The Smolt Passage Inseason Forecasts predict the arrival distributions of stocks of outmigrating juvenile salmon at several monitoring sites along the Snake and Columbia Rivers. The tool uses "real time" information about the current status of the runs along with current hydrographic information to predict the future progress of the migrating fish.

For the real time analysis, we use PIT tag, Smolt Index and hydrosystem data. In addition, stock-specific estimates of arrival distributions at the lower dams use flow forecasts provided by the Bonneville Power Administration and projected system operations (spill plans, transport operations, etc.) - taking into account the fraction of fish removed from the system for transport.

Current transport operations require that all fish collected at Snake River transport projects (Lower Granite, Little Goose, and Lower Monumental dams) be transported, except for a small fraction returned to the river at Lower Granite for a transport survival study. Any changes of these strategies will be incorporated into forecasts.

Throughout the migration season, the predictions are updated daily based on daily updated information. This tool is intended to provide information to the public and to help managers in decisions about mitigation efforts such as flow augmentation, spill scheduling and fish transportation. By providing current information on the status of particular salmon runs, the managers will be able to operate the Columbia River system in a manner that will maximize salmon survival while minimizing the costs of mitigation procedures.

The Smolt Passage Inseason Forecasts utilizes two separate programs to generate downstream passage distributions:

RealTime
RealTime uses an empirical pattern matching routine to predict arrival distributions at the first detection point in the migratory route (usually Lower Granite Dam on the Snake River) for a wide variety of wild salmon stocks.

COMPASS (implemented 2007)
The Comprehensive Passage (COMPASS) model takes the predictions from RealTime and uses hydrological, fish behavioral and dam geometry information to simulate the movement and survival of juvenile salmonids through the remainder of the Columbia River system. The downstream passage component of COMPASS represents downstream migration and survival of salmon populations through the Snake and Columbia rivers. It is written in the C programming language and was derived from CRiSP, a previous salmon passage model. COMPASS computes release-specific daily fish passage at all river segments and dams. The model is composed of four submodels: dam passage, reservoir survival, travel time, and hydrological processes. Parameter values and stock calibration provided by NOAA Fisheries.

CRiSP1 (used through 2006)
The Columbia River Salmon Passage model takes the predictions from RealTime and uses hydrological, fish behavioral and dam geometry information to simulate the movement and survival of juvenile salmonids through the remainder of the Columbia River system.

Program RealTime uses spill-adjusted detections of PIT-tagged fish to make predictions of run-timing and passage distribution of wild Snake River runs-at-large at Lower Granite. The COMPASS model uses the predicted passage distribution at Lower Granite to predict the passage at Little Goose, Lower Monumental, Ice Harbor, and McNary dams. Comparisons of PIT-tag counts and runs-at-large at Lower Granite Dam for historical years are available for wild subyearling fall chinook salmon (1993-1998), wild yearling spring/summer chinook salmon (1993-1999), and wild steelhead trout (1991-1999).

In addition, the program RealTime uses spill-adjusted detections of PIT-tagged fish to make predictions of run-timing and passage distribution at McNary of specific ESU populations in the Columbia and Snake basins. The COMPASS model uses the predicted passage distribution at McNary to predict the passage at John Day, The Dalles, and Bonneville dams.

Yearling Chinook Composite Stocks

Composites are the combined data of the streams they include, treated as a single stock.

• Select Composite Wild (2008 - present) - determined annually based on wild spring/summer stocks released above Lower Granite that have at least 3 historical years with 100 detections and a sufficient release size in the current year to expect 100 detections based on historical detection percentages for the stock.
• PIT-Tagged Wild Run-At-Large - all wild spring/summer stocks above Lower Granite.

For previous compositions of the composite stocks, please refer to the Publications web page for the post season analyses.

ESU Populations

ESU (Evolutionarily Significant Unit) is the distinct populations listed for protection under the Endangered Species Act (ESA). See ESA Listing Pages, Protected Resources, NMFS, NOAA, for detailed information on ESA listings and ESU status and descriptions of specific stocks.

