Klamath Coho
Integrated Modeling Framework
Model User Instructions
Prepared by:
Cramer Fish Sciences
Submitted to the Bureau of Reclamation, Klamath Basin Area Office
September 21, 2007
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SPREADSHEET MODEL OVERVIEW
The current version 1.1 of the Klamath Coho Integrated Modeling Framework (IMF) is designed
to facilitate direct comparisons between a given “Baseline Scenario” and an “Alternative
Scenario,” where these scenarios correspond to different flow releases from Iron Gate Dam
(IGD), and associated differences in downstream flow and temperature conditions within each of
the mainstem reaches. To do so, the model performs two sets of essentially identical life-cycle
calculations that differ only in terms of the flow and/or temperature data inputs and
corresponding survival estimates. Specifically, the spreadsheet contains 15 worksheets, as
summarized in Table 1.
The parameter settings in “Home,” “Inputs,” and “Subbasin_Inputs” guide the life-cycle
simulations, and apply to both the “Baseline” and “Alternative” scenarios. The “Baseline” and
“Alternative Scenario” calculations (sheets 7-10) are nearly identical but rely on different flow
and/or temperature data specified by the model user and defined in “Base_Data” and “Alt_Data.”
In the following, we describe some of the key features of the model for selected worksheets.
When the model file is first opened, a security warning message will appear prompting the user
to either disable or enable macros. Be sure to select “Enable Macros” to ensure correct model
functionality. Model parameters that can be modified by the user are highlighted in blue, while
all other parameters and descriptive information are highlighted in light yellow. Worksheet tabs
that are highlighted in red contain data and model functions that should not be modified by
model users.
“HOME” SHEET
Water Year Type and Flow Inputs
The “Home” sheet is designed as a synopsis page where users can manipulate key inputs and
view results. Model inputs that can be manipulated from the “Home” sheet include the
meteorological and tributary flow data (i.e. water year type), the amount of flow released at Iron
Gate Dam, and the flow and temperature functions used to estimate survival during key life
stages (e.g. pre-spawning survival and smolt migration survival). Graphs and summary tables
displaying the total number of smolts surviving to the ocean and adult returns in each simulation
year, as well as changes in smolt and adult production from the baseline to alternative scenario
are summarized at the bottom of the “Home” sheet.
The model currently contains meteorological and tributary flow data (i.e. natural flow inputs
downstream of IGD) for two water year types including 2001, which was characterized as a dry
water year, and 2004, an average water year. Model users are required to select the water year
type for the baseline (cell D9) and alternative (cell E9) flow scenarios. Inclusion of a wet water
year type (2006 data) is currently in progress and will be included in a revised version of the
model. To select the water year type, first click on cell D9 for baseline or E9 for alternative. A
drop-down list will appear, providing the option to select either a “1” for an average year (2004
data) or “2” for a dry year (2001 data). An example of the “Home” sheet is provided in Figure 1
with the top red arrow indicating the water year type inputs.
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Table 1. Summary of worksheets in the Klamath Coho IMF.
Sheet
Name
Summary Description
1
Home
Contains inputs for water year type (e.g. 2001 dry or 2004 average), IGD flow inputs
(by exceedance probability or user-defined), parameter inputs related to flow and
temperature functions, and summary results comparing example “Baseline” and
“Alternative” scenario simulations.
2
Effects
Contains summary tables and graphs of key model results such as pre-spawning
survival rates, adult distribution, summer parr production, and smolt migration survival.
3
Inputs
Contains numerous parameter inputs related to adult migration, juvenile migration, etc.
4
Subbasin_Inputs
Contains smolt capacity estimates for 50 tributaries, and several options for selecting
among alternative smolt-production models (e.g., Hockey-stick vs. Beverton-Holt, etc.).
5
Base_Data
Contains flow and temperature data corresponding to the “Baseline” scenario. These
data are selected from temperature and flow tables (e.g. 2004_temp, 2004_flow)
according to the specified water year type (i.e. 2001 or 2004) and IGD flows under the
“Baseline” scenario.
6
Alt_Data
Contains flow and temperature data corresponding to the“Alternative” scenario. These
data are selected from temperature and flow tables according to the specified water year
type and IGD flows under the “Alternative” scenario.
