This How-To guide provides guidance for the application of the Habitat Suitability Analysis features introduced in EFDC_Explorer 8.4. This guide will give the user an introduction to the Habitat Suitability Analysis features but is not intended to be comprehensive. As additional modules are added to a model, more parameters become available to be used in the habitat analysis. The demonstration model shown in this guide and the resources to conduct the habitat analysis are available for download from the Modeling Resources page.
This guide will show you how to:
- Determine the weighted usable habitat area based on defined criteria through time;
- Determine the habitat suitability index, for both the entire domain and for each cell, as a function of time;
- Analyze the weighted usable area and habitat suitability for the entire domain as a function of discharge using the Instream Flow Incremental Methodology (IFIM);
- Analyze the spatial distribution of suitable habitat as a function of time.
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 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 Habitat Suitability Analysis dialog
Figure 1. The Model Analysis form of EFDC_Explorer, with the Habitat Analysis tab selected.
From the main form of EE, go to the Model Analysis form and open the Habitat Analysis tab (Figure 1). Press the Habitat Suitability Analysis button to open the Habitat Suitability Analysis dialog (Figure 2).
Figure 2. The Habitat Suitability Criteria dialog.
Step 3: Define Habitat Suitability Curves
Habitat suitability curves are included in the HabitatAnalysisData.xlsx spreadsheet for the Muskellunge and Burbot species. Begin by entering in the first fish species and life stage into the Criteria ID text box (“Muskellunge Adult”). Next, select Water Depth from the drop-down menu under the Parameters list. A text box appears next to drop down menu for the model parameter once it has been selected. This text box is used to store the habitat suitability curves for the chosen parameter (Figure 3).
Figure 3. The Habitat Suitability Criteria dialog, with a Criteria ID, and Water Depth selected as the first parameter for analysis.
With the text box selected, press enter to open the XY Data Editing Tool. In this dialog, XY data can be entered and plotted graphically to assist the user in defining habitat suitability curves for the chosen parameter (Figure 4).
Figure 4. The XY Data Editing Tool (blank).
Begin entering XY data from the spreadsheet provided to define the habitat suitability curve for Water Depth for the Muskellunge Adult. Once finished, the curve should appear as shown below in Figure 5.
Figure 5. The XY Data Editing Tool with Habitat Suitability curve data entered and plotted.
Hit OK to return to the Habitat Suitability Criteria dialog.
Note that the XY data just entered now appears in the text box next to the drop-down menu. The user has the option to enter XY data in the text box, separating X and Y with a comma, and separating pairs of XY data points with a semi-colon.
You can now specify a layer of the model to focus on for a particular habitat suitability curve. Layer 0 (depth averaged) is entered by default in the Layer field of the selected parameter, but any model layer can be used in this field to refine the analysis.
Next, select Velocity from the next drop-down menu below Water Depth. Once XY data has been entered to define the habitat suitability curve for velocity, hit the Save button to save the criteria just defined for the Muskellunge Adult. This will write the habitat suitability curve information for this species to a .hsc file under the #habitat folder of the HabitatRiver model folder by default (Figure 6).
Figure 6. The Habitat Suitability Criteria dialog, with Suitability Curves defined for two parameters (Water Depth and Velocity).
Saved habitat suitability files can be reloaded into this dialog using the Load button.
Create .hsc files for all of the species listed in the HabitatAnalysisData.xlsx spreadsheet and save each one of them for use in the following steps of this How-To guide. You can skip this step by using the .hsc files already included with the demonstration model under the #habitat model folder.
Step 4: Generate Initial Time Series
Once habitat suitability curves have been generated and saved, the user can begin the analysis. With the desired .hsc file loaded into the Habitat Suitability Criteria dialog, press the Generate Initial Time Series button to extract data from the model output files. The user will be prompted to confirm the number of cells included in the analysis. Select Yes (Figure 7).
Figure 7. Prompt to confirm number of cells being analyzed, after pressing the Generate Initial Time Series button under the Initial Model Results Extraction Options section of the dialog.
Note that the number of cells included in the analysis can be refined using the Sub-Set option in the Habitat Suitability Criteria dialog. This dialog can utilize a .p2d or other shapefile to define a region of the model for analysis.
Once results have been extracted, a datafile is created in the #habitat folder containing data specific to the .hsc information entered in the form.
Step 5: View the Weighted Usable Area Time Series
Once model results have been extracted for the desired number of cells, Secondary Processing of Extracted Results options become available to the user in the Habitat Suitability Criteria dialog. From the drop-down menu, select WUA Time Series, and press View WUA Time Series to generate a plot of this data (Figure 8). The data displayed in this plot is automatically extracted to a data file under the #habitat folder in the model directory.
Figure 8. The Time Series Data Grapher with time series data plotted for Weighted Usable Area for the Muskellunge Adult.
Once you are finished inspecting the time series, press the Export button on the top bar to export this time series for use later. Give the time series a distinctive name that you will recognize later. For example, “TS_MuskellungeAdult_HSC_WUA.dat”.
