PHABSIM Laboratory Exercises

Preface

Chapter 1

Chapter 2

Chapter 3

Chapter 4

Chapter 5

Appendices

Lab Exercises 1-6

Lab Exercises 7-12

Lab Downloads

Laboratory 7. Habitat Suitability Criteria in PHABSIM

Objective

The objective of this laboratory is to introduce the use of habitat suitability criteria (HSC) within the PHABSIM for Windows system. The laboratory will illustrate the method used to input HSC for use within PHABSIM and examine several of the available criteria maintenance programs.

Data Files Used: Lab7.phb, Curvlib.phb

Introduction

The principal means by which PHABSIM integrates biological information for habitat modeling purposes is through the use of HSC (sometimes referred to as suitability-of-use criteria) within the various habitat models. The laboratory will not deal with the specifics of HSC development. However, the various means by which HSC can be entered and manipulated within PHABSIM will be examined. See Bovee et al. (1998) for a detailed description of HSC and their development.

In PHABSIM, HSC data are created, edited, and stored in the \Edit\Suitability Curves section of the program. These data contain the HSC coordinate data for species and life stages in terms of depth, velocity, channel index, and temperature.

HSCs for a particular species and life stage are typically grouped into three sets of HSC data representing the relationships between depth, velocity, and channel index and their corresponding suitability values.

In PHABSIM, HSC data are referenced by HSC numbers. Although these HSC numbers can be arbitrarily assigned within any PHABSIM project file, the structure of the numbers does control the format of the output results from the habitat programs as will be discussed later in this lab. The steps in this lab are designed to build basic skill in using HSC w/in PHABSIM.

Step 1. HSC Numbering

HSC numbering within PHABSIM allows the user to organize HSC curves by species groups. The basic format for HSC numbering is:

xxxxyy

The first four digits (i.e., xxxx) denote the >species=, while the last two digits (i.e., yy) denote the 'life stage'. Figure L7-1 contains a list of habitat suitability criteria for use in a particular study. This list is obtained by clicking \Edit\Suitability Curves\Curves\Select by ID.

The Graph button in the \Edit\Suitability Curves window allows you to view individual habitat suitability criteria graphically. To view all HSC for a species/life stage, select Display All Graphs in the \Edit\Suitability Curves\Curves menu. Figure L7-2 shows an example of the resulting plot. Note that there are no temperature HSC values in this curve set for Black Trout.

Figure L7-1. List of suitability curves showing species and life stage numbering.

Note that each HSC set (i.e., velocity, depth, and channel index) is associated with a unique HSC number for each species and life stage. In the example above, the user should identify that Rainbow Trout Fry has a HSC number of 21112. HSC number 21114, on the other hand, identifies the Rainbow Trout Juvenile curve set. Be sure you recognize how this follows the numbering convention described above.

Step 2: HSC Data Structure in PHABSIM

Move to \Edit\Suitability Curves in the SAMPLE.phb project and click Select\By ID. This displays a list (as in Figure L7-1) of the HSC curves that have been entered in the sample project including curve number, species, and life stage. New curves are entered by clicking the \Edit\Suitability Curves\File menu item, selecting New Curve, then filling in the boxes for Curve number, Species, and Life stage. Enter the HSC values in the table shown in that window (the first table is velocity). To change from velocity to depth, channel index or temperature, click the appropriate radio button in the Curve Type box to the upper right. Click the desired radio button (i.e., depth) and enter the HSC values in the table. Be sure to fill in all HSC tables before exiting. Habitat suitability criteria are discussed in Chapter 3 of the manual. Remember the PHABSIM convention that all HSC curves must begin at 0 and end at 100. In most situations the starting and starting values will be 0.0, 0.0 and ending values will be 100.0, 0.0. When might this not be the case?

In the suitability curve-editing portion of our Sample project, select Rainbow Trout Fry and note that the first velocity coordinate point at a velocity of 0.0 has a suitability value of 1.00. Note the last value. Again, failure to include the coordinate points with 100 for all curve sets will result in an error message indicating that the 100 value has not been entered. You cannot exit HSC data entry until all curves have final values of 100.

While in the \Edit\Suitability Curves window, each HSC set can be viewed graphically by clicking the Graph button. For Rainbow Trout fry, the HSC value of velocity descends from 1.0 at a velocity of 00.0 to 0.0 at a velocity of 0.5. For more complicated HSC graphs, using the zoom feature may enhance viewing of particular portions of the curve. The graph automatically updates when a different curve is selected. For example: click Graph and drag the plot to the lower right so the Curve box with radio buttons is revealed. Then click the Depth (or any other) radio button. The graph will update to show the depth curve at the same degree of zoom that was previously selected.

Figure L7-2. An example of displaying all HSC for a selected species and life stage.

When you are finished entering or viewing HSC curves, click OK to exit the \Edit\Suitability Curves window.

Step 3. Building HSC Libraries

The \Edit\Suitability Curves section of PHABSIM can be used for entering HSC data to create a set of HSC curves. Users of PHABSIM Version 2.0 (DOS) will recall the term FISHCRV libraries applied to such HSC sets. Table L7-1 lists HSC coordinate data for Brown Trout adult and fry for velocity, depth, and channel index which will be used to construct HSC data. The HSC numbers for each species and life stage are also indicated in this table.

Enter these HSC in the SAMPLE data set using \File\New Curve in the Suitability Curves Window. Examine the newly created HSC sets using the Graph feature. When finished, go back to the main menu and save the project.

The HSC in this project can now be used in other projects by importing the HSC data. In the \Edit\Suitability Curves window the ability to import from an existing project is found under \File\Import\From Existing Project. One may also import FISHCRV format text files prepared in DOS PHABSIM version 2 format using the Import From Text File menu item. You will be prompted to select which curves to import.

Thus, it is possible to create a project with the sole purpose of containing a library of HSC curves and import the desired HSC for each specific study from this library as needed. Try creating a new project and importing the HSC from this revised Lab7 project. Give the new project the name "New Curves". The "New Curves" project could become a library of curves by importing or building successive HSC data sets as described above. Note that any individual curve can be selected from the source project and placed in the receiving project as long as the curve ID numbers are unique.

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Laboratory 8. AVDEPTH and AVPERM Models

Objective

The objective of this laboratory is to introduce the user to the hydraulic parameter based model AVDEPTH/AVPERM. This concatenated name is retained for familiarity with past versions of the PHABSIM system. The laboratory will demonstrate the use of this model as well as illustrating the type of model outputs generated.

Programs Used: AVDEPTH\ AVPERM

Data Files Used: Lab8.phb

Introduction

The AVDEPTH \AVPERM model characterizes a study site channel in terms of hydraulic properties at each cross section. The AVDEPTH/AVPERM model can be used to characterize a stream in terms of a qualified wetted perimeter at each simulated discharge. The wetted perimeter can be reported for areas at least as deep as up to five user-specified depths. The output is provided for each cross section as well as for reach-aggregated results. In addition, the program produces summary output of average channel velocity, hydraulic depth, hydraulic radius, wetted width, wetted perimeter, Froude number, wading parameter, drag parameter, and cross sectional area. The wading parameter is calculated as the product of the depth times the velocity and can be used as an index of safe wading conditions at a cross section. The drag parameter is computed as the velocity squared times the depth.

The AVDEPTH/AVPERM model requires that the simulated hydraulic properties for use within the model have been generated by one of the hydraulic models (i.e., STGQ, MANSQ, or WSP). At least one of those models must have been run prior to use of AVDEPTH/AVPERM.

Simulate the Hydraulic Properties within the River

Ensure that the SAMPLE2.phb project file is available in the current working directory before starting the laboratory. At this point, STGQ, WSP, and VELSIM have been run in previous labs so the needed depth and velocity information is contained in the project database.

Run the Model and Examine the Output

Move to \Models\AVDEPTH/AVPERM and note the table for input of depth increments to be used in AVDEPTH/AVPERM. For this exercise, the five depth increments of 0.5, 1.0, 1.5, 2.0, and 2.5 ft. will be used. If the user does not supply any depths, the program computes the summary parameters based on all available depths at a cross section. Results are viewed in the Average Parameters and Depth Parameters tabs. Scroll these tables to see all entries. As with all PHABSIM for Windows output tables, these can be copied by dragging the mouse from the upper left to lower right corner, right clicking, and selecting copy from the pop-up menu. Figure L8-1 provides a partial Average Parameter and Depth Parameter table listing. Average parameters for the entire reach are available in text output only; click the Text File button to obtain this output. Figure L8-2 shows a reach level summary table produced by AVDEPTH/AVPERM.

Figure L8-1. Partial average parameter and depth parameter tables from AVDEPTH/AVPERM.

Figure L8-2. Whole study site average parameter table from AVDEPTH/AVPERM.