• Wild Snake River Spring/Summer Chinook ESU consists of 39 local spawning populations (subpopulations) of the following: Tucannon River Basin, Snake River Basin, Salmon River Basin, Lemhi, Pahsimeroi, Grande Ronde, and Imnaha River Basin, and includes all locations above river kilometer 522.000.
• Snake River Wild Fall Chinook ESU consists of the production from spawning populations of fall chinook in the Snake, Tucannon, Clearwater, Salmon, Imnaha and Grande Ronde Rivers.
• Snake River Sockeye ESU currently consists of Redfish Lake stock sockeye in the captive broodstock program at Eagle and Beef Creek hatcheries, and the hatchery fish released from this program into Redfish Lake, Pettit Lake, Pettit Creek, and Redfish Lake Creek; wild residual sockeye in Redfish Lake and their out-migrating progeny; any naturally-spawned progeny of broodstock adults released into Redfish Lake in 1993-94; and any adults returning to Redfish or Pettit Lake.
• Snake River Wild Steelhead ESU includes all naturally spawned populations of Summer run steelhead (and their progeny) in the Snake River Basin.
• Upper Columbia River Steelhead ESU includes all naturally spawned populations of steelhead (and their progeny) upstream from the Yakima River, Washington (above river kilometer 539), to the United States-Canada border and the Wells Hatchery stock of Summer run steelhead.
• Chinook Fall, Upper Columbia River consists of PIT tagged chinook where the run is designated as Unknown or Fall, the rearing type is designated as Unknown or Wild, the release site is on the Columbia River above the Snake Confluence, and the McNary detection date occurs after June 20^th of the same year the fish was released.

Subyearling Chinook

Since 2007, Subyearling Chinook predictions are generated by Program RealTime only. The predictions are based on detections of PIT-tagged wild subyearling fall chinook tagged and released from April to July, from 1993 to the present, by William P. Connor (U.S. Fish and Wildlife Service, Dworshak Fisheries Complex), with releases made along the Snake River between RK 268 and RK 224. Detections of these subyearling chinook at Lower Granite constitute a fairly good representation of the subyearling fall chinook run at large, particularly during the first and middle portions of the run. A Comparison of Historical Years (1993-1998) for PIT tag detections at Lower Granite Dam.

Sockeye

Predicted by Program RealTime only. For the year 2002, there were no PIT-tagged hatchery sockeye releases from Alturas Lake (ALTURL) or Redfish Lake (REDFL). Passage predictions are based on a composite of PIT-tagged hatchery sockeye releases from Alturas Lake Creek (ALTULC), Redfish Lake Trap (RLCTRP) and Sawtooth Trap (SAWTRP).

Combined Passage Indices at Rock Island, Lower Granite, McNary, John Day, and Bonneville dams

Program RealTime predictions are based upon the historical outmigration pattern detected at a specific point, and its estimation accuracy therefore depends on regularity in these patterns. The annual patterns of fish passage over McNary Dam are influenced by a number of elements, such as the transportion of fish by barge around upriver dams (Lower Granite, Lower Monumental, and Little Goose Dams), the release of hatchery fish at various times in the season, etc. This is true of Rock Island Dam as well, where irregularities in the patterns of fish passage over Rock Island Dam occur largely due to hatchery releases upriver from the dam. These unpredictable events increase the variability of outmigration patterns from year to year, making accurate predictions more difficult and resulting in wider confidence intervals for the RealTime predictions.

Notes on 2000 Inseason Forecasts

Fish Passage Center (FPC) passage indices of wild fish were once used by the RealTime forecasting project to make run-timing predictions of runs-at-large of ESA-listed fish to Lower Granite Dam. Beginning in 1999 with subyearling fall chinook salmon, and continuing this year with yearling chinook salmon and steelhead trout, hatcheries have released unmarked fish into the rivers, rendering obsolete the FPC's categorization by rearing-type. Currently, the RealTime forecasting project is using spill-adjusted detections of PIT-tagged fish to make predictions of run-timing and passage distribution of wild Snake River runs-at-large. Comparisons of PIT-tag counts and runs-at-large are available for wild subyearling fall chinook salmon, wild yearling spring/summer chinook salmon, and wild steelhead trout.

Notes on 1999 Inseason Forecasts

On June 3 and 5, 1999, Captain John Landing and Big Canyon hatcheries released 670,000 unmarked subyearling chinook above Lower Granite Dam. Without marks, the Fish Passage Center (FPC) is unable to distinguish these hatchery-reared fish from wild runs. Our methodology until that time depended on the accurate daily counts of wild fish from the FPC to reliably forecast the wild subyearling outmigration status. Forecasts for previous years based on Smolt Indices can be viewed from the Archive page.

