Russell W. Perry
Adam C. Pope
20230425
The North Delta Routing and Survival Management Tool (ver. 3.0, May 2026)
3.0
spreadsheet
Spreadsheet is based on:
Perry, R.W., Pope, A.C., Romine, J.G., Brandes, P.L., Burau, J.R., Blake, A.R., Ammann, A.J. and Michel, C.J., 2018. Flow-mediated effects on travel time, routing, and survival of juvenile Chinook salmon in a spatially complex, tidally forced river delta. Canadian Journal of Fisheries and Aquatic Sciences, 75(11), pp.1886-1901. https://doi.org/10.1139/cjfas-2017-0310
Perry, R.W., Brandes, P.L., Burau, J.R., Klimley, A.P., MacFarlane, B., Michel, C. and Skalski, J.R., 2013. Sensitivity of survival to migration routes used by juvenile Chinook salmon to negotiate the Sacramento-San Joaquin River Delta. Environmental Biology of Fishes, 96(2), pp.381-392. https://doi.org/10.1007/s10641-012-9984-6
https://doi.org/10.5066/P9OG5NX7
Understanding how routing modifications influence survival of juvenile Chinook salmon (Oncorhynchus tshawytscha) is complex because reach-specific survival and routing at key river junctions in the North Delta each have a different relationship with river flow. Therefore, to facilitate understanding of how routing modifications at key river junctions influence through-Delta survival, we developed this spreadsheet model to allow managers to explore the potential effects of modifying routing. The purpose is to provide a screening tool that allows managers to quickly run many different scenarios to understand how both routing and route-specific survival interact to affect overall survival through the Delta. In May 2026, version 3.0 was released, which allows managers to evaluate the sensitivity of through-Delta survival to different routing management actions at multiple locations in the North Delta. This tool may be useful in narrowing the range of potential scenarios that might be investigated using more complex modeling techniques (e.g., agent-based models) and eventually evaluated with field studies. Previous versions can be obtained from the authors.
To estimate survival and routing of juvenile Chinook salmon through the Sacramento-San Joaquin River Delta, California.
20071201
20110330
ground condition
None planned
Sacramento-San Joaquin River Delta
-121.9400
-121.2506
38.6040
37.7751
ISO 19115 Topic Category
biota
None
Salmon
USGS Metadata Identifier
USGS:6446bff0d34ee8d4adec6c01
None
Migration
Telemetry
Survival
None
Chinook salmon
Kingdom
Animalia
animals
Subkingdom
Bilateria
triploblasts
Infrakingdom
Deuterostomia
Phylum
Chordata
chordates
Subphylum
Vertebrata
vertebrates
Infraphylum
Gnathostomata
Superclass
Actinopterygii
ray-finned fishes
spiny rayed fishes
Class
Teleostei
Superorder
Protacanthopterygii
Order
Salmoniformes
salmons
Family
Salmonidae
salmonids
trouts and salmons
salmons
trouts
Subfamily
Salmoninae
Genus
Oncorhynchus
Pacific salmon
Species
Oncorhynchus tshawytscha
Chinook salmon
king salmon
TSN: 161980
None. Please see 'Distribution Info' for details.
None. Users are advised to read the dataset's metadata thoroughly to understand appropriate use and data limitations.
Russell W Perry
U.S. Geological Survey, NW-PACIFIC ISLAND REG
RESEARCH FISHERY BIOLOGIST
mailing address
5501 Cook Underwood Road
Cook
WA
98605
US
509-538-2942
509-538-2843
rperry@usgs.gov
Funding for the data and analysis were provided by:
California Department of Water Resources
U.S. Fish and Wildlife Service
U.S. Bureau of Reclamation
Delta Stewardship Council
Yes, the parameter estimates used for the model include estimates of uncertainty (95% Credible Intervals) provided on the "Model Parameters" tab of the spreadsheet.
The data are logically consistent and have been screened for errors and outliers.
The dataset uses parameter estimates from a statistical model to predict juvenile salmon survival and routing over a range of river flow conditions.
NA
NA
The statistical model parameter estimates used in this spreadsheet were estimated using a mark-recapture model applied to acoustic telemetry data of juvenile Chinook salmon migrating through the Sacramento-San Joaquin River Delta, California. More information is provided in Perry et al. (2013) and Perry et al. (2018) listed in the "Other Citation Details" section of this metadata.
20180101
"Model parameters" tab
Spreadsheet tab within Excel file (XLSX)
Producer Defined
Unnamed: 0
Name of model parameter.
Producer Defined
See "Model Metadata" tab in the spreadsheet for definition of each element of this column.
Lower95
Lower bound of 95% credible interval.
Producer Defined
NA
No Data
Producer defined
-8.81265
2.5645
Median
Median of posterior distribution of the parameter.
