Critical Limits Habitat Analysis

This How-To guide provides guidance for the application of the Critical Limits Time Series Habitat Analysis tool introduced in EFDC_Explorer 8.4. This guide will introduce the user to the basic functionality of the tool, but is not comprehensive. As additional modules are added to a model, more model parameters become available for use in the tool. The demonstration model shown in this guide and the resources to conduct the habitat analysis are available on the Modeling Resources page.

This guide will show you how to:

1. Determine area (or volume) of viable habitat for species through time based on defined criteria;
2. Determine the spatial distribution of viable habitat for species through time based on defined criteria.

Model Description

The HabitatRiver demonstration model provides a typical example of a large gravel bed river, with multiple vegetated islands, bars, and side channels. The upstream boundary of the model uses a stepped flow pattern fitting with the IFIM methodology, where flow is gradually increased from low to high flow conditions over a period of seven days. The downstream boundary condition utilizes a rating curve to define the relationship between the water level and flow in the channel. The model simulates the basic 3D hydrodynamics of the river system at various flow and stage combinations.

For this example, two species have been identified for analysis: Muskellunge (Esox masquinongy), and Burbot (Lota lota). At each life stage, these species seek out specific areas of the river which satisfy a broad set of habitat preferences. For this analysis, we focus on water depth and velocity as the primary factors in the habitat suitability for these species.

Step-by-Step Guide

Step 1: Run the Model

Once the model has been loaded into EFDC_Explorer, Run the model by pressing the Run EFDC button on the top bar of the main EE form. This step is required to conduct the habitat analysis in the following steps.

Step 2: Open the Critical Limits Time Series Analysis dialog

Figure 1. The Habitat Analysis Form under the Model Analysis tab in EFDC_Explorer 8.4.

From the main form of EE, go to the Model Analysis form and open the Habitat Analysis tab (Figure 1). Press the Critical Limits Time Series button to open the Critical Limits Series dialog (Figure 2).

Figure 2. The Critical Limits Series dialog.

Step 3: Define Critical Limit Parameters and Ranges

Critical limits for the species of interest are given in Table 1. Three live stages of the Muskellunge and two life stages of the Burbot will be analyzed in this exercise.

Table 1. Critical Limits for three life stages of Muskellunge and two life stages of Burbot.

Using the information provided, the user can begin to populate the Critical Limits Series dialog. Begin by entering the species name into the Criteria ID text box ("Muskellunge Adult"). Next, select Water Depth from the Parameters drop-down list below. Text boxes to enter the minimum and maximum critical limits will appear next to the selected parameter (Figure 3).

Figure 3. Critical Limits Series dialog with Criteria ID and Water Depth parameter ranges specified.

Continue by entering in critical limits for velocity, as shown in Table 1. When the form is populated with the desired critical limit parameters and ranges, press the save button to save this critical limits series profile for later. This file will have a .hcl extension and is saved in the #habitat folder of your model by default.

Step 4: Generate Initial Time Series

The next step after completing the Critical Limits Series profile for a given species will be to generate the initial time series. The user has the option to specify a window of time for analysis by changing the start and end date in the Initial Model Results Extraction Options. The Cell-by-Cell check box will write out results for each cell being considered in analysis. Using the Series check box next to any one of the selected parameters will plot the time series for that parameter, averaging by cells that meet the defined critical limits criteria.

Once the desired period of time for analysis has been specified, press the Generate Initial Time Series button. Once EFDC_Explorer has finished processing the initial time series, the results will be displayed in the Time Series Data Grapher (Figure 4).

Figure 4. Time Series Data Grapher with output from the Generate Initial Time Series option.

To use these data for comparison with other species, the user can write out the information in the plot by using the Export button on the top bar of the Time Series Data Grapher.

Step 5: Secondary Processing of Extracted Results

After generating the initial time series, and inspecting the resulting plot, return to the Critical Limits Series dialog by closing the Time Series Data Grapher window. Secondary Processing of Extracted Results options are now available in the Critical Limits Series dialog. The user has the options to run a Domain Average, a Running Average (using a user-defined averaging window), or Single Cell Time Series (using a user defined cell ID).

The Domain Average option will compute a composite habitat index as an average of suitable (1) and un-suitable (0) cells within the domain (Figure 5).

Figure 5. Composite Habitat Index based on suitable and un-suitable cells in the model domain.

The Running Average option allows the user to define a time window over a number of days and report the Average, Daily Maximum, Daily Minimum, or Twice-daily Maximum/Minimum. The user will be prompted to save the data for these analyses to a separate file.

Step 6: Combine Time Series Results for Comparative Analysis

Using the exporting and importing options in the Time Series Data Grapher, the user can compare results for the three life stages of Muskellunge and the two life stages of Burbot (Figure 6 and Figure 7).

Figure 6. Usable habitat area based on the defined critical limits criteria for three life stages of Muskellunge.

Figure 7. Usable habitat area based on the defined critical limits criteria for two life stages of Burbot.

Step 7: Spatial Analysis

The next step will use the Critical Limits Series profile that was created to display suitable habitat in the ViewPlan window. Press the Finished button on the Critical Limits Series dialog to return to the main form of EFDC_Explorer. Press the ViewPlan button to display the 2-D plan view of the model domain.

Use the Alt+H hotkey combination to open the selection dialog for the Habitat Analysis tools for the ViewPlan. Select option 2 by typing "2" into the text box and pressing OK. The user will then be prompted to open one of the ".hcl" files created earlier for the Critical Limits Series analysis (Figure 8). Select the desired ".hcl" file and press OK to load.

Figure 8. ViewPlan window showing cells which meet the defined critical limits criteria for the Muskellunge Adult.

The user can then use the Timing slider on the top right of the ViewPlan to view cells which meet the defined critical limit at any point in the simulation. With the stepped discharge pattern at the upstream boundary, the user can identify changes in suitable habitat at different discharge levels, as shown in FIgure 9, 10, 11, and 12.

Figure 9. Cells meeting the defined habitat criteria for the Muskellunge Adult at 350 cms.

Figure 10. Cells meeting the defined habitat criteria for the Muskellunge Adult at 750 cms.

Figure 11. Cells meeting the defined habitat criteria for the Burbot Adult at 350 cms.

Figure 12. Cells meeting the defined habitat criteria for the Burbot Adult at 750 cms.

Conclusion

This How-To guide provided an introduction to the basic function of the Critical Limits Time Series analysis tool, introduced in EE8.4. Utilizing the post-processing features available, estimates of the usable area and volume and habitat index were derived for two species of interest, the Muskellunge and Burbot. Comparisons were made between three life stages of Muskellunge, and two life stages of Burbot over a range of discharge values. The spatial distribution of suitable habitat was determined for both species using the ViewPlan viewing options for the habitat analysis results.

With more complex models, utilizing a wider range of simulation modules, the user can specify a parameters relating to temperature, sediment transport, water quality and others.