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The Getting Started documentation and associated Tutorials for this SyncroSim package currently reflects information for SyncroSim version 2. We are in the process of updating these pages to ensure compatibility with SyncroSim version 3. In the meantime, please note that some instructions, references, and/or images may not fully align with the latest version of SyncroSim. We appreciate your patience as we work to provide updated resources.


Measuring the impact of connectivity change with omniscapeImpact

This tutorial guides you through using the omniscapeImpact package, which extends omniscape SyncroSim. It covers the following steps:

  1. Installing the omniscapeImpact package
  2. Creating and configuring an omniscapeImpact SyncroSim Library
  3. Visualizing and comparing scenario results


Requirements

Before you begin, make sure that the omniscape SyncroSim package version 2.8.0 is installed, along with SyncroSim version 3.1.0 or greater. For more information, see Installing the omniscape SyncroSim package.

Note: omniscapeImpact shares its Conda environment with omniscape, so omniscape must be installed and its Conda environment created first.

The Baseline and Alternative Scenarios being compared must be directly comparable. omniscapeImpact will stop with an error if their output rasters differ in extent, resolution or projection, or if they disagree about which pixels hold valid data. If the two Scenarios were classified using different Category Thresholds, the connectivity category outputs are skipped and only the Normalized current comparison is produced.


Step 1. Installing the omniscapeImpact package

1. Open SyncroSim Desktop.

2. Select File > Packages.

3. The Packages window will open, listing all the SyncroSim packages installed in your computer. To install a new package from the Package Server, click Install.

4. A new window will open listing the packages available for install from the Package Server. To install omniscapeImpact, mark the checkbox beside the package name and click OK.

5. The omniscapeImpact package uses Conda to manage the package dependencies. Upon installing the package, you will be prompted to create or update the Conda environment for omniscapeImpact. Click Yes.

6. Return to the Packages window. omniscapeImpact will now be listed along with the other installed packages, and the Conda checkbox will be marked.


Step 2. Creating and configuring an omniscapeImpact SyncroSim Library

1. Open SyncroSim Desktop.

2. To create a new library, select File > New.

a. From the list of packages, select omniscape.

b. Select the Omniscape Impact template library. If desired, you may edit the File name, and change the Folder by clicking on the Browse button. Click OK.


A new library will be created based on the selected template, and SyncroSim will automatically open and display it in the Library Explorer window.

1. Note that the library contains two folders: omniscape and omniscapeImpact.

2. Expand the omniscape folder and note that it contains three scenarios.

The first two scenarios were covered in the tutorial Reproducing the Omniscape.jl example with omniscape SyncroSim.

The additional scenario, Decreased resistance, represents the case where resistance has been decreased by a similar magnitude as in the Increased resistance scenario.

3. Next, expand the omniscapeImpact folder and note that it contains two scenarios:

a. Impact of increased resistance – compares the Reference resistance and Increased resistance scenarios.

b. Impact of decreased resistance – compares the Reference resistance and Decreased resistance scenarios.

4. Double-click on Impact of increased resistance to open the scenario properties.

5. Under the General tab, navigate to the Pipeline datasheet.

Note that it lists one pipeline stage, Connectivity Impact Assessment.

6. Close the scenario properties and, in the Library Explorer window, expand the Impact of increased resistance scenario to expose its Dependencies folder.

The two scenarios to be compared are supplied as dependencies of the impact scenario, added by dragging each scenario onto the Dependencies folder. The order matters:
i. The first dependency is the Baseline – the reference connectivity state from which changes will be measured. For this example, it is the Reference resistance scenario.

ii. The second dependency is the Alternative – the changed connectivity state. For this example, it is the Increased resistance scenario.

To swap the Baseline and Alternative, reorder the dependencies. The run log for each run records which scenario was used as which. Adding a scenario (rather than one of its results) as a dependency automatically uses that scenario's most recent valid results.

7. Collapse the scenario.


Step 3. Visualizing and comparing scenario results

The Omniscape Impact template library already contains the results for all its scenarios. In SyncroSim, the results for a scenario are organized into a Results folder, nested within its parent scenario.

1. In the Library Explorer window, click on the arrow beside the Impact of increased resistance scenario to expose the Results folder; repeat the same action to expose the results scenario.

2. Double-click on the results scenario to open its properties.

3. Navigate to the Add-on tab and expand the Results node.


The omniscapeImpact package generates spatial and tabular outputs.

4. Under the Spatial node are the following outputs:

a. Overall – represents per pixels change in normalized current flow or connectivity category.

b. Per Category – represents per pixels loss, gain and no change for each connectivity category.

5. Under the Tabular node are the following outputs:

a. Differences Summary – represents the change in area and proportion between the baseline and alternative scenarios for each connectivity category.

b. Transitions Summary – represents the change in area and proportion between the baseline and alternative scenarios for all possible transitions between connectivity categories.

c. Jaccard Dissimilarity – represents the dissimilarity between the baseline and alternative scenarios for each connectivity category. For each connectivity category, the Jaccard Dissimilarity is calculated as 1 minus the ratio between the number of shared pixels across scenarios and the total number of pixels across scenarios.

6. Close the scenario properties and collapse the results and scenario folder.

You will now visualize the tabular outputs of omniscapeImpact

7. In the Library Explorer window, select the scenarios Impact of increased resistance and Impact of decreased resistance, right-click, and select Add to Results from the context menu.

8. Navigate to the Charts tab and double-click to view the Area difference chart.

Note that the two scenarios had opposite effects on connectivity.

The Increased resistance scenario led to an increase in area for Impeded and Channelized and a decrease in area for Diffuse and Intensified, relative to the Reference scenario.

The Decreased resistance scenario led to a decrease in area for Impeded and Channelized and an increase in area for Diffuse and Intensified, relative to the Reference scenario.

Note also that the magnitude of change in area was larger under the Decreased resistance scenario.

9. Close the Area difference chart and open the Jaccard dissimilarity chart.

Note that a similar pattern is reflected here, with Impact of decreased resistance showing greater dissimilarity to the baseline scenario compared to Impact of increased resistance.


Next, for a visual confirmation of the quantitative changes summarized by area and the Jaccard dissimilarity, you will inspect the spatial outputs of omniscapeImpact.

10. Navigate to the Maps tab and double-click to open the Normalized current difference and Cross-category difference maps.

The Normalized current difference summarizes continuous change in current between the baseline and alternative scenarios.

In turn, the Cross-category difference map highlights pixels where the change in current represented a change in connectivity category. For example, a change from Impeded to Diffuse would represent a 1 category gain, while a change from Channelized to Diffuse would represent a 2 category loss.

11. Close the Normalized current difference and open the Per-category difference map.

The Per-category difference map represents per pixel losses and gains for each category. Together with the Cross-category difference map, it can be used to identify transitions between connectivity categories.

Both maps also highlight that a decrease in resistance had a stronger effect on connectivity than an increase.