User guide for the CO$TING NATURE Policy Support System 

Documentation written by: 

Mark Mulligan with contributions from: 

Leonardo Saenz (KCL), Arnout van Soesbergen (KCL) , Rebecca Goldman (TNC) , Ruth Swetnam,(University of Cambridge), Sophia Burke (AmbioTEK)

Citation:

Mulligan, M. [year]  User guide for the Co$ting Nature Policy Support System [version]. Available online [https://goo.gl/Grpbnb].

This is a user guide to the Costing Nature PSS in the ecoengine framework.  Example images may be from Costing Nature or other ecoengine systems (eg WaterWorld) but the guide focuses on functionality available to Co$ting Nature.




Co$ting Nature is a web based tool for analysing the ecosystem services provided by natural environments, identifying the beneficiaries of these services and assessing the impacts of human interventions. This Policy Support System (PSS) is a testbed for the development and implementation of development and conservation strategies focused on sustaining and improving ecosystem services and their environmental foundations. It also focused on enabling the intended and unintended consequences of development actions on ecosystem service provision to be tested in silico before they are tested in vivo. The PSS incorporates detailed spatial datasets at 1-square km and 1 hectare resolution for the entire world, spatial models for biophysical and socioeconomic processes along with scenarios for climate and land use. The PSS calculates a baseline for current ecosystem service provision and allows a series of interventions (policy options) or scenarios of change to be used to understand their impact on ecosystem service delivery.  By combining more than 80 input maps Co$ting Nature calculates the spatial distribution of ecosystem services for water, carbon, hazard mitigation and tourism and combines these with maps of conservation priority, threatened biodiversity and endemism to understand the spatial distribution of critical ecosystems.  These data are combined with analysis of current human pressures and future threats on ecosystems and their services in order to assess conservation priority.    Further detail is given in Mulligan et al. (2010).

Mulligan, M. A. Guerry, K. Arkema, K. Bagstad and F. Villa (2010) Capturing and quantifying the flow of ecosystem services in Silvestri S., Kershaw F., (eds.). Framing the flow: Innovative Approaches to Understand, Protect and Value Ecosystem Services Across Linked Habitats. UNEP World Conservation Monitoring Centre, Cambridge, UK. ISBN 978-92-807-3065-4. [available here]

costing: present participle of cost (Verb)

Verb:        

1. (of an object or an action) Require the payment of (a specified sum of money) before it can be acquired or done.

2. Cause the loss of.

The thinking behind this system reads costing in both meanings  of the word. The eventual aim of most ecosystem services work is to understand the benefits derived from nature using the same broadly economic measures as are applied to those activities which compete for space with nature (agriculture, forestry, extractives etc.) in order to optimise the space for nature and economy in the landscape (meaning 1).  The role of Co$tingNature is to provide the biophysical basis for this accounting, leaving the economics to users, since valuation is highly context and perspective dependent.  The title, Co$ting Nature, also recognises that the lack of consideration of the value provided - for free - by natural systems is a root cause of their loss.  The $ indicates that valuation is often the end goal, but in fact valuation does not always have to be economic.

Models are learning tools which can provide guidance if their results are appropriately supported by experience and observations.  Look at the results of these models carefully and use them to better understand the outcomes of your baseline or intervention rather than as a numerical prediction of the present or future.  Read and understand the model descriptions carefully to be able to better interpret the behaviour of the model in response to spatial variability of input data, scenarios or policy options.  If in doubt ask us.

You can see a FAQ here

You can see a powerpoint presentation on the system here 


Index

User guide for the CO$TING NATURE PSS

Disclaimer

Commercial use

Fair Use

Citation and redistribution

VIDEO DEMONSTRATION QUICK START GUIDE

THEORY, the video links below describe the theory behind these systems:

PRACTICE, the video  links below describe the steps required for use:

TEXT QUICK START GUIDE

Creating an Account

Once Logged in

Step 1: Define Area.

Step 2: Prepare data.

Step 3: Start simulation.