After June 6, the 1999 forecasts were based on detections of PIT-tagged wild subyearling fall chinook at Lower Granite Dam. Subyearling chinook were tagged and released at regular intervals from April into July, or until water temperatures neared 20°C or catches neared zero, from 1993 to the present, by William P. Connor (U.S. Fish and Wildlife Service, Dworshak Fisheries Complex) with releases made along the Snake River between RK 268 and RK 224. Detections of these subyearling chinook at Lower Granite constitute a fairly good representation of the subyearling fall chinook run at large, particularly during the first and middle portions of the run.

Critical Parameters Used by COMPASS for Migration Seasons 2008-2009

Fish Guidance Efficiency

logit(FGE) = ₀ + ₁ * F_PH + ₂ * day

Spill Passage Efficiency

logit(P_SPILL) = ₀ + ₁ * logit(F_SPILL) + ₂ * F_TOTAL

For the full discussion of FGE and SPE, please refer to the Comprehensive Passage (COMPASS) Model Review DRAFT manual, 29 February 2008.

2008-2009 Critical Parameters Used by COMPASS
Project	Yearling Chinook					Steelhead
	Mortality					Mortality
	RSW	Spill	Sluiceway	Bypass	Turbine	RSW	Spill	Sluiceway	Bypass	Turbine
Lower Granite a
Little Goose b	0.02	0.028		0.036	0.077	0.02	0.028		0.050	0.070
Lower Monumental b	0.02	0.039		0.078	0.119	0.02	0.039		0.078	0.119
Ice Harbor	0.030	0.035		0.003	0.129	0.015	0.010		0.000	0.129
McNary b	0.021	0.038		0.087	0.097	0.021	0.041		0.048	0.110
John Day b	0.021	0.036		0.035	0.201	0.021	0.027		0.118	0.201
The Dalles		0.076	0.006		0.182		0.076	0.006		0.182
Bonneville		0.031	0.072		0.052		0.033	0.041		0.047
Bonneville II				0.020	0.052				0.047	0.122
a. For Inseason Forecasts, Lower Granite Dam is not modeled in COMPASS. Fish passage distribution and timing input into the COMPASS model at Lower Granite Dam is produced by Program RealTime based on historic and current PIT Tag detections. b. RSW parameters implemented for 2009 migration season.

Critical Parameters Used by CRiSP for Migration Seasons 1996-2006

2003-2006 Critical Parameters Used by CRiSP
Project	Yearling Chinook					Steelhead					Subyearling Chinook
	FGE	Spill Eff.	Mortality			FGE	Spill Eff.	Mortality			FGE	Spill Eff.	Mortality
			Turbine	Bypass	Spill			Turbine	Bypass	Spill			Turbine	Bypass	Spill
Lower Granite	75%	NL	7%	2%	2%	81%	NL	7%	2%	2%	53%	NL	10%	2%	2%
Little Goose	78%	NL	8%	1%	0%	81%	NL	8%	5%	0%	53%	NL	10%	2%	2%
Lower Monumental	49%	NL	8%	5%	3%	82%	NL	7%	7%	3%	49%	NL	10%	2%	2%
Ice Harbor	54%	1.0 L	10%	2%	2%	93%	1.0 L	1%	2%	2%	54%	1.0 L	10%	2%	5%
McNary	83%	1.0 L	10%	2%	2%	89%	1.0 L	10%	2%	2%	62%	1.0 L	10%	3%	2%
John Day	73%	1.6 L	10%	2%	2%	85%	1.6 L	10%	2%	2%	32%	2.0 L	10%	2%	2%
The Dalles	12%	2.0 L	19%	4%	5%	3%	2.0 L	19%	5%	5%	10%	1.8 L	16%	7%	6%
Bonneville	39%	1.0 L	10%	10%	2%	41%	1.0 L	10%	10%	2%	9%	1.0 L	10%	18%	2%
Bonneville II	48%	-	10%	2%	-	48%	-	10%	2%	-	28%	-	6%	2%	-

