SEFA was developed to provide an integrated set of tools for environmental flow assessment, as envisaged in the incremental flow analysis (IFIM).

- Data and presentation
- Development of habitat suitability curves and generalized additive models
- Hydraulic habitat model
- Water surface profile model
- Sediment analyses, including flushing flows and sediment deposition
- Water temperature modeling
- Dissolved oxygen modeling
- Time series analysis, including hydraulic habitat, riparian inundation, indicators of hydrologic alteration, and event analysis

The program provides a set of tools that allows the effects of flow alteration on various physical parameters to be assessed. For example, the various outputs can be graphs or tables showing how parameters like area weighted suitability (AWS, previously called WUA), dissolved oxygen, water temperature, inundation levels and sediment functions vary with flow. Changes to the flow regime can then be further examined using time series analysis to evaluate changes in the frequency, magnitude and timing of hydrological variables and variables such as area weighted suitability and inundation.

Details of the various calculation options for experienced users of PHABSIM.

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**Data**

Although it is possible to enter data directly, it is better to enter data in excel and import. In this way, you have a copy of the data in excel as well as in the SEFA rhbx file. The date entry/edit module allows data to be viewed and edited, if necessary.

**Units/Date**

Internally, all calculations are carried out in metric. However, results can be presented either in feet or metres. When files are imported, the units of the file will be requested, if not specified in the file.

A wide variety of date formats are recognized. Date can be in either day/month/year or month/day/year order. The default date/time presentation format is day/month/year order, but it can be changed to month/day/year order.

**Import/export**

Various file types can be imported and converted into a SEFA file. The types are delimited text (txt hab), excel (xls xlsx), RHYHABSIM (rhb), RHABSIM (rhb), PHABSIM DOS text (*.ifg) and PHABSIM windows files (*.phb etc.).

A SEFA file can be exported as a text file (.hab). The text file could then be imported to recreate the SEFA file. This is useful for creating a text backup of a file and its calibration. It also provides an alternative method of viewing the data, when you are familiar with the text format.

**Checking data**

A procedure is provided to check data and calibration. The results are listed in a text window and if there are any problems, they are shown as blue text. There are quite a number of checks. These include checking:

- substrate names that are entered against the substrate types that that the program assumes.
- rating curves.
- levels.
- % composition of substrate types sum to 100%.
- extreme of negative values of velocity.
- offsets are all in increasing or decreasing order.
- calibration gauging listing the stage change/flow change, highlighting exceptionally high or low values

**Presentation**

Results are usually displayed in as graphs. When any graph is displayed, a text window containing the data can also be displayed. Graphs and text can be copied to the clipboard.

**Habitat suitability curves and models**

A separate program module is provided for the analysis of habitat suitability data and the development of habitat suitability curves and statistical models. Habitat suitability curves are imported from text files into a library.

Multivariate statistical models (generalized additive models or GAMs) can be developed in TimeTrends and imported into the habitat suitability library for use in habitat analyses. These are usually generalized additive logistic or Poisson models, but other model types are possible. Typically, measurements of fish presence/absence or abundance would be used to develop a GAM based on habitat characteristics (e.g. depth, velocity and substrate).

**Hydraulic/Habitat suitability analyses**

The variation of hydraulic parameters and habitat suitability with flow can be shown at three scales, point, cross-section and reach. Most analyses can be carried out for any combination of reaches and cross-sections.

By default habitat is evaluated using depth, velocity and substrate criteria. It is possible to use any combination of these criteria. In addition, other criteria such as a substrate index or cover index can be included in the evaluation.

**Fluctuating flow analysis**

This produces a graph that shows how habitat reduces as the amount of flow fluctuation increases. The left axis is the area weighted suitability (AWS) and the bottom axis is the proportion of flow fluctuation.

The effect of flow fluctuations on hydraulic habitat is modeled about a base flow. The base flow is considered as the normal flow and that the fluctuation causes the flow to fall below normal and to increase above normal.

**Passage analysis**

The variation of passage width (total width and maximum contiguous width ) with flow can

be calculated.