Step 4, 5 and 6: View results

Glossary

TIPS AND TROUBLESHOOTING

FULL USER GUIDE

VIDEO:

TEXT:

Your browser:  Accessing the Policy Support System

Before logging in

Creating an Account

Access levels

Co$ting Nature functionality (Scientist interface)

VIDEO:

Setting up a simulation

Step 1: Define area

Step 2: Prepare data

Step 3: Start simulation (Scientist)

Step 4: Policy exercises (Scientist)

Manage simulations (Scientist)

Step 5: Results : maps (Scientist)

Step 6: Results : stats (Scientist)

Step 7: Results: narrative (Scientist)

Co$ting Nature functionality (Hyperuser interface)

Co$ting Nature  functionality (Megauser interface)

Ecoengine Functions by step (links to video demonstrations)

Step 1: Define area

Step 2: Prepare Data

Step 3: Start simulation

Manage Simulations

Step 4: Policy exercises

Step 5: Results maps

Step 6: Results stats

Step 7: Results narrative

Questions and Answers

GUIDANCE FOR PRE- and POST- PROCESSING OF DATA

Creating a Zone of Interest (ZOI) map from a  shapefile using SAGAGIS (by Mark Mulligan)

Combining tiles and clipping them to a shapefile in SAGAGIS (by Mark Mulligan)

Cutting and resampling your gridded data so that it is compatible with the PSS and ready for upload in SAGAGIS (by Mark Mulligan)



Disclaimer

No warranty or liability The developers of Co$tingNature provides this system and data without any warranty of any kind whatsoever, either express or implied, including warranties of merchantability and fitness for a particular purpose. The developers shall not be liable for incidental, consequential, or special damages arising out of the use of the system or of any data downloaded.  For the period that this system is is in beta please be aware that functionality can break and results can be incorrect - check them carefully and report any errors using the Beta, report problem link.


Commercial use


This tool uses datasets from suppliers who make these available for non-commercial use only  (e.g. the WDPA, IBA and EBA datasets).  This means that these datasets cannot be used if your project is a commercial one.  Most definitions of 'commercial use' include a) any use for profit or to generate revenue, or b) any use by an individual or entity operating within or on behalf of or to the benefit of or to assist the activities of any entity other than a not-for-profit organisation.  

If you need to use the tool for commercial use and do not have license to then you must license and use the commercial-use version, which excludes these datasets.


Fair Use

Each registered user can run one simulation concurrently.  Please do not open multiple accounts and tie up our servers running multiple runs simultaneously.  If you make significant and prolonged use of this system in your organisations operations you should consider funding a server to improve the service provided to all users.  Each user can store 3 simulations on our servers (since each simulation takes 5GB of space).  Please delete simulations once you have finished downloading results from them.


Citation and redistribution

A lot time and effort has gone into producing this PSS and making it freely available.  Please cite the source of any results, data, images etc that you use from this system as Mulligan, M [year] Results from the Co$ting Nature Policy Support System [version number]. http://www.policysupport.org/links/costingnature  Kings College London also request reprints of any publications.

Co$ting Nature is frequently updated so please do not redistribute datasets that you have taken from Co$ting Nature that would invariably be out of date very soon, but rather point interested users to Co$ting Nature so that they can generate those datasets anew.  If you wish to redistirbute WaterWorld data for any reason , please contact us.  Users are prohibited from any commercial, non-free resale, or redistribution.


VIDEO DEMONSTRATION QUICK START GUIDE

THEORY, the video links below describe the theory behind these systems:

Presentation:Comparison of ES tools (0h1m13s)

    Making Science accessible - advantages and objectives of WW /CN (0h5m35s)

CO$TING NATURE - Aim (0h25m40s)

    What Co$ting Nature does (0h27m30s)

    Summary of Co$ting Nature outputs (0h29m1s)

    ES and Nature Conservation priority maps and hotspots (0h29m31s)

WW/CN where they should(n't) be applied (0h30m30s)

PRACTICE, the video  links below describe the steps required for use:

Logging in and choosing the interface: Scientist and Licensed User, creating accounts (0h38m24s)

Step 1 Define area (0m19s)

Step 2 Prepare data (2m16s)

Step 3 Start simulation (4m56s)

Step 5 Results maps list (7m7s)

