Zonation in practice: tutorial and GUI

1. Zonation in practice: tutorial and GUI Federico M. Pouzols, Atte Moilanen, Joona Lehtomäki, Heini Kujala, Jarno Leppänen & Laura Meller C-BIG - Conservation Biology Informatics Group Dept. of Biosciences, University of Helsinki http://cbig.it.helsinki.fi

2. Simplified Zonation workflow Data collation and manual preprocessing (GIS) 1 Automated preprocessing using Zonation 2 Iterative landscape ranking (Zonation run) 3 Visualization, automated output & post-processing 4 Manual/external post-processing in GIS 5

3. Species distributions Biodiversity distribution data 1 Spatial (static) patterns of biodiversity

4. Manual pre-processing of data 2

5. INPUT: Zonation setup 3 • 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)

6. INPUT: a set of raster maps 3 • 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

7. 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 1 1 1 1 1 0 0 1 1 1 1 1 1 0 0 0 0 0 0 1 1 1 0 0 1 1 1 0 0 0 0 INPUT: a set of raster grids 3 Example: ascii raster files (as in the tutorial)

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

9. GUI: basic components Projects Results Process queue Messages (errors)

10. GUI quick start: open project (.bat file) 5 Right-click or Menu: File

11. GUI: run / queue a project 5 Right-click on a project

12. GUI: run and visualization of results 6 Shows run status

13. Output files generated automatically 7

14. Zonation teaching kit Unzip and you should get:

15. Teaching kit: software • Self-installing binary: creates icon and menu • If you choose the raw zip package, • Inside 4.software: GUI

16. Teaching kit: tutorial files Inside 5.tutorial_exercises:

17. Tutorial: so... let’s do it! • 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) 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.

18. Basic core-area Zonation • Open Zonation GUI (zig3gui.exe) • Open project: do_zig3.bat • It uses: • Features list file: splist.spp • Settings file: set.dat

19. Setup files: features/species list Species weights Feature raster maps Other parameters (only needed for more complex analyses)

20. Setup files: settings (.dat) If empty, defaults are used

21. Setup files: Project file (.bat) Project: all the pieces together BD features list file Output files name Call Zonation: run a setup Settings file

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

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

24. Output files • 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 othersfor post-processing in GIS

25. Example: change species weights • Open project do_w.bat • Open features list file splist.spp (right-click -> Edit) Change weights, save and re-run

26. Example: distribution smoothing • Open project do_ds.bat (then right-click -> Edit) Factor to multiply feature-specific (dispersal) parameters Distribution smoothing: ON

27. Multiple runs in a same project Open project do_multiple.bat You can use the tutorial files as templates for your own projects

28. Comprehensive manual I Introduction II Methods & algorithms III ZIG – The Zonation software - Running Zonation - Input files and settings - Outputs - Post-processing IV Graphical User Interface V Analysis setups for common planning needs VI Tutorial examples • PDF or browse from GUI

29. Things to do • 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”

30. Zonation website: http://cbig.it.helsinki.fi • Updates, more software, comments, bugs, forum, etc.