The summary table in Figure L8-1 shows the stream width at each of the simulated discharges at cross section 0.0, followed by the total width of the stream (i.e., the SUM column) with a depth greater than 1.0, as well as the maximum contiguous width with depths greater than 1.0. These summaries are repeated for each of the depths specified by the user in the AVDEPTH/AVPERM input tab. Use the scroll bars to view all of the output in the Average Parameters and Depth Parameters tables.

The final output summary at the bottom of the file (see Figure L8-2) contains this same information for depths aggregated over the entire study reach. The user should note that the AVDEPTH/AVPERM model computes the reach-aggregated results using the cross section weighting factors assigned in \Edit\Cross Sections. Therefore, changing the weighting given to particular cross sections will change the summary results displayed in this table.

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Laboratory 9. The HABTAE Model

Objective

The objective of this laboratory is to introduce the HABTAE model for calculating available habitat quantity and quality. The lab will explore several commonly used modeling options as well as demonstrate the sensitivity of habitat model predictions to different approaches taken in the hydraulic modeling phase of PHABSIM.

Programs Used: HABTAE

Data Files Used: Lab9.phb

Introduction

The HABTAE program allows integration of biological requirements of target species and life stages, represented in the form of Habitat Suitability Criteria (HSC), with hydraulic simulation results. This integration generates a number of indices of available habitat quantity and quality. These include weighted usable area, bed area, and volume. These results can be computed for each cross section, as well as for aggregated summaries at the study site level. A description of the calculations used in the HABTAE program can be found in Chapter 4 of the manual.

In this lab, we assume that water surface profile modeling has been finished and quality controlled so the VELSIM program will be used for all hydraulic simulations. However, several different modeling approaches for simulation of velocities will be explored to examine the impact on calculated available habitat. The lab is divided into several steps, which address a specific computational aspect or evaluation of HABTAE model sensitivity to different modeling options. The principal sections of the lab are:

a. Aggregation Method for Computing Combined Suitability
b. Computing Habitat for Cross Sections versus Reaches
c. Calculation of Habitat Quality
d. Effects of Velocity Simulations on weighted usable area (WUA) Results

The user is encouraged to examine the full range of computational capabilities for the HABTAE model contained in Chapter 4 of the manual and explore use of the options not covered in this lab manual. An effective way to determine whether a particular option has value to the user for a given problem is to run the HABTAE model with 'standard' or 'default' settings and then compare the computational detail listings in the output with other selected options. This is often the best way to determine how or what the program is actually calculating and whether or not a particular option is appropriate for the problem you are attempting to solve.

Compare Aggregation Methods for Computing Combined Suitability

In this section of the lab, three computational methods by which the HABTAE program combines individual suitability for depth, velocity, and channel index within a cell to derive WUA will be examined. The three approaches include multiplicative, geometric mean, and limiting value methods (see manual Chapter 4). Make sure that the requisite data files listed above have been copied to the current working directory prior to beginning the laboratory. The following steps proceed in the general order of a habitat analysis.

Step 1. Generate Hydraulic Characteristics for Selected Stream Flows using VELSIM

The Lab9.phb project contains the results of simulating water surface profile and velocity distributions for the sample study site. You may want to compare the results you obtained at the end of the previous laboratory with these results.

To determine if the Lab9 project is ready for this next step, go to \Reports\Graphs and view the longitudinal profile for all discharges. Then view the velocity distribution for the simulated and observed discharges at each cross section. When you have determined that these are the correct profiles, you can assume the project now contains the necessary hydraulic and channel geometry property information needed to proceed with this laboratory.

Step 2. Select Species and Life Stages

Prior to setting the HABTAE options, the target species and life stages to be used in the analysis must be determined. Specifically, HSC identification numbers must be selected or input to PHABSIM. Go to \Edit\Suitability Curves\Select\By ID to view a list of all of the HSC curve sets that have been loaded into the project thus far. Locate the HSC ID numbers for Bull Trout fry, juvenile, adult, and spawning life stages (i.e., 100101, 100102, 100103, and 100104). If Bull Trout HSC has not been loaded, you may load them now by importing them from an old PHABSIM format FISHCRV file. You will find FISHCRV.LAB in the working directory.

Step 3. Set the HABTAE Options

Next go to the HABTAE computational options tab at \Models\Habtae\Computations. Note that Habitat Calculations (old IOC Option 9) has been set to Standard Calculation so multiplicative combination of depth, velocity, and channel index HSC values for each computational cell will be the form of the WUA calculation. This option will be changed in subsequent HABTAE model runs as part of the laboratory to examine effects of different suitability aggregation techniques on WUA predictions. Note that WUA Calculations are set to Calculate WUA for Reach. Also note that Use Zero CI in calculations (IOC 18) has been selected so that a channel index code of '0' will match the associated HSC curve coordinate data of '0' for channel index.

Next go to the \Models\Habtae\Limits tab and select No restrictions on velocities to allow the HABTAE program to run if it encounters negative velocities or velocities that are greater than 15 feet/second.

Finish setting options by going to the ..\Life Stages tab and clicking on each HSC curve set ID number you wish to use in the habitat simulation. Select the 4 life stages of Bull Trout (i.e., 100101, 100102, 100103, and 100104) by clicking on each of them to highlight the Bull Trout entries.

Step 4. Run the HABTAE Program and Examine Output

Click the Run button in the ..\Output Options tab to run HABTAE. Move to the ..\Results tab where you will find tabular values indicating the combined suitability for each cell. Select the Discharge and Result you want to view and the table will update automatically. You may view a color graph of the habitat suitability distributed over the study site for the selected result by clicking on Graph.

Next move to the ..\ZHAQF Results tab to review tabulated WUA values calculated for the study site. As in the velocity and WSL sections, the results may be viewed by clicking on the Graph button. The relative differences in magnitude and shape of the WUA versus discharge curves for these life stages are a result of the habitat calculated from the HSC curves in response to the hydraulic properties at each discharge. The program also writes to a numbered ZOUT file as illustrated in Figure L9-1.

These summary tables are aggregated totals for all cross sections. This information is repeated for each life stage in the numbered ZOUT file produced by running HABTAE. To view this table, check the filename.history file for the number of the ZOUT file produced by the last HABTAE run and open the ZOUT with a text editor.

To easily view the ZOUTxx file, move to Windows Explorer and the working directory for your study. Then drag and drop the latest ZOUTxx file on to the Wordpad icon on the desktop. Highlight all text in the file and set the font size to 8 pt for ease of viewing the text without scrolling the lines.

The tabular listing in the ..\Zhaqf Results tab contains a tabular summary of total WUA for each species and life stage at each discharge. Clicking the check box marked Include total area will add a column for total surface area at each discharge. A list box for Species is provided so analysis results for different species can be displayed sequentially. Note that all life stages for Bull Trout are given in one table due to the format of HSC curve numbers used in the FISHCRV.LAB data file (i.e., 100101, 100102, 100103, etc.). If these HSC curve numbers had been 100001, 200001, 300001, 400001, then output for each life stage would have been displayed as a separate species.

As would be expected from the differences in HSC curves for different life stages, the WUA versus discharge plot found using the ..\Zhaqf Results\Graphs button shows that adults have the most habitat overall, and that as flows increase, fry and juvenile habitat availability tends to decrease (See Figure L9-2). This should make intuitive sense because velocities are increasing within the main channel areas, which makes these areas increasingly unsuitable for life stages with less swimming ability. Once this plot has been examined, return to the ..\Zhaqf Results and click Print to produce a copy (or copy and paste the table to a spreadsheet) of your Bull Trout results using multiplicative combination of HSC criteria. Label this copy "Standard Multiplicative WUA Results".

Figure L9-1. Aggregate habitat results for Bull Trout fry life stage at each of the simulated discharges.

Figure L9-2. Multiplicative WUA values for Bull Trout.

Step 5. Compare the Effect of Various Combined Suitability Values on Habitat Predictions

Changing the manner in which the HABTAE program computes combined suitability for each computational cell has the potential to change resulting predictions of WUA. In previous habitat simulations, WUA was computed using the multiplicative approach. In this step, the HABTAE program will use the geometric mean.

Go to the \Models\Habtae\Computations tab and click Geometric Mean; then move to the ..\Output Options tab and click Run. The results of this simulation are shown in Figure L9-3.

Comparing Figures L9-2 and L9-3 clearly demonstrates that the magnitude of WUA predictions change but in general the shape of the functional relationship in the WUA curves has remained essentially the same using both simulation options. The increased magnitude of WUA predictions should make sense since the geometric mean "compensates" for a single low suitability factor in a computational cell if the remaining two suitability factors are high. This should increase WUA values overall.

Finally, go to the ..\Computations tab and click Lowest Limiting Factor; and again click Run in the ..\Output Options tab. The results of this simulation are shown in Figure L9-4.