7
Base_LifeCycle
8
Base_Calcs
Contains complete life-cycle calculations across tributaries and simulation years based
on “Baseline” flow and temperature data.
Contains several intermediate calculations (e.g., temperature-related pre-spawn
survival, smolt migration survival) that are then used in “Base_LifeCycle.”
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Alt_LifeCycle
10
Alt_Calcs
11
2004_temp
Contains average and maximum daily stream temperature (˚C) by reach for every 50 cfs
increase in flow at IGD using 2004 meteorological and tributary flow data.
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2004_flow
13
2001_temp
Contains average daily flow (cfs) by reach for every 50 cfs increase in flow at IGD
using 2004 meteorological and tributary flow data.
Contains average and maximum daily stream temperature (˚C) by reach for every 50 cfs
increase in flow at IGD using 2001 meteorological and tributary flow data.
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2001_flow
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Defaults
Contains complete life-cycle calculations based on the “Alternative Scenario” flow and
temperature data.
Contains intermediate calculations that are then used in “Alt_LifeCycle.”
Contains average daily flow (cfs) by reach for every 50 cfs increase in flow at IGD
using 2001 meteorological and tributary flow data.
Contains all default model parameters. These values are used to restore default settings
and should not be modified by model users.
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Figure 1. Depiction of “Home” page in the IMF. The red arrow indicates inputs for water year type (i.e. average or dry) and the blue arrow indicates
drop-down lists for various Iron Gate Dam flow scenarios.
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Next, model users must specify the amount of flow released at IGD for both the baseline and alternative scenarios, which is expressed
as average cubic feet per second (cfs) for each biweekly period from October through September. Model users may select from a list
of predefined flow scenarios for both the baseline and alternative scenarios which correspond with a range of monthly flow
exceedance probabilities at IGD. Exceedance probability is defined as the probability that during a given month, the flow level at IGD
will be exceeded. Therefore, higher exceedance probabilities correspond with lower flows.
For the baseline scenario, flow exceedance probabilities were calculated from historical flow data at Iron Gate Dam from 1961 to
2006 (Data provided by the U.S. Bureau of Reclamation). Nine pre-defined flow scenarios are available in the IMF corresponding
with exceedance flows ranging from 10% to 90%. The inputs for each of these flow scenarios are given in cells H17:P40. In addition
to pre-defined flow scenarios by exceedance level, the model provides a column for model users to input flows of their choosing (cells
Q17:Q40 under “User”). To select a baseline flow scenario, the model user must click on the drop down list located in cell D13, and
select the desired exceedance probability or “User” to select the user-defined flow scenario. The location of the drop-down list for
selection of a flow scenario is indicated by a blue arrow in Figure 1.
Alternative flow exceedance scenarios were calculated by the Bureau of Reclamation using its Water Resources Integrated Modeling
System (WRIMS). The model utilizes 1961-2004 historical data for Upper Klamath Lake (UKL) inflows and Keno to Iron Gate
accretions, minimum lake levels and river flows, and estimated Klamath Project needs to estimate future UKL elevations and Klamath
River flows at IGD. Alternative flow scenarios provided in the model represent the estimated amount of flow released at IGD under
the proposed project operations for a range of flow exceedance probabilities from 2008-2018.
The inputs for each alternative flow scenario are given in cells T17:AD40. As with the baseline scenarios, the model user may input
flows of their choosing (cells AD17:AD40 under “User”). To select an alternative flow scenario, the model user must click a drop
down list located in cell E13, and select the desired exceedance probability or “User” to select the user-defined flow scenario. The
option to select the minimum flows as defined in the 2002 Biological Opinion for a dry water year type is also available under the
alternative scenarios, and is listed as “Minimum” in the drop down list. The selected flow scenarios for both the baseline and
alternative options are shown in cells D17:E40), and are contained within a table labeled “Baseline and Alternative Flow Scenarios
Used in the Model” (Figure 1).
The current version of the model contains certain limitations on the range of flow values that can be selected. The IMF currently
supports flow values ranging from 600 to 4,000 cfs from October through June, and from 600 to 2,600 from July through September.