2000-2002 Critical Parameters Used by CRiSP
Project	Yearling Chinook					Steelhead					Subyearling Chinook
	FGE	Spill Eff.	Mortality			FGE	Spill Eff.	Mortality			FGE	Spill Eff.	Mortality
			Turbine	Bypass	Spill			Turbine	Bypass	Spill			Turbine	Bypass	Spill
Lower Granite	78%	1.0	7%	2%	2%	81%	1.0	7%	2%	2%	53%	1.0	7%	2%	2%
Little Goose	82%	1.0	7%	2%	2%	81%	1.0	7%	2%	2%	53%	1.0	7%	2%	2%
Lower Monumental	61%	1.2	7%	2%	2%	82%	1.2	7%	2%	2%	49%	1.2	7%	2%	2%
Ice Harbor	71%	1.0	7%	2%	2%	93%	1.0	7%	2%	2%	46%	1.0	7%	2%	2%
McNary	95%	1.0	7%	2%	2%	89%	1.0	7%	2%	2%	62%	1.0	7%	2%	2%
John Day	64%	1.0	7%	2%	2%	85%	1.2	7%	2%	2%	34%	1.2	7%	2%	2%
The Dalles	46%	2.0	7%	2%	2%	40%	2.0	7%	2%	2%	46%	2.0	7%	2%	2%
Bonneville	38%	1.0	7%	2%	2%	41%	1.0	7%	2%	2%	16%	1.0	7%	2%	2%
Bonneville II	44%	-	7%	2%	0%	48%	-	7%	2%	0%	18%	-	7%	2%	0%

1996-1999 Critical Parameters Used by CRiSP
Project	Yearling Chinook					Steelhead					Subyearling Chinook
	FGE	Spill Eff.	Mortality			FGE	Spill Eff.	Mortality			FGE	Spill Eff.	Mortality
			Turbine	Bypass	Spill			Turbine	Bypass	Spill			Turbine	Bypass	Spill
Lower Granite	56%	1.0	7%	2%	2%	76%	1.0	7%	2%	2%	35%	1.0	7%	2%	2%
Little Goose	60%	1.0	7%	2%	2%	81%	1.0	7%	2%	2%	30%	1.0	7%	2%	2%
Lower Monumental	55%	1.2	7%	2%	2%	63%	1.2	7%	2%	2%	31%	1.2	7%	2%	2%
Ice Harbor	54%	1.0	7%	2%	2%	77%	1.0	7%	2%	2%	31%	1.0	7%	2%	2%
McNary	72%	1.0	7%	2%	2%	62%	1.0	7%	2%	2%	40%	1.0	7%	2%	2%
John Day	58%	1.0	7%	2%	2%	72%	1.2	7%	2%	2%	26%	1.2	7%	2%	2%
The Dalles	34%	2.0	7%	2%	2%	36%	2.0	7%	2%	2%	43%	2.0	7%	2%	2%
Bonneville	30%	1.0	7%	2%	2%	65%	1.0	7%	2%	2%	15%	1.0	7%	2%	2%
Bonneville II	54%	-	7%	2%	0%	52%	-	7%	2%	0%	24%	-	7%	2%	0%

The Adult Passage Inseason Forecasts predict the arrival distributions of adult chinook migrating upstream at several monitoring sites along the Snake and Columbia Rivers. The tool uses "real time" information about the current observed counts at Bonneville Dam along with current hydrographic information to predict the future progress of the migrating fish. For the real time analysis, we use adult passage counts and hydrosystem data provided by the U.S. Army Corps of Engineers and flow forecasts provided by the Bonneville Power Administration.

Throughout the migration season, the predictions are updated daily based on daily updated information. This tool is intended to provide information to the public and to fish managers.

The Adult Passage Inseason Forecasts utilizes two separate programs to generate upstream passage distributions:

Escapement Projector
The Escapement Projector is pattern matching algorithm that compares the current year's data to historical years of adult passage counts to predict arrival distributions at Bonneville Dam.

Adult Upstream Migration
The Adult Upstream Migration model takes the predictions from the Escapement Projector and uses information on reservoir and dam passage, fallback, straying and energy consumption with a physical river description and environmental data to simulate the movement and survival of adult salmonids from Bonneville through the remainder of the Columbia River system to the Snake or Upper Columbia river.

Adult Peak
The Adult Peak Predictor generates predictions for spring Chinook at Bonneville Dam that begin with a preseason prediction of run timing from a Genetics and Environment Timing model and a preseason run-size prediction based on the previous year's Jack returns. The daily, inseason methods to simultaneously estimate distribution parameters from the observations-to-date include use of up-to-date environmental conditions, historical bounds on parameters, and the mathematical properties of the gaussian distribution. The complete run of Chinook in the Columbia River is the sum of three sub-runs—spring, summer and fall—each well characterized by a gaussian distribution. A manuscript detailing the Genetics and Environment Timing model is in review (Anderson and Beer, submitted to Ecological Applications). For more information, please refer to Run timing of adult Chinook salmon passing Bonneville dam on the Columbia River. New in 2009, the run timing update is used as an input to the stock separation component of the AUM model.