Figure L9-3. Geometric mean WUA values for Bull Trout.

A comparison of all three simulation results illustrates several interesting patterns. The geometric mean always produces more habitat than either the multiplicative or limiting factor method as would be expected. The limiting factor approach is always greater than the multiplicative method. These differences are an interplay between estimated hydraulic properties from hydraulic modeling and the functional form of species and life stage HSC curves.

The user should carefully consider which option or combination of options to use when estimating habitat. Each of the computational approaches tells the user something different that, when interpreted in the context of the biology of the target species and life stages, may help in the evaluation of flow regimes.

Computing Habitat for Cross Sections versus Reaches

The HABTAE program can be used to calculate WUA, weighted usable volume, or weighted usable bed area either for an entire reach or individual cross sections. This is accomplished by selecting the appropriate item for WUA Calculations in the ..\Computations tab. In the next step of the laboratory, the HABTAE program will be used to produce results for each cross section. The analysis of habitat at particular cross sections can identify not only the amount contributed to total WUA by each habitat area but can also be used to focus your study on specific critical habitats.

Figure L9-4. Lowest limiting factor WUA for Bull Trout.

Step 6. Change Habitat Options to Produce Cross Section Output

In the ..\Computations tab, set WUA Calculations to Calculate WUA for Independent XSEC and set Habitat Calculations to Standard Calculation. Then click Run in the ..\Output Options tab.

Using this option in HABTAE will generate summary tables for each species and life stage for each cross section. These tables are only contained in the ZOUT file created after running this HABTAE option. View the latest numbered ZOUTxx file using Wordpad and scroll down through the output to examine these results. When finished, exit Wordpad and return to the HABTAE program in PHABSIM for Windows. In the output (see Figure L9-5), you will find terms for weighted width and percent WUA. These terms are provided because each cross section is treated independently and therefore, there is no longitudinal direction over which to compute area of the computational cells.

This option in HABTAE is particularly useful for understanding how predicted habitat changes for a given species and life stage within specific types of mesoscale habitats. This may be important when considering impacts of alternative flow regimes on spawning habitat in riffles or over wintering habitats in pools, for example.

Figure L9-5. Excerpt of habitat results for individual cross sections.

Evaluation of Habitat Quality

All HABTAE program runs to this point in the laboratory have estimated total WUA. For a given discharge the program may indicate that of a total stream surface area of 100 ft2 that there are 10 ft2 of WUA. WUA could be composed of a single 10 ft2 area with a combined suitability of 1.0 with the remaining 90 ft2 of habitat having a combined suitability of 0.0. Alternatively, all 100 ft2 of stream may have a combined suitability of 0.1. In both cases, total WUA would be 10 ft2. In this section of the lab, the HABTAE program will be used to set a threshold on the magnitude of combined suitability to compute the amount of "high quality" habitat at each discharge.

Step 7. Calculate Habitat With Minimum Combined Suitability Factors

Go to the ..\Limits tab and click Specify minimum factor by life stage in the Minimum Effective Composite Suitability Factor (IOC 19) box. Then move to the ..\Velocity Replacement Options tab and enter the minimum composite suitability factor value you will accept in the CFMIN column for each life stage HSC number shown. For this laboratory, use 0.75 for all life stages. Then click Run in the ..\Output Options tab.

The results for total WUA and "high quality" habitat can be compared for each species and life stage. In the ..\ZHAQF Results tab, click the Graph button, select Bull Trout Fry and click the Refresh button. Figure L9-6 displays the results for Bull Trout fry where the line labeled No Limit is total WUA and the line labeled CF Limit = 0.75 is WUA with a combined suitability greater than 0.75. Making two runs of HABTAE with and without composite suitability factor limits and copying the results to a spreadsheet produced this figure. The Bull Trout Fry graph in PHABSIM for Windows should look like the CF Limit = 0.75 line in Figure L9-6.

Note the apparent decline in WUA at 30.2 cfs (the second discharge) compared to 15.0 and 75.2 cfs. By clicking the Graph button in ..\Habitat Results you can view a plot of composite suitability for all cells in the study site. The color key allows visual evaluation of which cells have more than 0.75 combined suitability. At 30.2 cfs, only cross section 201 has a significant amount of Bull Trout fry habitat. Whereas at either 15.0 or 75.2 cfs, at least one other cross section has relatively large amounts of fry habitat with a combined suitability of 0.75 or greater. At these low flows, large relative changes in habitat may occur with changes in flow as highly suitable areas become wetted and those same areas develop high velocities at greater flows.

Display the results for the remaining life stages of Bull Trout in both the ..\Habitat Results and ..\ZHAQF Results tabs. Note that for this particular data set, high quality habitat is contributing to less than half of the total WUA over all ranges of discharge for all life stages. However, this is not always the case. In some instances, the amount of high quality habitat may make up only a small proportion of total available habitat over certain ranges of flows while dominating total available habitat at others. It is also not uncommon that the discharge at which high quality habitat is maximized may be different than the discharge at which total habitat is maximized. This type of analysis with HABTAE permits evaluation of tradeoffs between flows that may sacrifice total habitat to maximize high quality habitat at an alternative discharge.

Figure L9-6. Bull Trout fry habitat with and without composite suitability limits.

Evaluate the Effects of Velocity Simulations on WUA Results

To illustrate the effects of hydraulic simulations on computation of available habitat, this part of the laboratory will use four different calibration\simulation velocity data sets as input to HABTAE for the production of WUA. Setting a total of four different velocity simulation options and generating WUA for each of the resulting velocity distributions will accomplish this. We will simulate velocities using the high flow velocity calibration data set, the medium flow velocity calibration data set , the low flow velocity calibration data set, and the discharge range distributed set as templates. We currently have modeled velocities using the low flow velocity set as the template from 15 -75.2 cfs, the mid-flow velocity set for 139 cfs, and the high flow velocity set for 250 cfs and up. So we will begin there.

Step 8. Select different CAL sets within the VELSIM Program and Compute WUA with HABTAE for each Velocity Template

Set HABTAE to produce standard WUA for the entire study site by setting No limiting factor specified on the LIMITS tab and Calculate WUA for Reach and Standard Calculation on the Computations tab. Click Run, go to Zhaqf Results, and Print the table. Alternatively, you may copy the table into a spreadsheet. (Do not forget to enter the column and row headings.) Label the printed copy or spreadsheet block, "Combined Velocity Templates". Save the project using \File\Save Project before proceeding. We will come back to this project in the next lab so it is important to save the file now.

Next, go to \Models\Velocity Simulation\Velocity Calibration Set Assignments and set all combinations of discharge and cross section to 1. This will assign the low velocity set as the template for all velocity simulations. Click Run followed by OK to exit the velocity simulation window. Save this project under a new name using \File\Save As. Give the project the name "Lowvel" and ensure it is located in a directory subordinate to the working directory "Lab9".

In \Models\HABTAE, click Run (you have already set all the options). Go to the Zhaqf Results tab and print the table of WUA values. Label this copy or spreadsheet block "Low Velocity Template".

Repeat this process by setting all combinations of discharge and cross section to velocity calibration set 2 and then 3 with appropriate labels for middle and high velocity calibration set on the printed (or copied and pasted) tables of weighted usable area. Save the projects under new names using \File\Save As. Name the projects "Midvel" and "Highvel", and ensure they are located in directories subordinate to the working directory "Lab9". You should now have four sets of habitat results and four projects located in separate directories.

Examining the four sets of results for Bull Trout juveniles shown in Figure L9-7 shows convincing evidence that the choice of velocity calibration data set can impact the relationship between WUA and discharge over at least part of the flow range. Results for different species and life stage HSC relationships and different hydraulic calibration data can produce similar or widely differing results. The user needs to carefully consider her (his) choice of calibration data sets, HSC, and modeling options when applying PHABSIM. It is up to the investigator to justify the choice of options and data used in the context of the particular instream flow assessment. Usually these choices are made based on goodness-of-fit, reasonableness, and study objectives.

Figure L9-7. Bull Trout juvenile habitat produced by four different velocity set templates.

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Laboratory 10. Conditional (Adjacent) Velocity Habitat Simulations

Objective

The objective of this laboratory is to introduce calculation of habitat based on adjacent or "conditional" velocities using the HABTAE model.

Programs Used: HABTAE, Excel

Data Files Used: Lab10.phb, highvel.phb, midvel.phb, lowvel.phb, adjvelhab.xls

Introduction

In addition to "standard" Weighted Usable Area calculations, the HABTAE program allows the user to generate available habitat where adjacent velocity conditions are combined with the habitat suitability criteria to determine habitat worth.