Minimum flows of 600 cfs were based on identification of model limitations under low flow conditions. Specifically, model results
under flows of 500 cfs or less predicted maximum daily temperatures that were probably too high and minimum temperatures too low
compared with observed stream temperatures (Mike Deas, Watercourse Engineering, Personal Communication).
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Model limitations at the upper range of flows were based on historical data used to calibrate the hydrodynamic and temperature model
by Watercourse Engineering. Summer period flows greater than 2,600 have not been experienced historically. Thus, model predictions
of temperature have not been tested at flows equal to or greater than 2,600 cfs for the months of July, August and September. With the
inclusion of a wet water year type in a future version of the IMF, the maximum flow level of 4,000 cfs during other months (OctoberJune) will likely be increased. However, due to the current limitation of 4,000 cfs, IGD flow scenarios with exceedance probabilities
of 30% or less under the baseline scenarios, and 20% or less under the alternative scenarios are not supported by this version of the
model. Average biweekly flows outside of the specified range (600-4,000 from October-June, and 600-2,600 from July-September)
are highlighted in red, and care should be taken to avoid populating the model with flows outside of this range.
Specified flow values must also be in increments of 50 cfs. Flow increments of 50 cfs were chosen to maximize the level of flexibility
available to model users while simultaneously limiting the file size to a level that ensures reliable model performance and
manageability.
Temperature and Flow Functions
Parameters defining key temperature and flow functions in the IMF, as well as corresponding plots of these functions are also
provided on the “Home” sheet. Model users should refer to the final IMF report for a detailed description of these functions.
Briefly, pre-spawning survival, summer parr capacity, and smolt emigration survival are all described by logistic scalar functions that
range from 0 to 1. The shape of these functions are defined by lower and upper threshold values for the independent variable (i.e.
temperature or flow), and the corresponding lower and upper survival limits. For example, the pre-spawning survival scalar under the
default model settings has lower and upper threshold values of 16°C and 26°C, with corresponding survival scalars of 0.95 and 0.05
respectively. Under these parameter settings, the pre-spawning survival scalar equals 0.95 at an average stream temperature of 16°C,
and declines steadily to a low of 0.05 as stream temperature increases to 26°C. Model users have the flexibility to modify these
parameters to test different assumptions about the exact form of these functions.
In addition to the temperature- and flow-related survival functions, the “Home” sheet also contains the slope parameter for the lengthbased scalar function for the parr-to-smolt survival rate. This function only applies to parr rearing in mainstem reach 1 (MS1). More
information about this function can be found in the Klamath coho life-cycle model final report (Final Report).
Results
The first set of results provided on the “Home” page are the changes in smolt production and adult production between the “Baseline”
and “Alternative” scenarios, summarized for mainstem reaches (MS1 to MS6), miscellaneous tributaries (MST1 to MST6), and major
tributaries (Shasta, Scott, Salmon, and Trinity). To the right of these are the percentage changes. Below these are the actual simulated
smolts and adult production values for the “Baseline” scenario (left side) and “Alternative” (right side). We included results for the
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differences and relative changes between the “Baseline” and “Alternative” scenarios at the top because these results are much easier to
grasp when exploring the effects of “Alternative” scenarios.
“EFFECTS” SHEET
The “Effects” sheet contains summary tables and graphs of key model results with particular emphasis on model outputs that are likely
to be influenced by changes in flow and/or temperature. Model outputs presented in the “Effects” sheet include temperature-related
pre-spawning survival rates, distribution of adult returns in simulation year 10, summer parr production in the mainstem in year 10
(including temperature and flow effects on parr capacity in MS1), smolt migration survival to the ocean, and total smolt production in
year 10 by smolt type (i.e. Type I-III). Figure 2 depicts an example of model results for smolt migration survival. The summary tables
and graphs provide a clear comparison of survival rates (by reach of origin) between baseline and alternative flow scenarios. In
addition, these data explicitly show the independent effects of flow and temperature survival scalars on overall smolt survival to the
ocean.