Run Size Confidence Intervals

Starting with the 2005 Adult Fall Chinook Run Size forecasts, a new method was employed to calculate the 90% confidence intervals for the next day cumulative run forecast and the final day total run size forecast. Mean squared error (MSE) of the total run forecast was calculated using deviations of actual runs from run predictions made for each day in all historical years (1982-present). Run predictions were generated using the same methods employed for the current year's forecast. MSE is used to estimate the standard error and 90% confidence intervals (depicted by the gray lines -) of the run forecast. These same methods are applied for the next day cumulative run size forecast.

Stock Specific Migration Timing

For information on the preseason forecasts and methods, please refer to Preseason adult spring Chinook peak arrival timing and run size prediction for Bonneville Dam, 2009.

Since 2005, the Daily Run Size & Passage Prediction (Date-based) is for the period March 15 - June 15 to best match the Columbia River Fisheries (CRM) spring management period. The U.S. v Oregon Technical Advisor Committee 2009 Upriver Spring Chinook Forecast is 298,900 fish.

Starting with the 2005 migration season, the Passage Predictions are available for four stocks: Snake River, Upper Columbia River, Lower Columbia River, and Hanford Reach/Yakima. Percent of the run arriving at Bonneville Dam is based on historic run timing and observed visual count data (courtesy of U.S. Army Corps of Engineers, NWD). Stock separation of the run at Bonneville is based on stock composition, reach conversion rates, and run-timing of selected PIT-tagged stocks for all available years of adult detections at PIT Tag observation sites.

• Snake River: Predicted percent passage of Adult Chinook through the projects on the Columbia mainstem and the lower Snake River. Arrivals to the upstream dams (The Dalles, John Day, McNary, Ice Harbor, Lower Monumental, Little Goose, and Lower Granite) are forecast with the Adult Upstream Model.
• Upper Columbia River: Predicted percent passage of Adult Chinook through the projects on the Columbia River with destination above Priest Rapids Dam. Arrivals to the upstream dams (The Dalles, John Day, McNary, Priest Rapids, Wanapum, Rock Island, Rocky Reach, Wells) are forecast with the Adult Upstream Model.
• Lower Columbia River: Predicted percent passage of Adult Chinook through the projects on the Lower Columbia River with destination above Bonneville but not above McNary Dam. Arrivals to the upstream dams (The Dalles, John Day) are forecast with the Adult Upstream Model.
• Hanford Reach/Yakima: Predicted percent passage of Adult Chinook through the projects on the Columbia River with destination above McNary Dam but not above Priest Rapids Dam, these include Yakima and Hanford Reach stocks. Arrivals to the upstream dams (The Dalles, John Day, McNary) are forecast with the Adult Upstream Model.

Temperature Forecasts

The "real time" Temperature Algorithm was originally developed in 1996 to predict the current year's water temperature values. The Temperature Algorithm is a multi-method algorithm that uses historical mean data, year-to-date observed data, and a forecast of flow to predict temperature values at multiple locations in the Columbia and Snake Rivers. Lower Granite, Priest Rapids, and The Dalles pools were selected as representative temperatures of the Snake, Mid-Columbia, and mainstem Columbia, respectively. Rock Island was added in 2001 due to the inconsistent reporting of temperature at Priest Rapids dam. Temperature predictions are run bimonthly during the juvenile migration season, April to September. The dotted black line on the forecast graphs indicates the date on which the forecast was produced. The observed data is updated daily which allows for the comparison of early forecasts to the actual observed values.

Output from the temperature forecasts are used as input to the Total Dissolved Gas forecasts as well as the Smolt Passage and Adult Passage forecasts.

Total Dissolved Gas Forecasts

Total Dissolved Gas forecasts are produced by the COMPASS model using gas production equations developed as a part of the U.S. Army Corps of Engineers "Gas Abatement Study." Gas production equations implemented in CRiSP included equations developed by Waterways Experiment Station (WES) and Columbia Basin Research. The equations predict tailwater gas production as a function of spill. Temperature forecasts, flow and spill forecasts, and year-to-date observed data are inputs to the gas modeling forecasts.