    The map view window (8m15s)

    View map by region (eg watershed, protected area) (9m14s)

    Viewing in Google maps/Earth (9m57s)

    Query points on a map and viewing the component inputs of a map (10m36s)

    Comparing potential and realised bundled services (12m31s)

    Examining the relative threat index (13m41s)

    Examining the relative conservation priority index (14m23s)

    Examining conservation priority metrics (15m18s)

    Examining the development priority metrics (16m23s)

Step 4 Policy exercises (scenarios/policy options, valuatiion) (18m32s)

Accessing the model and system documentation (19m31s)


If you prefer text use the:

TEXT QUICK START GUIDE

written by Mark Mulligan and Rebecca Goldman

Creating an Account

Sign up: Click “Create an Account” link in the left hand Nav Bar and complete the details

  1. The system will send an email to the account you have entered. Once you get the email, click the link and log in.  If the email does not arrive within a few minutes check your spam folder and if it is not there contact us and we will confirm your account manually.. 
  2. Note default for log in is “policy analyst interface” – choose scientist interface to log in with more details
  3. Note default interface is google maps
  1. Will run more quickly
  2. Can still choose google earth once in the program but can change the selection at the beginning too.

Once Logged in

Step 1: Define Area. 

In the left hand nav-bar under “Set-up” click “Define area”

  1. Choose 10 degree tile
  2. Provide a short name for the run
  3. Latitude/Longitude fields
  1. If you have the latitude and longitude for your site, enter it, then Click “Submit Choice”.  Note that western hemisphere longitude start with a minus and southern hemisphere latitudes start with a minus. Use decimal degree i.e. -2.65727 not degrees, minutes and seconds.  
  2. If you do not know the latitude and longitude you can search the Google map manually or enter the location name into the search box and click Go> - the latitude and longitude at the top right of the Google map are for the centre of the map (indicated with a cross-hair) and can be cut and paste into the form.

Step 2: Prepare data.

Getting all data about your site

  1. The system will list the datasets available for the simulation.  If some are not available they will appear as red crosses in the Available column.  If any are missing you will need to build them so click 'Build missing map tiles'.  They will then be build and you will be asked to click 'prepare data' again to list them.  You can look at the input datasets by clicking geobrowse. Once all input datasets are ready, click “Copy data to your workspace” at the bottom of the page.  This will copy all the data to your workspace on the computer, not to your local machine.
  2. For the system to  prepare the maps may take a couple of minutes - when done,  the screen will indicate “data ready” and there will be a long list of available maps
  3. Each of these can be looked at using “geobrowse
  4. If the data is available to be re-distributed then the link “download” will be active
Step 3: Start simulation.

Run the PSS for your site

  1. Click “start simulation” in the left hand nav bar under “Simulation”
  2. Click the “Start” button
  3. Click “Yes” to accept that by running the model you will delete the results of any previous run of this simulation.
  1. If the screen does not indicate that the model is running and provide a progress bar with updates, go back to the main screen and click 'start simulation' again to refresh this screen.
  1. The model will take some time to run
  1. If this is a region/tile in the Andes it  will take about 10 mins to run the simulation
  2. If in an area that has never been run beforeit will take 1 day, so you may close the windows and come back tomorrow to see progress
  3. Click “Refresh” to see what the simulation is doing – it should refresh every 10 seconds anyway
Step 4, 5 and 6: View results
  1. To see results
  1. Click on the type of results you want to see back on the original screen
  1. Step 5 “Maps”
  2. Step 6 “Stats” (will be timeseries)
  3. Step 7 "Narrative" (will be a narrative of the model outcome)
  1. Can look at Results before the run finishes – can see them as they become available by clicking “Results – maps” and then refreshing that window with the refresh button
  2. To see maps from the maplist
  1. Click on “geobrowse”
  2. To get data click “download” – will be in zipped GIS Arc ASCII grid format
  1. Looking at Maps in Geobrowse
  1. Can Look at the maps in 6 ways (buttons below the map)
  2. Button 1: Google earth (will overlay data on google earth – must have google earth on your computer)
  3. Button 2: Google maps (overlay on google maps)
  4. Button 3:  Makes the mapped results “full size”
  5. Button 4: Change the color scheme
  6. Button 5: Shows Frequency Distribution
  7. Button 6: Will pop the map out into a separate window so can compare side by side with other maps
  8. Can change the scale to log scale for results that have a very large range of values
  1. Click “shifted log scale”
  2. Click “accept”
  1. Other
  1. Units are usually found at the top of the map screen, citations at the bottom of the map screen
  2. Can see the Google maps in 3 “styles” (click box next to Style label in the upper right of the map)
  1. Satellite
  2. Map – with cities, roads, etc
  3. Hybrid – labels in satellite version
  1. The model will first generate  map data for each timestep
  2. The last maps to be generated will be averages or totals for the year
  3. Description of map variables will come up next to each result with units links to glossary.  Hold the mouse over the concatenated name to see the full anme in a 'tool-tip'
  4. In the Google maps or Earth visualisations, one can zoom into a particular city by typing in the location or entering lat and lon
  5. When looking at a map can always click the “go back” button (or right click white space in window and choose back from context menu that appears) to be able to select other maps from the map list