**Sediment modeling**

Flushing flow requirements can be estimated by calculating the area of stream bed flushed (deep, and surface) using Milhous flushing criteria. Velocity, shear velocity, dimensionless shear stress, suspended sediment size and bed load size can also be displayed.

The % area of the river in which silt or sand will deposit can also be calculated using Shields curve for initiation of movement (i.e., movement/deposition occurs when dimensionless shear stress is 0.056.

The longitudinal variation in suspended sediment concentration can be calculated assuming no input of sediment. This models the settling process of fine particles (sticky river bed) in water following Einstein’s (1968) work on siltation of redds.

** Water Temperature modeling**

Two methods (Lagrangian and Theurer) can be used to calculate the variation of maximum, minimum and daily mean water temperature with distance downstream. It is also possible to use meteorological and water temperature time series data for calibration and modeling.

**Dissolved oxygen modeling**

Procedures are provided to calculate dissolved oxygen parameters (re-aeration, respiration and production) from recorded data and to use these parameters to calculate the effect of flow on dissolved oxygen.

**Water surface profile modeling**

Procedures are provided for calibration and modeling using water surface profile

modeling.

The main innovation is the ability to change Manning’s N with flow. And there are a number of ways of doing this (e.g., use the beta value of the first section for all, use the calculated beta between each pair of sections, use the average beta value for all).

A series of WSP profiles can be saved for as rating curves and used for subsequent analyses.

**Flow analyses**

An import wizard is used to import a text or EXCEL file containing date and flow data. A wide variety of date formats are recognized. Date can be in either dd/mm/yy or mm/dd/yy order. Many of the following analyses are applicable to other types of times series data.

These data can be displayed as graphs and used to calculate flow duration statistics, seasonal flow statistics and indicators of hydrologic alteration.

Similar analyses can be carried out for area weighted suitability (AWS previously called weighted usable area).

The frequency, timing and duration of riparian inundation can be calculated for a specified height above base flow.

The frequency and duration of events can be calculated. Multiple criteria can be specified for events (e.g. flow > 10 and flow < 100).

**Calculation details and PHABSIM options**

The default methods are recommended for general use, but preferences can be set to allow an emulation of IFG4 methods for Manning’s N calibration, calculation of velocity and calculation of rating curves.

By default, SEFA calculates habitat suitability by interpolating linearly at between cross-section measurements points. For example if one point is measured at the water’s edge and the next in the water at a depth of 0.5 m, the program will calculate habitat suitability at 0.025 m increments from 0 to 0.5 m, If this is not checked, habitat suitability will only be calculated at measurements points, as it was in **PHABSIM**

Log-log rating relationships are derived for stage-discharge pairs of measurements. The default method is to fit the curve through the survey flow and the best least square fit to other stage-discharge pairs. This method is most appropriate if the survey cross-section is based on measured water depths, because it does not introduce spurious depth errors in depth when predicting water levels at the survey flow.

The alternative method is that used in IFG4 (PHABSIM) to fit the curve through all stage-discharge pairs. The default velocity calibration and prediction method is to calculate Manning’s N and VDF from conveyance (a function of hydraulic radius) at measurement points. When predicting velocities for a given flow, they are calculated from conveyance and are then adjusted so that the they give the given flow times the ratio of measured to survey flow. Using this default method and the default log-log rating method predicted velocities at the survey flow will be the same as measured velocities.

The alternative method is that used in IFG4 (PHABSIM), where Manning’s N values are calculated from water depth at each measurement point and the slope for the cross-section (usually the

default slope of 0.0025). When predicting velocities for a given flow, they are calculated using manning’s equation (N, depth and slope), with the velocities are then adjusted so that the they give the given flow.**Calculation of habitat suitability. **

Three methods of calculating the combined suitability index are available. The default is for CSI values to be multiplied to form a single combined index.

When a water level is higher than the left or right bank, the water edge is estimated by linear extrapolation. However, if the bank slope is less than 0.05 (the default), a vertical bank is created. PHABSIM always creates vertical banks.

Stage discharge relationships calculated using Manning’s equation (MANSQ) assume that hydraulic roughness varies with discharge. The alternative method is to allow roughness to vary with hydraulic radius.