In this lab, the VELSIM program will be used for all velocity distribution simulations using four different velocity simulations to explore the impact on calculation of available habitat within HABTAE. To facilitate presentation of the material, the lab has been broken into several sections, which address a specific computational aspect or evaluation of model sensitivity with HABTAE. The principal activities of the lab are:

• Creation and Modification of HABTAE Options Control Files for Simulations
  
• Conditional Velocity Simulations
  
• Generation of Hydraulic Properties using Different Velocity Simulation Approaches
  
• Conditional Velocity Simulations with Different Velocity Modeling Approaches

  The user is encouraged to examine the complete listing of computational capabilities for the HABTAE model contained in Chapter 5 of the manual and explore use of computational options not covered in this lab exercise. The best way to determine whether a particular option has value to the user for a given problem is to run the HABTAE model with 'standard' or 'default' settings and then compare computational detail listings in the output with other selected options. The laboratory is presented in 7 steps that lead you through the conditional velocity analysis process.

  Step 1. Run HABTAE with Standard Options

  In the ..\Output Options tab, set the following items:

• Click the Write Computational Details check box to cause computational details to be printed to the next numbered ZOUT file.

• Click the Write WUA or WUV radio button in the ZHAQF Options box to write WUA calculation results to the ZOUT file.

• Click the Write Flow Data check box so the ZOUT file will also contain the flow data used to generate these habitat results.

  In the Computations tab, set the following items:

• Click the Use Zero CI in Calculations check box, as channel index values of zero should calculate as zero.

• Click the Calculate WUA for Reach radio button in the WUA Calculations box to produce aggregated weighted usable area as the final habitat result.

• Click the Standard Calculation radio button in the Habitat Calculations box to ensure that the "standard" multiplicative calculation of composite suitability is performed.

  In the Life Stages tab scroll the table and click on each of the four life stages of Bull Trout. For this exercise, do not include any other species. Only the four Bull Trout lines should be highlighted. Make a note of the HSC numbers for each life stage as you will use them later.

  Return to the \Models\Velocity Simulation\Velocity Set Assignments window and check that Cal Set 3 has been assigned to all discharges at all cross sections. If this has not been done, do it now and rerun the velocity simulation.

  These settings prepare the HABTAE model to perform the standard habitat calculation for four life stages of Bull Trout. In the ..\Output Options tab, click the Run button. Move to the ZHAQF Results tab. On the Windows Desktop, start Microsoft Excel (or your preferred spreadsheet package) and open the file adjvelhab.zls. Drag the mouse from the upper left to the lower right corner of the ZHAQF Results table, right click, and select Copy. Move to Excel and paste to the first block of values starting at cell A9. This places the "standard" habitat calculation results in the spreadsheet.

  Step 2. Select HABTAE Options for a Minimum Adjacent Velocity Limit Calculation

  In the Adjacent Velocity tab, set the following items:

• In the Use VLIM as box, click the Minimum radio button to search for a velocity that is greater than or equal to the velocity you will define below as VLIM. That is, VLIM is set to act as a lower (minimum) bound.

• In the WUA Calculation when VLIM not found box, click WUA = 0 to cause no WUA to be calculated in the current computational cell if the user-defined minimum velocity is not found within a user specified distance.

  Enter scan distances and threshold velocities to be used for each species and life stage in the Dist and VLIM columns of the table in the Scan distance, velocity limit, and initial velocity box. These values are entered next to the appropriate HSC curve ID numbers for Bull Trout; 100101 for fry; 100102 for adult; 100103 for juvenile; and 100104 for spawning. (Scroll the table using the scroll bar until the needed HSC curve numbers are displayed.)

  For the purposes of this lab exercise, enter a restrictive scan distance (Dist) for fry (5 feet), a larger distance for juveniles and adults (10 feet), and zero distance for the spawning life stage to simulate immobility of incubating eggs in the analysis. It is incumbent on the investigator to determine an appropriate distance to scan for particular species and life stages when using the adjacent velocity calculations in the HABTAE program.

  Similarly, enter a different threshold velocity (VLIM) value for fry (0.5 fps) and adults (1.0 fps), and the same value for juvenile and spawning (1.5 fps). The choice of limiting velocity is again a matter of professional judgement. Examining the HSC curves for velocity can often provide insight as well as searching published literature on sustained swimming speeds or related life history information. The values chosen in this laboratory are for illustrative purposes only.

  In the Velocity Replacement Options tab, leave all values set to zero as only mean column velocity is being considered and no nose velocity issues are being explored at this point. It is possible, however, to base adjacent velocity calculations on nose velocities as long as you have habitat suitability criteria that reflect nose velocity, search distance and velocity limit information that is appropriate to such a calculation. Little research has been done in this area so such information may be scarce.

  This sets up the Adjacent Velocity as Minimum Limit calculation for four life stages of Bull Trout. In the ..\Output Options tab, click the Run button. Move to the ZHAQF Results tab. On the Windows desktop, start Microsoft Excel (or your preferred spreadsheet package) and open the file adjvelhab.xls. Drag the mouse from the upper left to lower right corners of the ZHAQF Results table, right click, and select Copy. Move to Excel and paste to the first block of values starting at cell A21. This places the "VLIM is Minimum" habitat calculation results in the spreadsheet.

  Step 3. Run HABTAE With a Maximum Adjacent Velocity Limit

  In the Adjacent Velocity tab set the following items:

• In the Use VLIM as box, click the Maximum radio button to search for velocity less than or equal to the velocity you will define below as VLIM. That is, VLIM is set to act as an upper (maximum) bound.

  Leave all other options the same as in Step 2 above. Click the Run button as above and copy and paste the habitat results into the spreadsheet at cell A33. This places the "VLIM is Maximum" habitat calculation results in the spreadsheet.

  Step 4. Compare Standard and Adjacent (Conditional) Velocity Simulations

  This section of the laboratory will compare HABTAE habitat predictions based on both maximum and minimum threshold conditional velocity simulations. In the previous steps, results have been generated using the standard habitat calculation, conditional velocity simulation using a minimum threshold, and conditional velocity simulation using a maximum threshold. In each instance high flow calibration velocity simulation results from VELSIM were used.

  To begin this evaluation, move to the ..\Habitat Results tab. There you will find dialog boxes for Curve ID, Cross Section and Discharge. Clicking the triangular down arrow at the right of each box displays a menu of the options available for Curve ID. Select 100101 Bull Trout fry. For Cross Section, select 0.000, and for Discharge select 139.0 cfs. The table now displays the velocity suitability index value (VEL SI), the Depth SI, the channel index suitability value (Sub SI), the adjacent velocity suitability factor (Ad Vel), the combined suitability factor for each cell (Factor), the cell area and the cell weighted usable area (WUA). A separate table of results will be displayed for each combination of Curve ID, Cross Section, and Discharge selected as shown in Figure L10-1.
  

  

  Figure L10-1. Habitat results table.

  This table may be copied by dragging the mouse from the upper left to lower right corner, right clicking and selecting copy in the menu provided. The table may then be pasted to a spreadsheet or report as needed. Table headings are not included in the copy operation, so it is often useful to prepare a spreadsheet containing the headings as a template to receive this information.

  The habitat results may be graphically viewed by clicking the Graph button. Both plan view and 3-D rotatable graphics are provided. The graphical display gives an indication of where on each transect the most suitable conditions exist. At the top of the graph window, dialog boxes similar to the Habitat Results tab allow the user to select which Curve ID and Discharge are to be viewed. Click Refresh to update the plot when each menu change is made.

  Note the areas of high quality Bull Trout fry habitat at 139 cfs. Red is used for the highest value range. You can see that the highest composite suitability is less than 1.0. Why is this?

  Now select 15 cfs and click Refresh. What differences do you see between this view and the 139 cfs view? Reduce the size of this graph window by dragging a corner so you can see the HABTAE window, but leave the graph window open for later use.

  In the HABTAE Habitat Simulation window, go to the ZHAQF Results tab and click the graph button. In the Species dialog box select Bull Trout fry. Note the shape of the habitat-discharge relationship. Resize both this and the Habitat Results graph window so both can be viewed on screen at the same time. (On smaller monitors, it may be necessary to overlap the two graph windows and alternately click them to bring one or the other to the foreground or you may find it convenient to print the ZHAQF plot.)

  While viewing the ZHAQF plot, select (and refresh) each discharge in the Habitat Results graph. How do the composite suitability values explain the resulting ZHAQF plot?

  Note that at the lower discharges, the area of fry habitat occupies much of the stream bed. However, at the higher discharges, fry habitat is relegated to the stream margins. As the flow increases, the number of cross sections with suitable fry habitat at the stream edges decreases and the amount of area represented as high quality habitat (i.e., displays in red) decreases. Figures L10-2 to L10-4 illustrate the difference between the standard, minimum and maximum limit habitat for one discharge.

