referencing relevés with Google Maps
33
Getting started
10
Google Maps - geo-referencing relevés
33
Graphics export to
84
Keyboard usage
-HHeader data - edit
32
Header data export to Ascii file
75
Header data export to CANOCO inputfile
51
74
12
-LLatitude/Longitude
33
Linking an ecological database to a species list
Longitude/Latitude
33
Longitude/latitude - format
93
Lookup tables
16
16
75
© 1998-2016 Stephan Hennekens
Index
-MMapping file - export to
80
MEGATAB export header data to input file
Modify attributes database
26
Modify database structure
23
Modify ecological database
92
Modify header data
32
Modify popup lists
88
Modify species data
33
Modify species list
89
Modify user privileges
93
Mouse usage
12
MS Access database - export to
72
MULVA export to inputfile
79
-Nnested plots - combining
New database
20
New relevé
37
39
-OOpen database
20
-PPopup lists
16
Popup lists - backup/restore
Popup lists - modify
88
Privileges - modify
93
Privileges of users
13
28
-QQuery - build
67
-RRandom select relevés
66
Re-index database
22
Relevé - new
37
Relevé data sheets - export to
Remove database
21
© 1998-2016 Stephan Hennekens
82
75
Remove selection
68
Rename database
21
Renumber relevés in database
21
Replace all synonyms with valid names
Replace header data
38
Replace species
33
Restore databases
28
Retrieve selection
68
Richness
36
33
-SSave selection
68
SDF formatted table export to
77
Search a relevé
42
Search and replace header data
38
Search and replace species
33
Select all relevés in current database
Select current relevé
66
Selection - clear
68
Selection - remove
68
Selection - retrieve
68
Selection - save
68
Shannon diversity
36
Shapefile - export to
80
Shapefile - import XY-coordinates from
Simpson's index of diversity
36
SORT - Import export table
58
Species check list - export
79
Species data - edit
33
Species data import
52
Species data - modify
33
Species list - create new
89
Species list - delete
92
Species list - import from file
89
Species list - modify
89
Species lists - backup/restore
28
Spread sheet table - export to
76
Statistics
27
subplots - combining
39
Switch edit mode
32
Synchronize species list and ecological
92
Synonyms - replace with valid names
Synsystematic identification
28
SYNTAX-5 export to input files
79
SYNTAXON export to input files
79
66
62
database
33
99
100
Turboveg for Windows
-TTAB export to input file
78
TAXAL export to input file
79
Trouble shooting
17
Turboveg database - export to
72
Turboveg standard XML file standard - import
TurbovegCE - import XML file
49
TWINSPAN export species data to input file
46
74
-UUsage of keyboard and mouse
User privileges
13
12
-VVegetation table - add to database
37
VEGRO export species data to input file
74
VEGRON export species data to input file
74
-XXML- export to ESVeg compatible file
74
XML file (standard) - export to
72
XML file TurbovegCE - import
49
XML project file for TurbovegCE - export to
73
© 1998-2016 Stephan Hennekens
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