Step 6: View the WUA vs. Q plot
Close the Time Series Data Grapher to return to the Habitat Suitability Criteria dialog. Select WUA versus Q from the Type of Processing drop down menu. This will bring up a text box which is used to enter time and discharge data to plot the weighted usable area as a function of discharge (Figure 9). Click the text box and press Enter to open the XY Data Editing Tool to enter time and discharge data.
Figure 9. When WUA versus Q is selected for the Type of Processing, the T vs. Q text box appears to allow the user to populate that field.
For this guide, the user can copy and paste time and discharge data from the spreadsheet provided or enter time and discharge points as desired. The time and discharge data provided for this exercise was chosen to reflect steady flow conditions in the model reach by choosing times at the end of each step in the discharge curve (Figure 10).
Figure 10. Example data for Time versus Discharge, in order to plot weighted usable area versus discharge.
Press OK to return to the Habitat Suitability Criteria dialog once the time and discharge data has been entered, then press the View WUA versus Q button to show the data (Figure 11).
Figure 11. Weighted Usable Area as a function of Discharge for the defined discharge values.
Once you are finished inspecting the time series, press the Export button on the top bar to export this time series for use later. Give the time series a distinctive name that you will recognize later. For example, “TS_MuskellungeAdult_HSC_WUAvsQ.dat”.
Step 7: View HSC Time Series
Close the Time Series Data Grapher and return to the Habitat Suitability Criteria dialog. From the drop-down menu options for Secondary Processing of Extracted Results select HSC Time Series and press the View HSC Time Series button. The Time Series Data Grapher will appear again with a time series of the Habitat Suitability Index for the species of interest (Figure 12).
Figure 12. Habitat Suitability Index as a function of time for the Muskellunge Adult.
Once you are finished inspecting the time series, press the Export button on the top bar to export this time series for use later. Give the time series a distinctive name that you will recognize later. For example, “TS_MuskellungeAdult_HSC_Index.dat”.
Step 8: Additional Secondary Processing Options
From the Habitat Suitability Criteria dialog, there are some remaining options to explore under the Secondary Processing of Extracted Results drop-down. These are:
- Weighted Usable Volume (WUV) Time Series: The weighted usable volume time series provides another measure of the usable habitat within the area of interest by taking the Weighted Usable Area and multiplying by the depth of each cell.
- Volume Time Series: Like the Weighted Usable Volume, but without utilizing the weighting criteria.
- Parameter Time Series: A time series of the selected parameter for all cells satisfying the habitat suitability criteria.
Explore these remaining options and see how they compare with the same parameter for other species or life stages.
Step 9: Compare Habitat Suitability for Different Life Stages
Repeat Steps 3 through 7 for all life stages of the Muskellunge, and the life stages of Burbot. After that task is completed, we can put together the habitat suitability information for analysis.
In the Habitat Suitability Criteria dialog, select the type of plot desired from the drop-down menu under Secondary Processing of Extracted Results and view the series. From the Time Series Data Grapher, press the Import button on the top bar. Navigate to the #habitat folder where the other series for that species are saved. Load each of the series into the Time Series Data Grapher to overlay the time series on same axes.
You can modify the line styles and axis labels by right clicking on the Legend or Axes.
Below are examples of resulting plots from this step of the How-To guide:
Figure 13. Weighted usable area as a function of Discharge for three life stages of the Muskellunge.
Figure 14. Habitat Suitability Index as a function of Time for two life stages of the Burbot.
Step 10: Spatial Analysis of Habitat Suitability
From the main form of EE, open the ViewPlan to load the 2-D plan view of the model domain and display simulation results. The keyboard shortcut Alt+H can be used to open the habitat analysis tools for the 2-D plan view (Figure 15).
Figure 15. ViewPlan options for the EEMS Habitat Tools. This menu is accessed by pressing Alt+H from the ViewPlan window.
Select the Habitat Suitability Indices option by typing 3 in the text box and pressing OK. The user is then prompted to load a Habitat Suitability Criteria file. Select one of the files in the #habitat folder that was created in Step 3.
Habitat suitability index values between 0 and 1 will then be displayed for every cell in the model domain at the selected model snapshot (Figure 16). To change model snapshots, user the Page Up and Page Down buttons on your keyboard or use the Timing slider on the right side of the ViewPlan Window.
Figure 16. ViewPlan showing the the spatial distribution of suitable habitat based on Habitat Suitability Index values (between 0 and 1) for the Muskellunge Adult.
Below are examples showing the comparison between habitat suitability for the Burbot species at who different discharge levels in our model:
Figure 17. Spatial distribution of suitable habitat for the Burbot Adult at 350 cms.
Figure 18. Spatial distribution of suitable habitat for the Burbot Adult at 750 cms.
This How-To guide provided an introduction to the basic function of the Habitat Suitability Criteria features, introduced for EE8.4. Utilizing the post-processing features available, estimates of weighted usable area and the habitat suitability index were derived for two species of interest, the Muskellunge and Burbot. Comparisons were made between three life stages of the Muskellunge, and two life stages of the Burbot. The spatial distribution of suitable habitat was determined for both of these species using the ViewPlan options available for displaying Habitat Suitability Criteria.
Using these features, the user can utilize a wide range of model parameters depending on the modules currently in use in a given model. These could include information regarding temperature, water quality, sediment characteristics, or toxics.
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