  Note the loss of habitat at the fourth cross section (168 to 201 ft upstream) between the standard and "minimum" adjacent velocity calculations. This accounts for the lower conditioned habitat value at 15 cfs seen in the habitat flow relation displayed at the upper right. Also note that the fourth cross section has a large area of good habitat under the conditions of the "maximum" calculation. When the limiting velocity (VLIM) is treated as a lower bound (minimum) no cells are found within the search distance with velocities higher than VLIM at the fourth cross section. Thus, the final weighting factor is zero due to the adjacent velocity condition. In contrast, when VLIM is treated as an upper bound (maximum), there are ample cells with velocities lower than the limit and the habitat at the fourth cross section at 15 cfs is substantially the same as the standard calculation.

  You can use the graphical display to determine the cause of the trend toward less fry habitat at higher discharges by selecting from the Depth SI, Velocity SI, and Channel Index SI radio buttons in the Habitat Results plot. If you select the Depth SI button and click refresh while displaying habitat results for 250 cfs, you will see a large area of the stream turn red. Thus, it is unlikely that Depth is the limiting factor. However, if you select Velocity SI, the plot shows minor changes from the composite suitability plot. Thus, it appears that velocity is the limiting factor that causes the fry suitability to decline with increasing discharge. This is true for the standard and both conditional velocity calculations. Why?

  Now that we have considered how the habitat suitability for depth and velocity influences the shape of the habitat-discharge relation, we are ready to compare the three adjacent velocity limit approaches chosen earlier. Return to the adjhabvel.xls spreadsheet and note the graphs displayed to the right of the data entry area. (If you did not have time to complete this portion of the lab, a worked example is contained in Sheet 2 of the spreadsheet.)

  

  Figure L10-2. Bull trout fry habitat plan view, standard calculation.

  

  Figure L10-3. Bull trout fry habitat plan view, minimum adjacent velocity calculation.
  

  

  Figure L10-4. Bull trout fry habitat plan view, maximum adjacent velocity calculation.

  These examples should demonstrate that for part of the flow range some life stages were not affected by use of conditional velocity simulations based on the criteria specified for either the maximum or minimum thresholds in conjunction with the user-specified scanning distances. The greatest impact on WUA across the entire range of discharges was obtained for the spawning life stage. Note that spawning was the only life stage where scan distance was set to >0'. The combination of threshold velocity and scan distances using the minimum threshold gave similar results to the standard velocity simulations for all life stages except spawning. This suggests that for most flows, HABTAE was able to find a velocity value above the threshold velocity within the specified scan distance for these life stages. This was not true at the very lowest discharges, but it is reasonable that fewer high velocity cells would be encountered at the very lowest flows.

  Conversely, using the maximum threshold, there were more instances where HABTAE was not able to find a velocity that was less than the specified maximum (upper bound) within the scan distance for fry, adult, and spawning. Therefore WUA totals were reduced compared to the standard velocity simulations. Refer to the adjacent velocity calculation example in Chapter 4 of the manual if you have questions about the effect of these conditional velocity simulations. Again, the spawning life stage was most strongly affected due largely to the zero scan distance.

  The degree to which conditional velocity simulations will affect WUA relationships will be a function of the form of the HSC curve for velocity, velocity limits specified, and the scanning distance supplied by the user. These factors will also result in either greater or lesser changes between target species and life stages. It is the responsibility of the investigator to justify his (her) choice of modeling options and, in particular, choice of velocity limits and scanning distances used for the species and life stages involved in each project analysis.

  Step 5. Effects of Changing Threshold Velocities

  To better illustrate the ideas discussed above, move to the Adjacent Velocity tab and change VLIM for Bull Trout juvenile and adult to 4.0 feet/second and select the Minimum radio button in the Use VLIM as box. From the comparison of simulation results in Step 4, relatively small differences between minimum and standard velocity simulations were obtained for juvenile and adult Bull Trout. To generate results for the higher VLIM, move to the Output Options tab and Run the simulation, then move to the ZHAQF Results tab and view the graph. Select Juvenile and Adult life stages only. You may also copy and paste the ZHAQF table into the adjvelhab.xls spreadsheet in the space identified as REVISED VLIM FOR JUVENILE AND ADULT, row 50.

  By viewing the graphs to the right of the data table, it is apparent that setting the minimum threshold to a higher value has dramatically altered simulation results for both of these life stages. In fact, at lower discharges the results would indicate that velocities greater than 4.0 feet/second simply do not exist in the channel. Why? Confirm this is true by reviewing the velocity distribution plots for the lower discharges in either \Models\Velocity Simulation\Results\Cross Section or \Reports\Graphs\Bed Profile with WSL/Velocities. You should find there are no velocities greater than 4.0 fps until a discharge of 650 cfs is simulated.

  The fact that WUA for Bull Trout juvenile (and adult) is 0.0 at discharges 250 cfs and below, means that HABTAE was unable to locate velocities greater than 4.0 feet/second within the given scan distance for each computational cell. Therefore set the computational cell WUA to zero (i.e. in ..\Habtae\Adjacent Velocity the WUA = 0 button was selected in the WUA calculation when VLIM not found box.) At simulated discharges of 650 cfs and 1,250 cfs, hydraulic predictions are generating velocities in at least some computational cells that are greater than 4.0 feet/second and, therefore, a small amount of conditional WUA is predicted for these life stages.

  Step 6. Generation of Hydraulic Properties using Different Velocity Simulation Approaches

  You have already run the VELSIM program to produce the four velocity simulation alternatives that will be used in this lab. For convenience, you will find them in the Sample folder as noted in Table L10-1 below:

  Table L10-1. Project names for different velocity simulation options.
  Directory	Project name	Contents
  Sample	Sample.phb	Three velocity calibration sets applied to three flow ranges
  Sample/highvel	highvel.phb	High flow calibration velocity set used for all flows
  Sample/midvel	midvel.phb	Medium flow calibration velocity set used for all flows
  Sample/lowvel	lowvel.phb	Low flow calibration velocity set used for all flows

  To use any of these projects in PHABSIM for Windows, use \File\Open Project and move to the desired project directory using Browse. Once in that directory, the file projectname.phb will be visible in the Open File dialog box. Double click the project file to open the project.

  In previous laboratory steps, effects of different conditional velocity simulation approaches were examined to compare the HABTAE habitat predictions using these options. In this step, the effect of different hydraulic simulation approaches on conditional velocity simulations using a minimum threshold approach will be compared. First we will examine the effect of using the "best" velocity simulation by applying each of the three calibration velocity sets to their appropriate range of discharges.

  Return to the \Models\Velocity Simulation\Velocity Calibration Set Assignments tab and assign the appropriate cal set 1 to all discharges up to 75.2 cfs and cal set 2 to 139 cfs. Run the velocity simulation again by clicking the Run button in the ..\Options tab. Then move to the \Models\Habtae\Adjacent Velocity tab and remove the check from the Scan for velocity in adjacent cells check box. Click the Run button in the ..\Output Options tab. Move to the ZHAQF Results tab and copy the Results table for Bull Trout. Paste these results into the range beginning at row 72 in the adjhabvel.xls spreadsheet.
  
  Compare the results of the standard habitat calculation for bull trout juveniles and adults (using the three cal set velocity simulation) to the standard habitat calculation using a single cal set. Are the results significant? How might this change in velocity simulation affect the outcome of any decision being based on the habitat analysis?

  What effect does use of three cal sets have on adjacent velocity calculations? To examine this, move to the \Models\Habtae\Adjacent Velocity tab and check the Scan for velocity in adjacent cells check box. Click the Run button in the ..\Output Options tab. Move to the ZHAQF Results tab and copy the results table for bull trout. Paste these results into the range beginning at row 91 in the adjhabvel.xls spreadsheet.

  Again, compare the results using the graphs provided. Comparing these results with the results generated earlier using a single cal set, you can see that the effect of the adjacent velocity condition is greater at low flows in both sets of results. For this particular data set, it appears that the habitat results are more strongly influenced by the adjacent velocity condition than by the choice of velocity calibration set.

  What about the first decision you made in the hydraulic modeling process, the choice of hydraulic model? The results obtained to this point were based on the "best" water surface results we could obtain by combining models at the control and across the pool. To examine the sensitivity of the habitat simulation process to choice of water surface model, we will run the WSL simulation using STGQ for all combinations of cross section and discharge.

  Return to the \Models\WSL\Methods tab, select the STGQ radio button, and click the Select All button followed by the Run button. Move to the ..\Velocity Simulation window and click the Run button in the Options tab. Next, move to the \Models\Habtae\Output Options tab and click the Run button there. Move to the ZHAQF Results tab and copy the Results table for Bull Trout. Paste the results into the space provided in row 113 of the adjvelhab.xls spreadsheet.

  Comparing the graphs in spreadsheet you will again find that the choice of hydraulic simulation option has less effect than the choice of adjacent velocity calculation.