If you have problems see troubleshooting 


Glossary



TIPS AND TROUBLESHOOTING


1. Use Mozilla Firefox - we cannot ensure that all features will work properly on other browsers 

2. If a page stops loading for more than a few seconds press F5 to reload 

3. If a model simulation is running and the progress bar is not being updated then click the 'start simulation' link from the main page again to refresh the simulation screen 

4.  System errors are automatically reported and will be fixed, please report any missing data where the system advises this and please use the 'Beta, report problem' from the main page to make us aware of any difficulties you are having with the system or changes that you would like to see made. 



FULL USER GUIDE

VIDEO:

Logging in and choosing the interface: Scientist and Licensed User, creating accounts (0h38m24s)

Step 1 Define area (0m19s)

Step 2 Prepare data (2m16s)

Step 3 Start simulation (4m56s)

Step 5 Results maps list (7m7s)

    The map view window (8m15s)

    View map by region (eg watershed, protected area) (9m14s)

    Viewing in Google maps/Earth (9m57s)

    Query points on a map and viewing the component inputs of a map (10m36s)

    Comparing potential and realised bundled services (12m31s)

    Examining the relative threat index (13m41s)

    Examining the relative conservation priority index (14m23s)

    Examining conservation priority metrics (15m18s)

    Examining the development priority metrics (16m23s)

Step 4 Policy exercises (scenarios/policy options, valuatiion) (18m32s)

Accessing the model and system documentation (19m31s)

TEXT:

written by Mark Mulligan and Leonardo Saenz 

Your browser:  Accessing the Policy Support System 

Co$tingNature PSS is supported to run under Firefox  or Chrome web browsers only. You may be able to access Co$tingNature PSS with other web browsers but success it is not guaranteed.

1. Start Firefox. Firefox is freely available from http://www.mozilla-europe.org/en/firefox/ 

2. To get access to the System visit http://www.policysupport.org/links/Co$tingNature

3. Allow pop ups from Agua Andes PSS if your browser requests this.

5. Enable Javascript in the unlikely event that it is not enabled in your browser.

6. Use Alt-Tab to navigate between the different pop-up windows as you interact with the system.

If you have problems see troubleshooting 

Before logging in 

An initial screen will allow you to log in to the system. Logging in allows us to store your simulations and provide you with full access to the system and simulation results.

To create an account use the Create account link.  If you have an account already provide your username and password in the fields stated. 

 

Creating an Account 

In order to sign up to Agua Andes PSS you need to hold a user account. To create an account, please follow the following steps.

  1. Click  the "Create an Account” link at the bottom of the control panel.

 

This option will open up the "Create a New Logging Account" screen in which you are requested to submit the following details.

 


2. The system then will send an email to the account you have entered. Please click the link you are provided with by email to authorize the activation of your account. This action will open up Co$tingNature PSS and log you in.  If the email does not arrive within a few minutes check your spam folder and if it is not there contact us and we will confirm your account manually.. 

