SacPAS: Central Valley Prediction & Assessment of Salmon

UW Columbia Basin Research
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SacPAS Fish Model v.2.1:  Spawning to Emergence and In-river Migration  

Beta version for testing and evaluation This model is in testing phase. Currently it works best with a modern browser.

WARNING: Certain functionality may not be available in older browsers.

The SacPAS fish modeling process begins with egg deposition at the time of spawning. Development rate and survival can be modeled by various methods to determine fry emergence from the gravel. On this page you can control temperature inputs, redd counts/timing/location and survival details for egg development modeling.

Developed by:
W. Nicholas Beer CBR,UW

You can skip emergence modeling and input fish directly into the migration model.
You can model egg development in other California rivers.

Temperature data inputs 

Historic (KWK to CCR):
Historic Single Site:   Note.

Input or upload
READ about formats. Temperature and redd counts share a format. Both upload and input formats are multi-column, comma separated variables. Day-of-year is first column. Blocks of days can be condensed with format: "first_day:final_day" Subsequent columns are values at different river positions identified by River Kilometer.

Column name format MUST be: "RKMxxx" where xxx is numeric. E.g.Day,RKM483,RKM479,...

2 years worth of temperature values are required due to the calendar-year-spanning life history of Winter Run Chinook Salmon. If you Upload data, it will be placed in the text area as input values awaiting "Run".

For plotting purposes, temperatures outside of the selected range are truncated. This does not affect calculations.

To use "Density by Reach": You must query the database OR upload redds with specific headers:

RKM483 = Keswick to ACID dam (5.5 Km)
RKM479 = ACID dam to Hwy44 (3.3 Km)
RKM470 = Hwy44 to Airport Rd. (19.7 km)

"Plot days" and "RKM range" control plotting of temperature heatmap and timeseries.

TCrit is the temperature below which there is no temperature induced mortality.

"Crit period" is the critical number of days prior to and including hatch day when temperature exposure is computed.

"Crit type" selects how the exposure is identified during the critical period.

Use SHINY Tool to create temps.


Units: Centigrade Farenheit

Winter Chinook redd inputs

Historic Look-up locations
Input or upload
READ about formats. Temperature and redd counts share a format. Both upload and input formats are multi-column, comma separated variables. Day-of-year is first column. Blocks of days can be condensed with format: "first_day:final_day" Subsequent columns are values at different river positions identified by River Kilometer.

Column name format MUST be: "RKMxxx" where xxx is numeric. E.g.Day,RKM483,RKM479,...

2 years worth of temperature values are required due to the calendar-year-spanning life history of Winter Run Chinook Salmon. If you Upload data, it will be placed in the text area as input values awaiting "Run".

For plotting purposes, temperatures outside of the selected range are truncated. This does not affect calculations.

To use "Density by Reach": You must query the database OR upload redds with specific headers:

RKM483 = Keswick to ACID dam (5.5 Km)
RKM479 = ACID dam to Hwy44 (3.3 Km)
RKM470 = Hwy44 to Airport Rd. (19.7 km)

"Plot days" and "RKM range" control plotting of temperature heatmap and timeseries.

TCrit is the temperature below which there is no temperature induced mortality.

"Crit period" is the critical number of days prior to and including hatch day when temperature exposure is computed.

"Crit type" selects how the exposure is identified during the critical period.



Survival to RBDD (Temperature)

Eggs sensitive prior to hatching
   Time to hatching method:
   Default Use ATUs (°C days)
TCrit: °C = °F
Crit days:
b (rate): b(rate) = 0.5 applies to "Eggs sensitive prior to hatching" (the default).

This is daily mortality rate when the critical temperature is exceeded, but only applies during the hatching critical period.

°C-1d-1 = °F-1d-1
Eggs sensitive ALL incubation
TCrit: °C = °F
b (rate): b(rate) = 0.0239 applies to "Eggs sensitive ALL incubation" from Martin et al. 2017. This mortality rate is applied for any day during the entire incubation period when the temperature goes above the critical temperature.
°C-1d-1 = °F-1d-1

Survival to RBDD (Other factors)

Beverton-Holt (2018)
Base rate: (maximum survival)
Carry cap: per KM (averaged by reach).
Beverton-Holt (2017)
Base rate: (maximum survival)
Carry cap: total redds.
Original paper: 9107 spawners.
Linear (SRTT/Martin 2016)
Base rate: (maximum survival)
Rate per redd:
Original paper: rate per spawner = -0.0000188.
None. Only temperature effects
 A Heat Map here.
Show above:

 A Temperature Plot here.
Plot days to

RKM range to
Temp range °C:
Hatching Critical type: Critical Value type affects display of exposure metrics. During the Critical period near hatching: Show the mean or the maximum temperature.

Run egg model.

Redd dewatering (optional)

NO dewatering
Dewater w/ observed KWK flows  (no boards @RBDD)
Dewater w/ Input or Upload  (no boards @RBDD)

Column:
Units: CFS KCFS.


More controls and information below.
-- Additional Details--

Results summary

-- Show Additional Details --

Summary results

Redd distribution

Pre-hatching exposure

All incubation exposure

Emergence timing

Hatch timing

Survivals to emergence

-- Download CSV file --

Summary results

Redd distribution

Pre-hatching exposure

All incubation exposure

Emergence timing

Hatch timing

Survivals to emergence

Temperatures


Chinook egg to emergence timing model

Mechanistic (Beer and Anderson 1997): Egg mass mg.
Empirical (Jensen et al. 1999)
Power law (Beacham/Murray 1990) Days = e10.404 - 2.043*log(T°C + 7.575)
Linear (Zeug et al. 2012): Target ATUs degree C days.

Additional inputs

Eggs per Redd Oppenheim (2014)
-- Further information --

Details, clarification, usage tips, and FAQs...(HTML)

"Using river temperature to optimize fish incubation
metabolism and survival (Anderson 2018) (PDF)"

Methods to compute time to hatching (PDF)

Temperature profile maker (SHINY)

Explore Egg/Fry survival models (SHINY)

View egg growth models comparison (PNG)

SHO-WR: Winter Run Chinook salmon management site (SHINY)


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POC: web@cbr.washington.edu

SacPAS: Central Valley Prediction & Assessment of Salmon, University of Washington, Columbia Basin Research, www.cbr.washington.edu/sacramento/

Monday, 14-Oct-2019 10:13:03 PDT