  At least two conclusions can be drawn from this exercise. First, in the particular circumstances of this study site, the choice of hydraulic simulation has less influence than the choice of adjacent velocity conditions for Bull Trout adult and juvenile. This may not be true for all study sites or all HSC. (You may wish to create spreadsheet graphs for the other life stages to see if they are more or less affected by these choices.) Second, use of the adjacent velocity simulation can be a good tool to help determine which ranges of flow produce substantial and/or insignificant amounts of habitat when adjacent conditions are important. This information may be very useful in the instream flow decision arena.

  When using conditional velocity based habitat simulation, it is especially important to ensure that the various adjacent velocity conditions used have a strong biological basis. The IFIM process emphasizes obtaining agreement among stakeholders as to the form of the analysis prior to beginning the PHABSIM application. This ensures that the critical questions about use of habitat simulation options such as conditional velocity are asked before the analysis begins.

  Step 7. Including Adjacent Velocity Conditions That Lie Just Outside The Search Distance
  
  As a final step in this laboratory, the Scan for initial velocity (VO) and interpolate radio button in the ..\Habtae\Adjacent Velocity tab will be checked to cause the program to interpolate a weight for suitable habitat if the threshold velocity is not found within the user-specified scanning distance. In previous simulations, the WUA = 0 radio button was checked, which caused the WUA to be set to 0.0 if the threshold velocity was not found. Choosing the interpolation option directs the program to locate a velocity that is closest to the threshold velocity and less/greater than the user specified velocity (V_o) within the scanning distance. The program then interpolates a 'combined suitability' between 0.0 and 1.0 to modify WUA in the computational cell rather than setting it to 0.0. Whether the program finds a suitable velocity which is less than (VLIM acts as a maximum) or greater than (VLIM acts as a minimum) Vo is determined by the option selected in the Use VLIM as box.

  In PHABSIM for Windows, move to the \Models\Habtae\Adjacent Velocity tab and enter V_o values of 0.4, 0.5, 1.0, 1.0 for bull trout fry, juvenile, adult, and spawning life stages, respectively, in the input table. Set VLIM to act as a minimum, select Scan for initial velocity (VO) and interpolate, and be sure that the Scan for adjacent velocity box is still checked. Move back to the Output Options tab and click Run. Copy and paste the ZHAQF table to row 137 of the adjvelhab.xls spreadsheet.

  Note that V_o values have been entered for each life stage to be analyzed and, in this particular application, the values are less than the VLIM values since the minimum threshold option is being used in the simulations. Remember the minimum threshold option directs the program to look for values greater than VLIM so a relaxed V_o must be less than VLIM to make sense. Refer to the example in Chapter 4 of the manual if you have questions about this.

  Plots of the Scan for initial velocity (VO) and interpolate and the WUA = 0 options for adult and juvenile Bull Trout are included in the spreadsheet at row 130. The results for all life stages show slightly greater habitat over part of the range of discharges with the Scan for initial velocity (VO) and interpolate option compared to the WUA = 0 option. This is a result of including the additional interpolated WUA that had weighting factors assigned between VLIM and V_o when the interpolation option was selected.
  

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  Laboratory 11. Habitat Modeling - HABTAM

  Objective

  The objective of this laboratory is to illustrate the use of the HABTAM program where the investigator wishes to examine available habitat at two different flows and the species and life stage of interest can migrate laterally within a cross section.

  Programs Used: . HABTAM

  Data Files Used: Lab11.phb

  Introduction

  The HABTAM program is used to simulate conditions at a cross section where fish are allowed to migrate laterally to find suitable habitat when two separate flows are compared. The user supplies a starting flow, an ending flow, and an appropriate maximum migration distance. The program will compute the WUA for each pair of discharges and compute the amount of WUA that is used at the ending flow assuming that all the WUA (i.e., habitat) at the starting flow was used. The program can also be used with a maximum allowable migration distance of 0.0, which might be appropriate for incubation life stages or benthic invertebrates. In this latter case, the program will compute the minimum of the WUA of the starting or ending flow. The use of the HABTAM program should not be confused with "migration" analyses within a reach or river segment, since only lateral migration on a given cross section is considered in the HABTAM program. PHABSIM for Windows does not contain any reach or river segment migration analytical capabilities.

  The required hydraulic and channel properties information for this lab has already been generated in previous exercises. We will use the Lab11 project that contains three calibration sets assigned to their representative discharge ranges as the starting point for this lab. The laboratory implements the following processes four steps:

• Ensure the best WSL and velocity simulations have been performed
  
• Set HABTAM Options
  
• Simulate habitat using HABTAM

  Step 1. Open the Lab11 Project

  Use /File/Open to move to the lab11 working directory and open the lab11 project file. You now have the sample project as it was at the end of Lab 6 with the velocity distribution determined by three velocity templates applied to three ranges of flow.

  For later use, it is a good idea to open the project and make a note of the curve ID numbers and which life stage and species they represent. Table L11-1 contains the curve ID numbers in the project. Note that some have three digits for the species ID number.

  Table L11-1. HSC ID numbers and life stages provided in the sample project.
  Curve number	Species	Life stage
  11300	Brown Trout	Spawning
  11301	Brown Trout	Fry
  11302	Brown Trout	Adult
  11303	Brown Trout	Adult-escapement
  11304	Brown Trout	Incubation-ice formation
  21112	Rainbow Trout	Fry
  21114	Rainbow Trout	Juvenile
  21115	Rainbow Trout	Adult
  100101	Bull Trout	Fry
  100102	Bull Trout	Juvenile
  100103	Bull Trout	Adult
  100104	Bull Trout	Spawning
  500101	Brook Trout	Adult
  500102	Brook Trout	Juvenile
  500103	Brook Trout	Fry
  500104	Brook Trout	Spawning

  Step 2. Set HABTAM Options

  Go to /Models/HABTAM/Options and put a check in the boxes for Write migration calculation details, Write cross section data, Write flow related data, and Write computational details. Selecting these options will allow the examination of the computational details in the output file listing to better understand how the HABTAM program functions. Check that Velocity Calculation Options in the Velocity Calculations tab is set to Mean column velocity because the HSC curves used in the laboratory are based on mean column velocities. The remaining options can be left in their default condition. We recommend you compare the defaults with the option choices for a full understanding of the choices available in HABTAM.

  Next, go to the Migration tab. Here you will find a table containing all species/life stages for which HSC have been entered in this project. You can supply the allowable migration distance for each life stage. For this lab we will use Brown Trout spawning, fry, and adults, HSC curve numbers 11300, 11301, and 11302. Enter migration distances of 0.0 for spawning, 5 for fry, and 15 for adults. Note that a distance of 0.0 is entered for spawning since incubating eggs cannot migrate.

  In the Options tab you can enter starting and ending discharge pairs representing the range of flow to be considered in the analysis. In an actual application, you would enter flow ranges relevant to the purpose of your study. For example, the range of high and low flows due to a hydropeaking operation. For this lab, enter three sets of flow pairs: 15, 30, 75.2, 139, 250 versus 625; 15, 30, 75.2, 139, 250 versus 1,250 and 1,250 versus 15, 30, 75.2, 139, and 250. That is, enter a starting flow of 15 and an ending flow of 625. In the next row, enter a starting flow of 30 and an ending flow of 625, etc. For the third set, enter a starting flow of 1,250 and an ending flow of 15. Continue similar entries until finished.

  Step 3. Simulate Habitat Using HABTAM

  With these options selected, click the Run button. When the program finishes click OK and go to the Migration Results tab. There you will find a table of WUA values that reflect the amount of habitat area that was available to an organism that could migrate the specified distance when the flow changed over the ranges shown on the table axes. The Graph button provides 2- and 3-dimensional plots of the results. The entries in the Migrations Results table represent the habitat area derived for the species/life stage shown in the Curve - species/life stage box and the distance shown in the Migration Distance box. You may scroll through the possible entries for those boxes to view the results for all life stages and migration distances set in the options. For example, to view the table or graph for Brown Trout adults, scroll the species box to Brown Trout adults and the migration distance box to 15 ft. (We only specified a single entry of 15 feet for them earlier, so you must select that distance to fill the table with the Brown Trout Adult results.)

  The ZOUTn file contains the selected output items and can be viewed using Wordpad. The Zout file contains computational detail summary tables for each cross section, a summary table output listing for the selected life stages for each set of paired flows for each cross section in sequence, and, following the final flow pair computational summary table for the current life stage, HABTAM provides reach level summary tables.