Access levels 

You also need to indicate the kind of Co$tingNature PSS user you are: there are two kinds of users: Policy Analyst and Scientist.  Other user levels are licensed.  In addition, you should select the language for your session (currently English or Spanish). Co$tingNature is available in English and Spanish.  You can leave the viewer as the default Google Maps.

I am a:  

Though the same tools are used, the interface changes for different users so the level of detail shown is for example much greater when signed in as scientist compared with policy analyst.

  

Once logged in you are ready to use Co$tingNature PSS!


 


Co$ting Nature functionality (Scientist interface) 

This section describes the functionality of Co$tingNature from the perspective of the ‘scientist’ interface.

VIDEO:

Step 1 Define area (0m19s)

Step 2 Prepare data (2m16s)

Step 3 Start simulation (4m56s)

Step 5 Results maps list (7m7s)

    The map view window (8m15s)

    View map by region (eg watershed, protected area) (9m14s)

    Viewing in Google maps/Earth (9m57s)

    Query points on a map and viewing the component inputs of a map (10m36s)

    Comparing potential and realised bundled services (12m31s)

    Examining the relative threat index (13m41s)

    Examining the relative conservation priority index (14m23s)

    Examining conservation priority metrics (15m18s)

    Examining the development priority metrics (16m23s)

Step 4 Policy exercises (scenarios/policy options, valuatiion) (18m32s)

Accessing the model and system documentation (19m31s)

TEXT:

Setting up a simulation

There are a series of instructions under the option "Set-up" of the control panel, which will allow you to set up a model simulation. These instructions are: define area and prepare data.

Step 1: Define area 

Allows you to define the area of interest for the future simulation. Move the Google map until the crosshair in the centre of the map is above your area of interest.  To search for a location type the location name or coordinates (latitude,longitude) into the Location box above the map and click Go>. Note that western hemisphere longitude start with a minus and southern hemisphere latitudes start with a minus. Use decimal degree i.e. -2.65727 not degrees, minutes and seconds.  Provide a short name for the run in the box labelled Run name. Choose whether the run will be tiled 1km resolution (over a 10 degree tile) or tiled 1-hectare resolution (over a 1 degree tile).

Step 2: Prepare data 

Once you have defined the area of interest, it is necessary to prepare the data required to run hydrological and soil erosion models for that area. The PSS performs this automatically after clicking the link "Prepare Data", which organizes around 150 files at 1km spatial scale that correspond to the geographical 10 degree tile containing the area of interest. All raw files are extracted from SIMTERRA database that powers the PSS. Through Agua Andes PSS you can benfit from these data, however not all raw data are available for downloading depending upon restriction agreements. Data produced by the PSS can by used by users with no restriction by giving necessary credits to the the PSS project.             

Getting the Data for that Tile 

  1. Click “Prepare Data” in the Left Hand Nav Bar (Under “Define Area”) 
  2. A new window will appear with many layers listed 
  3. For each layer there will be two icons. The first will be a red “x” if you have not run this tile before, the second should be a green “check mark” 
  4. Scroll down and make sure all the layers have a green check mark in the column next to “doc” link.  If they all do then you will be able to run the PSS for that tile. If any are missing click the report missing tile link 
  5. To see the data for any layer click “geobrowse” but this will be the data ONLY for what is specified by the geobrowse you choose 
  6. If all the tiles are available then you should be able to copy data to your workspace

Step 3: Start simulation (Scientist) 

Once data have been prepared, clicking start simulation allows the baseline or alternative (scenario or policy option) simulation to be run.  If no-one has ever run the tile before then the simulation may take a number of hours as the system prepares a series of input datasets.  If the tile has been run before then the simulation will take only a few minutes and will write results as it runs.

Step 4: Policy exercises (Scientist) 

The different scenario and intervention tools for Co$ting Nature are accessed through this option   

Manage simulations (Scientist)

Under manage simulations you can change the current simulation to a previous (baseline or alternative) simulation, view the number of alternatives (scenarios and policy options) associated with a particular baseline or delete previous simulations that you no longer need.  Use this option to ensure that you have no more than three simulations stored at a time.

Step 5: Results : maps (Scientist)

Here you can visualise, compare and download results of the system in map form.