“INPUTS” SHEET
The “Inputs” sheet (Figure 3) contains most of the other parameters related to the life-cycle calculations. Changes to these parameters will affect the
life-cycle calculations for both the “Baseline” and “Alternative” scenario simulations. In general, these values are organized for easy viewing, but would
not be changed or manipulated often. Model inputs included on the “Inputs” sheet include parameters associated with: 1) Adult entry and migration; 2)
Spawner survival rates; 3) Juvenile production from tributaries; 4) Iron Gate Hatchery (IGH) contributions; 5) Smolt migration; and 6) Marine factors
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(i.e.
smolt-to-adult
survival
and
ocean
harvest
rate).
Parameter
values
for
each
of
these
categories
are
shown
in
Figure 3. Depiction of the “Inputs” sheet in the IMF. This sheet contains a “Restore Defaults” button (circled in red) which allows users to reset all
model parameters to the default settings. Parameters that can be modified are highlighted in blue.
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Table 2 and are described in detail in the Final Report.
In addition to the input parameters shown in Table 2, the “Inputs” sheet contains migration
timing information for both adults and smolts. These inputs define the start dates and duration of
migration for weekly (adults) and biweekly (smolts) cohorts of fish migrating through the
mainstem Klamath River. Model users can quickly examine model sensitivity to migration
timing by adjusting the migration start dates.
The model includes three options for mainstem parr capacity, representing different methods and
assumptions used to estimate parr capacity in mainstem reaches (Table 3). Parr capacity in MS1
under all three options was estimated using the Habitat Limiting Factors Model (HLFM)
modified by flow, temperature, and alkalinity scalars (option 2 only) as described in Technical
Memorandum 5 and the Final Report. Parr capacity in all other mainstem reaches (MS2-MS6)
was either estimated using HLFM (options 1), HLFM modified by an alkalinity scalar (option 2),
or was based on abundance estimates from snorkel survey data (option 3). Model users can select
from these three options by clicking on the drop-down list in cell C95 and selecting either “1”,
“2”, or “3” for options 1, 2, or 3 respectively.
The “Inputs” sheet contains an option to restore all model parameters to their default settings. To
restore model defaults, click on the button titled “Restore Defaults” located at the top of the
“Inputs” sheet (Figure 3).
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Figure 2. Depiction of the “Effects” sheet in the IMF showing summary tables and a graph of smolt migration survival rates by model reach. These
results provide a comparison between baseline and alternative flow scenarios and also indicate the independent effects of flow and temperature survival
scalars.
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Figure 3. Depiction of the “Inputs” sheet in the IMF. This sheet contains a “Restore Defaults” button (circled in red) which allows users to reset all
model parameters to the default settings. Parameters that can be modified are highlighted in blue.
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Table 2. Summary of default model parameters located on the “Inputs” sheet in the IMF.
Model parameters
Adult entry and migration
Initial abundance of naturally produced adults (first three brood years)
Initial abundance of hatchery produced adults (all brood years)
Proportion females
Spawner survival rates
Pinniped predation
Yurok tribal harvest
Karuk tribal harvest
Pre-spawn (temperature-independent)
Juvenile production from tributaries
Survival rates
Fry-to-fingerling
Fingerling-to-parr
Summer parr-to-smolt
Winter parr-to-smolt
Movement survival
Migrant fingerling production (i.e. slope (b) of linear regression where fingerlings = b* migrant fry)
Shasta River (MS2)
Scott River (MS3)
MS1 parr growth model
Starting weight (g)
Feeding ration
Maximum allowed migration distance (up cool non-natal tributaries)
Distance (km)
Mainstem parr capacity
MS1
MS2
MS3
MS4
MS5
MS6
IGH contribution
Smolt release number
Smolt post-release survival
Relative fitness of spawners
Stray rate
Value
5,000
1,200
0.55
0.983
0.958
0.997
1.000
0.81
0.86
0.45
0.90
0.90
2.589
2.589
1.4
1.0
1.6
7,705
186
659
7,834
2,302
1,761
100,000
0.50
0.50
0.10
Smolt migration
Baseline survival (per 100 Km)
0.95
Marine factors
Smolt-to-adult survival rate
Ocean harvest rate
0.04
0.065
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Table 3. Total estimated parr capacity in mainstem reaches for each of the three different options
Reach
MS1
MS2
MS3
MS4
MS5
MS6
Option 1 (default)
Option 2
HLFM (no alkalinity scalar) HLFM (with alkalinity scalar)
7,705
11,558
186
280
659
991
7,834
12,142
2,302
3,568
1,761
2,643
Option 3
Snorkel data
7,705
879
1,093
281
63
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“SUBBASIN_INPUTS” SHEET
The “Subbasin_Inputs” sheet contains smolt capacity estimates for the 50 tributaries included in
the model, and several options for selecting among alternative smolt-production models. Details
of the methodology used to derive these capacity estimates and the rational for examining
alternative smolt-production models is described in Technical Memorandum 5 and the Final
Report. A depiction of the “Subbasin_Inputs” sheet is shown in Figure 4.