  Examine the Migration Results tab summary table listing shown in Table L11-2 that contains the pair-wise flow comparisons for each life stage. It should be apparent from these results that the order of the paired flows can make a difference on program results. This should make sense since the initial flow is being compared to the ending flow and the actual difference is a function of not only the user-specified migration distance but also the combined suitability of available habitat cells at the ending discharge. Note that for both the adult and spawning life stages the "habitat used" areas are identical for these two sets of flow comparisons. For spawning, a migration distance of 0.0 should, by definition, produce the same result. In the case of adults, it is apparent that a migration distance of 15 feet is large enough to allow access to most, if not all, of the cross sections' computational cells between the changes in discharge. Now select the spawning life stage and 0 migration distance. What kind of changes do you see in comparison to the adult migration habitat?

  Table L11-2. HABTAM weighted usable area results for Brown Trout adults for the study site with 15 feet search distance.
  Starting discharge	Ending discharge
  	15	30.1	75.2	139	205	625	1250
  15	0	0	0	0	0	2808.99	451.24
  30.1	0	0	0	0	0	2930.99	1107.54
  75.2	0	0	0	0	0	3886.65	2185.41
  139	0	0	0	0	0	5167.13	3645.41
  205	0	0	0	0	0	6624.82	4622.36
  1250	223.98	545.69	972.18	2336.49	3380.58	0	0

  Two- and 3-dimensional plots of the migration-based weighted usable area can be viewed by clicking the Graph button. The 3-D plot can be rotated for better viewing by holding down both mouse buttons and moving the mouse. It takes some trial-and-error experimentation to get familiar with the movement mechanism. Try it, and see.

  The ZHAQF output from HABTAM contains the reach level summary results of WUA and can be accessed at the ZHAQF Results tab.

  Step 4. Influence of Migration Distance on HABTAM Model Predictions

  To illustrate the sensitivity of the HABTAM model to proper choices of migration distance, this step of the laboratory will alter the migration distance used for fry, juvenile, and adult life stages and compare the resulting computations at the 139 cfs and 15 cfs flow combinations. Change the migration distance for fry and adults to 3 feet and 25 feet respectively. The results of this change for Brown Trout adults are shown in Table L11-3.

  What effect did changing the migration distances have on fry and adult life stages compared to the previous habitat simulations?

  It should be apparent that sensitivity in model predictions occurs over a range of migration distance between 0.0 and some upper threshold that is dependent on the shape of the HSC criteria and, therefore, different for different species and life stages. The selection of an appropriate migration distance is a matter of professional judgment. Remember, this migration distance only applies to computational cells at a given cross section.

  Table L11-3. HABTAM weighted usable area results for Brown Trout adults for the study site with 25 feet search distance.
  Starting discharge	Ending discharge
  	15	30.1	75.2	139	205	625	1250
  15	0	0	0	0	0	3266.24	1396.92
  30.1	0	0	0	0	0	3540.05	2227.93
  75.2	0	0	0	0	0	4072.22	2720.29
  139	0	0	0	0	0	5729.13	4263.98
  205	0	0	0	0	0	6624.82	4688.58
  1250	552.11	585.30	1040.32	2798.86	3446.80	0	0

  
  

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  Laboratory 12. Habitat Modeling - HABEF

  Objective

  The objective of this laboratory is to illustrate use of the HABEF program for simulation of effective habitat for each of six options available to the user. The HABEF program can be used to examine differences between available habitat for a given species and life stage at different flows or comparisons between different species and life stages at a specific flow.

  Programs Used: HABTAE, HABEF

  Project Used: Lab12.phb

  Introduction

  The HABEF program can be used to examine a number of relationships between habitat conditions at two stream flows and/or for two life stages at a specific discharge. In this laboratory, each of the six computational options available within the HABEF program will be examined.

  In the HABEF program different hydraulic property arrangements can be used depending on the option selected. The HABEF program will compute two different indices of habitat. The first is WUA, which is derived from the combined suitability factor computed by the initial habitat simulation program. (You must have run HABTAE or HABTAM prior to using HABEF.) The second index, UA (usable area) is derived from the sum of computational cell areas where the combined suitability in the computational cell is >0.001. Usable areas can be considered to be a measure of the area where all of the HSC variables have suitability that is marginally greater than zero. Can you explain why this may not be the same as the wetted surface area of the stream?

  The six steps in this laboratory guide the student through these basic options of the HABEF program:

• Union of Life Stage 1 with Life Stage 2
  
• Stream Flow Variation Analysis (Minimum WUA)
  
• Competition Analysis
  
• Stream Flow Variation Analysis (Maximum WUA)
  
• Effective Spawning Analysis
  
• Stranding Index Analysis

  Step 1. Ensure Needed Hydraulic And Habitat Model Results Have Been Run

  Habitat analysis results from HABTAE or HABTAM are required prior to executing HABEF. Open the Lab12.phb project in the Lab12 directory and note that WUA Results exist for Rainbow Trout adult. This indicates one or the other of these programs has produced results earlier. If you are uncertain which program was used, check the Habitat Results table. In this case, the Habitat Results table in the HABTAM window is filled with [NULL] entries while the table in the HABTAE window has numerical values. Hence, HABTAE was run.
  
  Step 2. Set Appropriate Simulation Options and Run HABTAE Model

  This step is provided as an example of the actions you would perform when the initial modeling steps have not yet been performed. For this laboratory, you may go directly to Step 3 as the HABTAE model has been run and the needed result files are already in the Lab12 folder.

  Move to the HABTAE program window by clicking /Models/HABTAE. Go to the Life Stages tab and click as many life stages on or off until only the Brown Trout adult and Rainbow Trout adult (or other desired) life stages remain. Click the Run button to run the model. You will now have habitat results for adult Brown and Rainbow trout.

  At this point, two files have been created in the Lab12 directory containing computational cell details at each cross section for each simulated discharge for each of the species and life stages used in the simulation. Those files have the naming convention: Projectname.HSCnr(e or m). The habitat suitability criteria number (HSCnr) is used to the identify species and life stage contained in each particular results file. The suffix 'e' or 'm' indicates whether the files were produced by HABTAE or HABTAM, respectively. The HABEF program uses these files for cell-by-cell computations. In this case, they should be named Lab12.11302e and Lab12.21115e, respectively, for Brown and Rainbow trout adult results produced by HABTAE.

  Step 3. HABEF Simulations for Union (Option 1) and Competition (Option 3) Analyses

  The HABEF program will now be used to simulate the union of two life stages and competition between two species. In the union analysis for two species and life stages (Option 1) HABEF computes total weighted usable area represented by combined habitat of the two species or life stages. The total habitat quantity computed at a specific discharge will always be greater than or equal to the highest amount for a single species or life stage but always less than or equal to the sum of the two habitat totals. Why is this? In answering this question, consider adding the largest WUA value regardless of species in each cell to the HABEF union sum. If species/life stage "a" has the dominant WUA in all cells and there are no cells where the species/life stage "b" alone has WUA greater than zero, then the WUA reported by HABEF will be equal to the WUA for species/life stage "a". If both species/life stages dominate in some cells, the sum will be greater than the sum for species/life stage "a" alone. Will this general statement still be true for two species/life stages that use very different habitats with little or no overlap?

  The analysis of competition (Option 3) computes the amount of habitat for a particular species or life stage for two conditions. First, it calculates habitat for species/life stage "a" in cells where habitat for the species/life stage "b" is zero. This is combined with the amount of habitat occurring in computational cells where combined suitability is greater than 0.0 for both species but where species "a" has a higher combined suitability value than species "b". Thus, the competition option describes the total WUA for cells where a species dominates.

  Select /Models/HABEF and enter a descriptive name for the comparison being run in the Job Title text entry box. This name will be used to label all output tables (both text files and on-screen). In the species/life stage 1 text entry box, click the down arrow button to the right and select Brown Trout adult. In the second text entry box, click the down arrow and select Rainbow Trout adult, then click the Union of life stage 1 with life stage 2 radio button. Note that this assigns Brown Trout adults to species/life stage 1 and Rainbow Trout adults to species/life stage 2. Finally, click the Run button and view the Results tab. You may also produce a named HABEF results file using the Text File button in the Results tab and view it using Wordpad. PHABSIM for Windows does not retain subsequent sets of results in the database, so it is convenient to create result text files for each run to allow later comparison when numerous HABEF options are generated in the course of an analysis. It is also wise to change the job title for each run to avoid later confusion among options where the numerical results are similar.
  

  The table in the Results tab contains a summary for each life stage at each discharge of their respective UA and WUA values and the WUA associated with the union of the two life stages. Note that the WUA associated with the union of two life stages is less than the total WUA if the two life stages had been simply added together at a given flow. A comparison of the Total Area column (i.e., total stream surface area) and the respective UA columns for each life stage shows that at discharges below 139 cfs all computational cells have a combined suitability greater than 0.001. Why is this?

  Table L12-1 contains an example of the union analysis output table. Click the Graph button at the bottom of the HABEF Results tab to view graphical results.