Step 6: Results : stats (Scientist)

Here you can visualise, compare and download results of the system in timeseries form.

Step 7: Results: narrative (Scientist)

Here the system provides a narrative on the outcomes of a particular baseline or scenario simulation.


Co$ting Nature functionality (Hyperuser interface) 

Demonstration of CN getting started (0h27m8s)

Demo Step 1: Define area (0h29m20s)

Demo Step 2: Prepare data (0h31m13s)

    Running tiles that have not been run before - building tiles (0h32m20s)

    Mask using rules (0h32m45s)

Demo Step 2: Copying data - limited storage space for runs (0h35m40s)

    Summary statistics for input maps (0h37m20s)

Demo Step 3: Start Simulation - Indexing locally or globally (0h38m25s)

Demo Step 5: Results maps - list (0h40m24s)

    Example: Relative Total Realised services. GIS functionality (CN and WW), view by function (0h40m44s)

    Viewing in Google Maps, Query points to determine values of input (0h44m40s)

    Compare Potential vs Realized Bundled Services (0h47m2s)

    Future Threat and Current Pressure (0h48m28s)

    Biodiversity Index and Conservation Priority Index (0h49m59s)

    Pressured and Threatened Conservation Priority index (0h51m8s)

Step 4: Changing Priorities and Values - setting weights (0h52m6s)

Free version and licensed features (1h36m15s)


Co$ting Nature  functionality (Megauser interface) 

Step 1 Define area (0m29s)

Step 2 Prepare data (1m49s)

Step 3 Start simulation (4m34s)

Step 5 Results maps list (5m43s)

    View maps available to Megauser: Total relative realised water provisioning services (6m17s)

    Carbon sequestration maps (7m12s)

    Total relative realised bundled services (7m51s)

    Comparing potential and realised bundled services (8m32s)

    Examining the relative conservation priority index (9m58s)

    aggregrate nature conservation priorities based on realised services (10m45s)

    The map view window (11m18s)

    View map by region (eg watershed, protected area) (11m54s)

    Viewing in Google maps/Earth (12m30s)

    Query points on a map and viewing the component inputs of a map (12m37s)

Step 4 Policy exercises (scenarios/policy options, valuation) (14m29s)

    Changing the Priorities and Values of conservation priorities (15m0s)



Ecoengine Functions by step (links to video demonstrations)

This section describes the generic functionality of the ecoengine framework and how to use it.

Step 1: Define area

Step 1 Define area (0m40s)

Step 2: Prepare Data

Use alternative SIMTERRA input maps (0h0m40s)

Masking data (1h23m56s)

Masking an area by a region of interest (ROI) (2m28s)

Mask by Watersheds of points (0h58m15s)

Investigating input maps - show workspace data (6m33s)

Examining the input data, for example Landsat 2000 Treecover (1h27m14s)

Step 3: Start simulation

Write monthly output maps option (7m44s)

Manage Simulations

Selecting previous runs and managing simulations (8m45s)

Deleting old simulations to free up space (1h20m55s)

Looking at a previously saved run. Looking at monthly impacts (1h55m31s)

Step 4: Policy exercises

Climate Change scenarios(1h14m53s)

Land Cover and Land Use Change (1h20m57s)

Run land use change model (including multiple deforestation monitoring products and management effectiveness) (0h6m55s)

Land and Water Management options (1h53m18s)

Land and Water Management, bench terraces, scenario by uploading your own maps (1h27m27s)

Extractive Scenarios for mining concessions and Oil and Gas. (1h29m15s)

Population growth and urbanisation scenarios (1h29m54s)

Change input maps (1h54m10s), Replace input maps (1h28m7s)

Show baseline and scenario, List alternative workspace data and compare to baseline (1h17m9s)

Run land use change model - deforestation (0h0m0s)

Run progressive deforestation scenarios (0h7m38s)

Compare alternatives (compares baseline and multiple alternatives for a given map) 

Step 5: Results maps

Results list (1h40m8s)

The map view window (7m26s)

Examining water balance (10m37s)

Examining water quality (11m5s)

Examining runoff (11m54s)

Viewing in Google maps/Earth (8m50s)