Producer Defined
NA
No Data
Producer defined
-3.559815
3.056515
Upper95
Upper bound of 95% credible interval.
Producer Defined
NA
No Data
Producer defined
-0.995313
5.74664
Mean
Mean of posterior distribution of the parameter.
Producer Defined
NA
No Data
Producer defined
-4.215915777
3.0816291
SD
Standard deviation of posterior distribution of the parameter.
Producer Defined
NA
No Data
Producer defined
0.009417319
3.052032652
MCerr
The Monte Carlo standard error.
Producer Defined
NA
No Data
Producer defined
0.000171936
0.179445546
MC%ofSD
The Monte Carlo standard error as a percentage of the standard deviation.
Producer Defined
NA
No Data
Producer defined
1.8
12.2
SSeff
Effective sample size
Producer Defined
NA
No Data
Producer defined
68
3134
AC.200
The auto-correlation of the sample.
Producer Defined
NA
No Data
Producer defined
-0.033120206
0.562133774
psrf
Potential scale reduction factor.
Producer Defined
NA
No Data
Producer defined
0.999646932
1.125591576
"Model Calculations" tab
Spreadsheet tab within Excel file (XLSX)
Producer Defined
Flow at Freeport
Flow of the Sacramento River at USGS gage 1144765
Producer Defined
5000
80000
Cubic feet per second
Std flow
Flow standardized by subtracting the mean flow and then dividing by its standard deviation
Producer Defined
-0.575
2.033
standard deviation
DCC pos
Position of the Delta Cross Channel Gate (0 = closed, 1 = open)
Producer Defined
0
1
Binary
SAC-FPT
Logit transform of reach specific survival for SAC-FPT -- Sacramento R. from city of Sacramento to Freeport
Producer Defined
1.552
3.547
FPT-J1
Logit transform of reach specific survival for FPT-J1 -- Sacramento R. from Freeport to junction with Sutter/Steamboat Sloughs
Producer Defined
2.717
4.256
J1-J2
Logit transform of reach specific survival for J1-J2 -- Sacramento R. from junction with Sutter/Steamboat to junction with DCC/Georgiana Slough
Producer Defined
2.717
4.256
J2-RIO
Logit transform of reach specific survival for J2-RIO -- Sacramento R. from junction with DCC/Georgiana to Rio Vista
Producer Defined
1.069
7.735
RIO-MAL
Logit transform of reach specific survival for RIO-MAL -- Sacrammento R. from Rio Vista to Chipps Island
Producer Defined
1.099
1.132
SUT
Logit transform of reach specific survival for SUT -- Sutter Slough from junction with Sac. R. to Miner Slough exit at Cache Slough complex
Producer Defined
-0.402
5.668
STM
Logit transform of reach specific survival for STM -- Steamboat Slough from junction with Sac. R. to exit at Cache Slough complex
Producer Defined
0.852
5.703
DCC
Logit transform of reach specific survival for DCC -- Delta Cross Channel from junction with Sac. R. to Lower Mokelumne R.
Producer Defined
-0.625
2.158
GEO
Logit transform of reach specific survival for GEO -- Georgiana Slough from junction with Sac. R. to Lower Mokelumne R.
Producer Defined
-0.073
5.231
INT
Logit transform of reach specific survival for INT -- "Interior Delta", all routes/channels from junction of Georgiana Sl. and Mokelumne R. to Chipps Island
Producer Defined
-0.507
-0.448
SAC-FPT.1
Reach specific survival for SAC-FPT -- Sacramento R. from city of Sacramento to Freeport
Producer Defined
0.825
0.972
FPT-J1.1
Reach specific survival for FPT-J1 -- Sacramento R. from Freeport to junction with Sutter/Steamboat Sloughs
Producer Defined
0.938
0.986
J1-J2.1
Reach specific survival for J1-J2 -- Sacramento R. from junction with Sutter/Steamboat to junction with DCC/Georgiana Slough
Producer Defined
0.938
0.986
J2-RIO.1
Reach specific survival for J2-RIO -- Sacramento R. from junction with DCC/Georgiana to Rio Vista
Producer Defined
0.744
1.0
RIO-MAL.1
Reach specific survival for RIO-MAL -- Sacrammento R. from Rio Vista to Chipps Island
Producer Defined
0.75
0.756
SUT.1
Reach specific survival for SUT -- Sutter Slough from junction with Sac. R. to Miner Slough exit at Cache Slough complex
Producer Defined
0.401
0.997
STM.1
Reach specific survival for STM -- Steamboat Slough from junction with Sac. R. to exit at Cache Slough complex
Producer Defined
0.701
0.997
DCC.1
Reach specific survival for DCC -- Delta Cross Channel from junction with Sac. R. to Lower Mokelumne R.