  Table L12-1. HABEF output for union analysis.
  Q	Area	UA(1)	WUA(1)	UA(2)	WUA(2)	WUA(1 or 2)
  15.0	40049.24	9164.18	2,926.54	40,049.24	3,986.22	4,869.38
  30.1	51654.74	18582.09	5,291.70	51,654.74	6,036.19	7,512.03
  75.2	59558.40	34597.02	9,434.51	59,558.40	12,864.07	14,397.67
  139.0	64810.89	50776.12	10,796.20	64,482.53	14,374.42	16,641.56
  205.0	68096.85	59678.32	8,980.34	52,992.38	11,189.20	13,551.44
  650.0	74003.04	68891.79	7,471.48	25,375.71	9,357.60	11,691.81
  1250.0	77031.06	45363.88	6,732.50	20,628.08	8,537.55	10,091.42

  You can see that the total amount of WUA in the union of two species is greater than that for either individual species WUA and less than their sum would be. You may wish to view the graph of results and print it for later reference.

  Next, the HABEF program will be run again with the same input data but will be used to compute effective habitat based on selection of the competition analysis option.

  Go to the HABEF Options tab and select the Competition analysis radio button. Make sure that the first input file is ZHCF1 and the second file is ZHCF2, as in the previous example. Change the Job Title to indicate the next results are for the competition analysis. Click the Run button and move to the Results tab.

  Table L12-2 shows output from the competition analysis. Note that the HABEF output is different when selecting competition analysis versus union analysis (Table L12-1). The program shows summary results at each simulation discharge in terms of total stream area, UA and WUA where each species has the only suitable habitat. Summary output is also provided for amount of usable area for both species and area associated with habitat conditions where each species is dominant (i.e., combined suitability for species "1" is greater than the combined suitability for species "2"). The program also computes the amount of habitat area with equal worth for both species as noted earlier.

  Table L12-2. HABEF output for competition analysis.
  Q	Area	UA(1)	WUA(1)	UA(2)	WUA(2)	WUA(1 or 2)	WUA (1=2)	WUA(1 in 1&2)	WUA(2 in 1&2)	WUA (1>2 in 1&2)	WUA (2>1 in 1&2)
  15.0	40049.24	0.00	0.00	30885.06	1626.35	9164.18	0.00	2926.54	2359.87	2031.87	1211.16
  30.1	51654.74	0.00	0.00	33072.66	1669.93	18582.09	0.00	5291.70	4366.26	3412.54	2429.57
  75.2	59558.40	0.00	0.00	24961.39	1550.70	34597.02	0.00	9434.51	11313.37	3527.26	9319.71
  139.0	64810.89	328.36	25.04	14034.77	788.40	50447.76	0.00	10771.16	13586.02	4400.39	11427.72
  205.0	68096.85	15104.48	1041.23	8418.54	497.36	44573.84	0.00	7939.11	10691.84	3722.10	8290.75
  650.0	74003.04	48626.87	1861.00	5110.79	356.60	20264.93	0.00	5610.48	9001.00	1328.08	8146.12
  1250.0	77031.06	25641.79	660.65	905.99	65.11	19722.09	0.00	6071.85	8472.44	1883.55	7482.10

  The competition results for 15.0 and 30.1 cfs show Brown Trout adults have more suitable habitat at the low flow range. However, from 75.2 cfs and up, Rainbows have significantly more habitat than Browns.

  The dominance of Rainbow Trout adult habitat at higher discharges is related to their tolerance for lower depth as reflected in the depth HSC reaching 1.0 at a lower depth for Rainbows than for Browns. Go back and check the HSC to confirm this. For the 15 and 30.1 cfs discharges, Rainbow Trout adults have between 50% and 70% as much habitat as Brown Trout adults. However, from 75.2 cfs and up, the Rainbow habitat is three or more times as abundant as Brown habitat. Assuming the HSC have been verified to accurately describe behavior of the two species, from these results can you conclude that higher flows favor Rainbow Trout adults? How would the results be affected if the depth HSC for each species had a ± 25% error and the full range of the uncertainty was considered in the analysis?

  Step 4. Streamflow Variation Minimum and Maximum Analysis

  Streamflow variation analysis for minimum and maximum WUA in HABEF can be used to explore which species and life stage has either the maximum or minimum WUA at each discharge on a computational cell-by-cell basis. When HABEF minimum variation is selected, the composite suitability factor used to compute WUA for a computational cell is the minimum composite suitability value in that computational cell in each of the two species/life stages being compared. The maximum streamflow variation HABEF option is identical except that the maximum composite suitability from the computational cell within the two ZHCF files is used to compute WUA.

  Make sure that the first species/life stage you wish to consider is entered in the first dialog box and the second species/life stage is in the second box. Select the Streamflow Variation Analysis (minimum WUA) radio button, change the job title to indicate minimum WUA analysis, and click the Run button to execute the HABEF program. Move to the Results tab to view the output. You may wish to save the results for later comparison, click the Save button to do so.

  For comparison, perform a maximum streamflow variation analysis. Enter a job title indicating maximum WUA, click the Streamflow Variation Analysis (maximum WUA) radio button, and click Run. Again, click the Results tab to review results.

  A comparison of these streamflow variation results with the previous minimum analysis shows a marked difference in the relationship between minimum or maximum WUA and discharge. The minimum WUA analysis declines as discharge increases, while maximum WUA increases then decreases with flow.

  When these results have been examined, return to the HABEF window.

  Step 5. Effective Spawning Analysis Using HABEF

  HABEF effective spawning analysis allows an investigator to examine the effects of flow alterations on spawning and incubation life stages. The program computes effective spawning habitat based on the concept that available habitat at an initial (spawning) discharge must also be available at the second (incubation) discharge. In this analysis, the HABEF program computes combined suitability in a computational cell at the starting and ending discharges (i.e., for each set of paired discharges in respective HABTAE or HABTAM results). If composite suitability at the second discharge is greater than 0.0, then the composite suitability factor for that computational cell at the first or starting discharge remains unchanged and WUA for that computational cell is added to the total for the cross section and, hence, the reach. Simply put, if the spawning area maintains minimal incubation conditions (stays wet with needed velocity) then the spawning area is accumulated in the total. However, if the composite suitability factor at the second discharge is 0.0, then suitability at the first discharge is set to 0.0 and that amount of available habitat is 'removed' from the total at the cross section. This is similar to using the minimum streamflow analysis option but differs in that WUA at the first flow is dependent on the analysis of the second flow.

  To make this example of effective spawning more realistic, new results using Bull Trout spawning HSC will be generated with the HABTAE program.

  Return to /Models/HABTAE, move to the Life Stages tab and click all of the Brown and Rainbow Trout life stages to turn them off. Now click the four Bull Trout life stages to turn them on. Click Run and return to the HABEF program when HABTAE is finished.

  Change the job title to indicate you are performing an effective spawning analysis and select Bull Trout spawning in both species/life stage dialog boxes. Then click Run and move to the Results tab. Click the Graph button to view the results. Which combination of discharges produces the greatest effective spawning habitat values? Which produce the lowest values?

  The plot also shows that if the starting flow is 1250.0 cfs and flows are reduced, the amount of effective spawning habitat is substantially reduced at 250.0 cfs and non-existent below 75.2 cfs. As the starting and ending flow difference is reduced, the effective spawning is less affected as would be expected (Why?). It should also be apparent that starting at a lower flow such as 75.2 and ending at a higher flow such as 139.0 cfs has less impact on effective spawning (Why?). If you have difficulty reading the 3-dimensional plot, return to the results table and examine it in drawing your conclusion.

  Step 6. Stranding Index Analysis Using HABEF

  Stranding analysis with the HABEF program employs essentially the same computational logic as described above for effective spawning analysis. The composite suitability of a computational cell at the second flow must be greater than 0.0 for composite suitability of the computational cell at the first flow to contribute to effective WUA. Thus, when evaluating stranding, one should only compare flow pairs that show a decrease in discharge. For this analysis, the same species and life stage is selected in both dialog boxes on the /HABEF/Options tab. Typically, the selected life stage would be one that has only a small capacity to move with changes in discharge, though the analysis can be conducted for any life stage.

  While a stranding analysis will not be run in the laboratory due to time considerations, the following general approach can be used for all life stages. To ensure that the analysis is focusing on available depth alone, you can create a new set of suitability curves for stranding. To do so, make copies of the HSC in the /Edit/Suitability Curves window and edit suitability curve coordinates for velocity and channel index, setting all suitability values are 1.0. There is no need to change the number of coordinate pairs. Change depth suitability curve coordinates for depth such that depth suitability is 0.0 below some threshold (e.g., 0.5 feet) and then change the remaining depth SI values to 1.0.

  Save these changes and run the new HSC in the HABTAE program. Then move to the HABEF program and run the stranding index analysis using the same HSC in both dialog boxes. The results will show the chance of stranding when depth for that species/life stage drops below the selected threshold value.

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