Query input components for a map at a point (12m40s)

Examining change from the baseline (2h2m57s)

Examining monthly maps, view and download (1h5m50s)

Citation information (1h39m5s)

Permalink for export of (google) maps (1h48m29s)

Analyse map - scatterplot and stats (1h49m39s)

POIs ROIs and ZOIs (1h11m10s)

Regions of interest (copy/paste points of interest and show on output maps) (0h18m30s)

Create ZOI with bounding box (0h0m0s)

Step 6: Results stats

Results time series (1h51m41s)

Step 7: Results narrative

Results narrative (1h52m31s)

Questions and Answers

Running the model over multiple tiles and combining using ArcMap and ArcHydro or SagaGIS (1h32m36s)

Run times in new areas (1h38m43s)

Free version and licensed features (1h36m15s)



GUIDANCE FOR PRE- and POST- PROCESSING OF DATA

Creating a Zone of Interest (ZOI) map from a  shapefile using SAGAGIS (by Mark Mulligan)

- Download and install the free and open source SAGAGIS GIS (if you do not already have it).

- Download any of the available input or output maps in ARCASCII format to use as a template and unzip it.

- Use your file manager to pick up the ARCASCII file and drop it into the SAGAGIS window.

- Ensure that your shapefile is in the Geographical Coordinate System (GCS, latitude longitude) and uses a WGS84 DATUM (Use Modules > Projection - Proj.4 > Coordinate Transformation (Shapes) to reproject if necessary)

- Use your file manager to pick up the file with .shp extension in your polygon shapefile and drop it into the SAGAGIS window

- Check that the grid and the shapefile overlap by double clicking the name of the grid under the  tab and choosing to display in a new window.  Then go back to the  tab and double click the name of the shapefile and choose to display in the window named as your grid is.  Does the shapefile overlay the grid?  If not then you may need to run another tile in the PSS or check that the shapefile is really in The geographic coordinate system (GCS) and WGS84 datum.

- In SAGAGIS from choose the Grid-gridding collection and double click the Shapes to Grid module.

- Under Shapes choose the name of your loaded shapefile

- Under attribute choose the field that will be used (choose any since we will convert the grid to zero (outside)  and 1 (inside) the area of interest

- Under Preferred target grid type choose integer (1 byte)

- Under Target grid choose the grid that you have loaded (to do this choose grid here and you will be asked to define the grid system in the next step)

- Click Okay. In the next window, you will be asked to choose the Grid system, so, choose the only one available, which is the system of the grid you loaded and to which the shapefile must be converted.

- Under Number of Values choose [create], and then click Okay.

- Now go to the tab and double click in the new grid with the [Count] tag, which will be named the same as your shapefile.  Choose New to display in new map.  You should see your shapefile shape as a grid with values of 1 where the area of interest is, and 0 elsewhere (it may be clipped to the edge of the tile if it extends beyond it).  This will now be used to set your ZOI in the PSS. If you see a blank map then either your shapefile is not a polygon or it is in a different coordinate system to the GCS, WGS84 of the grid.  Fix it and try again.

If your shapefile has small polygons which are lost on conversion to grid cells then you need to download the latest version of SAGAGIS (at least 2.1.1 here) and when using Shapes to Grid choose output values as data/no-data, polygon should be set to cell and fit to cells  should be ticked.  Note that you will not need to install SAGAGIS, just download the zip file, extract it and run the file called SAGA_GUI.exe.

- You now need to save the map as a zipped ARCASCII to include it in the PSS. Go back to  and choose Import/Export - Grids and then double-click Export ESRI ARC/Info Grid.  

- Under grid system choose your only available grid system.  

- Under grid choose the name of the grid that you created with the the [Count] tag at the end.  

- Under file choose a folder and file. Make sure to include the .asc extension. Click Okay and the file will be written.

- Under ASCII Precision choose 0.  

- In your file manager (e.g. Windows Explorer) find the .asc file and zip it, giving the .zip file the same name as the .asc file.  This can now be used to set a ZOI using upload ZOI in the PSS.