In brief, the model allows the user to select among two smolt-production models (cell B4): (1)
the Hockey-Stick model in which smolts/female (the “α” parameter) remains constant across
female abundances until smolt capacity (K) is reached (i.e., smolt production increases linearly
as females increase and then plateaus at K); and (2) a variant of the Beverton-Holt function in
which smolts/female increases more steeply at low female abundance than assumed under the
Hockey-stick model, but at a declining rate such that the Beverton-Holt curve meets the HockeyStick curve at the inflection (K), which is again the maximum smolt production. To select the
smolt production model, click on the drop-down list in cell B4, and select a “1” for Hockey-Stick
or “2” or Beverton-Holt.
Model users also have the option to assume a fixed “α” for the Hockey-stick model (cell B12)
instead of the default “α” which is estimated using the formula α=K/N*, where N* is the number
of female spawners needed to fully seed the habitat which is a function of stream length. To do
this, simply click on cell B12 and select “1” for the females/km function or “2” for the fixed α
option. The value for the fixed α option can be specified by the user in cell B15 (default = 40
smolts per female). By modifying the values in cells B4 and B12, model users can specify each
of the four stock-recruitment functions as summarized in Table 4 and described in detail in the
Final Report.
Alternative choices for parr capacity estimates are also provided (B8 and B9, with data
beginning in column AG). Parr capacity estimates can be modified by an optional alkalinity
scalar by selecting a “1” from the drop-down list in cell B8. Similarly, the form of the
temperature-capacity scalar can be modified by entering the appropriate value in cell B9. Three
different options are available for the temperature-capacity function, corresponding with
differences in the assumed lower and upper temperature thresholds (i.e. temperatures at which
the capacity scalar equals 0.95 and 0.05). Model users must enter a “1” for temperature
thresholds of 15°C and 22°C, a “2” for thresholds of 16°C and 23°C, and a “3” for thresholds of
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17°C and 24°C. A detailed description of the alkalinity and temperature capacity scalars are
provided in the Final Report.
Although the various options in the “Subbasin Inputs” sheet provide a large amount of flexibility
in the tributary smolt production functions, we emphasize that some of these options are tentative
and exploratory in nature. These aspects of the model have been a recent “work-in-progress”
designed primarily to assess some underlying assumptions that will be resolved and revised in
future versions of the model.
Table 4. Optional stock-recruitment functions used in the model to predict tributary smolt production.
Options
Stock-recruit
form
Spawners at full
seeding
(N*)
Smolts per spawner at low
seeding (α)
Option 1
(default)
Hockey stick
Function of stream
length
Option 2
Hockey stick
N* = K/α
Fixed α
(default 40 smolts/spawner)
Option 3
Beverton-Holt
Same as Option 1
Scaled value of Option 1 (a = c*α)
Option 4
Beverton-Holt
Same as Option 2
Scaled value of Option 2 (a = c*α)
α
/N*
Note: c = 1.5 under default model settings.
REMAINING SHEETS
These sheets contain model functions and supporting flow and temperature data that should NOT
be manipulated by the user. They provide opportunity for the user to view model calculations.
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Figure 4. Depiction of the “Subbasin Inputs” sheet in the IMF. Smolt production functions and parr capacity estimates can be modified by changing the
parameters circled in red.
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