Zonation in practice: tutorial and GUI

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Federico M. Pouzols, Atte Moilanen, Joona Lehtomäki, Heini Kujala, Jarno Leppänen & Laura Meller

C-BIG - Conservation Biology Informatics GroupDept. of Biosciences, University of Helsinki

http://cbig.it.helsinki.fi

Zonation in practice: tutorial and GUI

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Simplified Zonation workflow

1 Data collation and manual preprocessing (GIS)

2 Automated preprocessing using Zonation

3 Iterative landscape ranking (Zonation run)

4 Visualization, automated output & post-processing

5 Manual/external post-processing in GIS

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Species distributionsBiodiversity distribution data1

Spatial (static) patterns of biodiversity

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Manual pre-processing of data2

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• In the GUI, setups are included in “projects”• A minimum setup requires

• Define a project (potentially several variants/runs)• Features/species list• A set of raster maps: one for each feature in the list• Settings definition (if empty, defaults are used)

3 INPUT: Zonation setup

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• Biodiversity feature raster• Example: .tif, .img or .asc file; standard GIS formats

as supported by GDAL (http://www.gdal.org/)• Raster showing the species occurrences and the

dimensions of the raster

• Basic setup: one raster for each feature

3 INPUT: a set of raster maps

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3 INPUT: a set of raster grids

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Example: ascii raster files(as in the tutorial)

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• Biodiversity feature (e.g. species) list file• text file, frequently with extension .spp for distinction • List of all those biodiversity feature raster map files

included in the analysis

• Trick: same map can entered multiple times for connectivity, retention etc. analyses

• More details about files, later

INPUT: features/species list file (.spp)4

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GUI: basic components

Projects

Processqueue

Results

Messages(errors)

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GUI quick start: open project (.bat file)5

Right-click orMenu: File

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GUI: run / queue a project5

Right-click on a project

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GUI: run and visualization of results6

Showsrun status

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Output files generated automatically7

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Zonation teaching kit

Unzip and you should get:

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Teaching kit: software• Self-installing binary: creates icon and menu

• If you choose the raw zip package, Inside 4.software:

GUI

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Teaching kit: tutorial files

Inside 5.tutorial_exercises:

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• Our species rasters as figures: tutorial_input/species_maps_jpg

• 120*140 km2 region in Hunter Valley, eastern Australia

• Habitat suitability for 7 species• 649*555 cell grid, 200m resolution

• Courtesy of Dr. Brendan Wintle, University of Melbourne, and Hunter Region Organization of Councils (HROC)

Tutorial: so... let’s do it!

Wintle, BA, Elith, J, Potts, JM. 2005. Fauna habitat modelling and mapping: A review and case study in the Lower Hunter Central Coast region of NSW. Austral Ecology, 30(7): 719-738.

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• Open Zonation GUI (zig3gui.exe) • Open project: do_zig3.bat

• It uses:• Features list file: splist.spp• Settings file: set.dat

Basic core-area Zonation

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Feature raster mapsSpecies weightsOther parameters (onlyneeded for more complex analyses)

Setup files: features/species list

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Setup files: settings (.dat)

If empty,defaults are used

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Call Zonation:run a setup

Settings file

BD features list file

Output files name

Project: all the pieces together

Setup files: Project file (.bat)

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• The .spp, .dat and .bat files are actually text files that can be edited with any text editor, including notapad. The .spp and .dat extensions have been used for distinction. The .bat is the extension of a dos/windows batch command file.

Note about .spp, .dat and .bat files:

23 Explore settings and input files in the project tree

Right-click on files to edit

Expand settings and files included in an instance/setup

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• Prefix of names: fourth parameter to zig3.exe• Priority ranking map (raster and image: .jpg)• .curves.txt performance (representation) of each

feature during the cell removal • .run.info.txt keeps track of analyses, files and

settings (details how the software runs)

• .rank.asc, .prop.asc, .wrscr.asc, and others for post-processing in GIS

Output files

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• Open project do_w.bat• Open features list file splist.spp (right-click -> Edit)

Example: change species weights

Change weights, save and re-run

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• Open project do_ds.bat (then right-click -> Edit)

Example: distribution smoothing

Distribution smoothing: ON Factor to multiply feature-specific (dispersal) parameters

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Multiple runs in a same project

• Open project do_multiple.bat

You can use the tutorial files as templates for your own projects

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Comprehensive manualI IntroductionII Methods & algorithmsIII ZIG – The Zonation software

- Running Zonation- Input files and settings- Outputs- Post-processing

IV Graphical User InterfaceV Analysis setups for common

planning needsVI Tutorial examples

PDF or browse from GUI

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• Fire up the GUI and open project do_abf.bat• Explore the project tree:

• Display some of the input raster files• open the .spp and .dat files. What’s there?

• Run (queue) the project• Explore the results (in GUI and output files)• Compare top areas with ABF (do_abf) against

CAZ (do_zig3). Tip: use ”merged maps”• Plot results using ”interactive plots”

Things to do

30 Zonation website: http://cbig.it.helsinki.fi

Updates, more software, comments, bugs, forum, etc.