Combining tiles and clipping them to a shapefile in SAGAGIS (by Mark Mulligan)

If your study area covers more than one PSS tile you may need to combine tiles and then clip them to an area of interest such as a watershed

Download and install the free and open source SAGAGIS GIS (if you do not already have it).

Download any of the available input or output maps in ARCASCII format and unzip them.

Use your file manager to pick up the ARCASCII file and drop it into the SAGAGIS window.

Ensure that your shapefile is in the Geographical Coordinate System (GCS, latitude longitude) and uses a WGS84 DATUM

Use your file manager to pick up the file with .shp extension in your polygon shapefile and drop it into the SAGAGIS window

In SAGAGIS from choose the Grid-Merging.  Choose the grids to merge.  Under “target-grid” give a name to the grid that you wish to create from the merged grids.  Click Okay.  The grids will load and merge.  Now go to the tab and double click the new grid and choose New to view it and check that it is Ok.  

To clip the grid, from the  tab choose Shapes-Grid, Clip grid with Polygon.  Choose the grid system of your merged grid (it will be the one with the most rows and columns.  Under Input choose the name of the merged grid.  Under Polygons choose the name of the shapefile.  Click Okay and your merged grid will be cut to the polygon shapefile.

You must now export this merged, clipped grid.  Under  choose the Import/Export - Grids and double-click Export ESRI Arc/Info Grid.  Choose the grid system of your merged grid.  If you are unsure go to the  tab and right click the grids that you no longer need and choose close to close them and remove their grid systems from view.  Choose the grid to be exported.  Under File choose a location to save the exported ARCASCII file and click Okay.  The merged, clipped grid will be saved.


Cutting and resampling your gridded data so that it is compatible with the PSS and ready for upload in SAGAGIS (by Mark Mulligan)

If your gridded data are not the same cellsize or extent as those in the tile that you are running in the PSS, so long as your data are in the same coordinate system (GCS WGS84) and cover the tile area, you can use SAGAGIS to resample them so they can be uploaded.  

- Download and install the free and open source SAGAGIS GIS (if you do not already have it).

- Download any one of the PSS input or output maps that you will use as a template map and unzip the ARCASCII

- Use your file manager to pick up the ARCASCII file and drop it into the SAGAGIS window.

-Open your own gridded dataset in SAGAGIS by drag and drop or using the import functions

- From the  tab choose Grid-Tools, Resampling

- In the dialogue that appears, for GRID, choose the grid system and grid for  your data grid that you want to resample

- For PRESERVE DATA TYPE, uncheck the box

- For TARGET GRID, choose GRID (which means we will name a grid later). Click OK and this window closes.

- A choose grid window then opens.  Here choose the grid system for the template grid downloaded from the PSS.  For grid choose create as we will build a new grid for the output resampled data. Click Okay.  If your grids do not overlap at all then SAGAGIS will not ask any more questions and will not be able to produce useful output (you may see a blue grid but it will be of no use).  

If your data do overlap,  a new window opens in which you need to specify the resampling method. For continuous data, f there are no no-data areas, then use BICUBIC SPLINE INTERPOLATION.  If there are some no-data areas if you are resampling to a grid cell size that is very close to the original size, then choose NEAREST NEIGHBOUR to avoid the creation of false cell values in no-data areas.  If you are resampling to a radically different cell size, then use an interpolation method like BICUBIC SPLINE INTERPOLATION.  If the data are a classified map (discrete data) such as land use then choose Majority as we want to retain the same classes.  Click Okay.

- You will now see a resampled new map under the grid system associated with the map that you downloaded from the PSS.  It should be a square tile with the same footprint as the PSS tile that you downloaded.

If your original data are higher spatial resolution than the PSS template and this process leads to loss of features then instead of using interpolation choose Maximum value as the interpolation method.

You must now export this resampled, clipped grid.  Under  choose the Import/Export - Grids and double-click Export ESRI Arc/Info Grid.  Choose the grid system of your merged grid.  If you are unsure go to the  tab and right click the grids that you no longer need and choose close to close them and remove their grid systems from view.  Choose the grid to be exported.  Under File choose a location to save the exported ARCASCII file and click Okay.  The merged, clipped grid will be saved.


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