Producer Defined
0.349
0.896
GEO.1
Reach specific survival for GEO -- Georgiana Slough from junction with Sac. R. to Lower Mokelumne R.
Producer Defined
0.482
0.995
INT.1
Reach specific survival for INT -- "Interior Delta", all routes/channels from junction of Georgiana Sl. and Mokelumne R. to Chipps Island,
Producer Defined
0.376
0.39
SUT.2
Routing linear predictor for Sutter Slough
Producer Defined
-0.864
1.556
STM.2
Routing linear predictor for Steamboat Slough
Producer Defined
-1.155
1.596
DCC.2
Routing linear predictor for the Delta Cross Channel.
Producer Defined
-4.083
-0.771
GEO.2
Routing linear predictor for Georgiana Slough.
Producer Defined
-9.63
-1.842
SUT.3
Routing probability for the baseline scenario for Sutter Slough.
Producer Defined
0.134
0.244
STM.3
Routing probability for the baseline scenario for Steamboat Slough.
Producer Defined
0.1
0.255
SAC_J1
Routing probability for the baseline scenario for the Sacramento River at its junction with Sutter and Steamboat Slough.
Producer Defined
0.501
0.766
DCC.3
Routing probability for the baseline scenario for the Delta Cross Channel
Producer Defined
0
0
GEO.3
Routing probability for the baseline scenario for Georgiana Slough
Producer Defined
0.305
0.4
SAC_J2
Routing probability for the baseline scenario for for the Sacramento River at its junction with Georgiana Slough and the Delta Cross Channel
Producer Defined
0.6
0.695
SUT.4
Modified routing probability based on user-defined settings for Sutter Slough.
Producer Defined
0.134
0.244
SUT_dif
Difference between basiline and modified routing probability based on user-defined settings for Sutter Slough
Producer Defined
0
0
STM_new
Intermediate calculattion for modified routing probability based on user-defined settings for Steamboat Slough
Producer Defined
0.1
0.255
SAC_J1_new
Intermediate calculation for modified routing probability based on user-defined settings for Sacramento River at junction with Sutter and Steamboat Slough
Producer Defined
0.501
0.766
STM.4
MNodified routing probability based on user-defined settings for Steamboat Slough
Producer Defined
0.1
0.255
SAC_J1.1
modified routing probability based on user-defined settings for Sacramento River at junction with Sutter and Steamboat Slough
Producer Defined
0.501
0.766
chksum J1
Checks that the sum of routing probabilities = 1.
Producer Defined
1
1
DCC.4
Modified routing probability based on user-defined settings for the Delta Cross Channel
Producer Defined
0
0
GEO.4
Modified routing probability based on user-defined settings for Georgiana Slough.
Producer Defined
0.305
0.4
SAC_J2.1
Modified routing probability based on user-defined settings for Sacramento River at junction with Georgiana Slough and the Delta Cross Channel
Producer Defined
0.6
0.695
chksum J2
Checks that the sum of routing probabilities = 1.
Producer Defined
1
1
SUT.5
Survival to Chipps Island for baseline scenario for fish using Sutter Slough
Producer Defined
0.233
0.722
STM.5
Survival to Chipps Island for baseline scenario for fish using Steamboat Slough
Producer Defined
0.407
0.722
DCC.5
Survival to Chipps Island for baseline scenario for fish using the Delta Cross Channel
Producer Defined
0
0
GEO.5
Survival to Chipps Island for baseline scenario for fish using the Georgiana Slough
Producer Defined
0.131
0.366
SAC
Survival to Chipps Island for baseline scenario for fish using the Sacramento River.
Producer Defined
0.405
0.714
YOLO
Baseline probability for using the Yolo bypass migration route.
Producer Defined
0
0
SUT.6
Baseline probability for using the Sutter Slough migration route.
Producer Defined
0.134
0.244
STM.6
Baseline probability for using the Steamboat Slough migration route.
Producer Defined
0.1
0.255
DCC.6
Baseline probability for using the Delta Cross Channel migration route.
Producer Defined
0
0
GEO.6
Baseline probability for using the Georgiana Slough migration route.
Producer Defined
0.153
0.307
SAC.1
Baseline probability for using the Sacramento River migration route.
Producer Defined
0.348
0.474
chksum
Checks that sum of all migration route probabilities = 1
Producer Defined
1
1
YOLO.1
Modified probability for using the Yolo Bypass migration route.
Producer Defined
0
0
SUT.7
Modified probability for using the Sutter Slough migration route.
Producer Defined
0.134
0.244
STM.7
Modified probability for using the Steamboat Slough migration route.
Producer Defined
0.1
0.255
DCC.7
Modified probability for using the Delta Cross Channel migration route.
Producer Defined
0
0
GEO.7
Modified probability for using the Georgiana Slough migration route.
Producer Defined
0.153
0.307
SAC.2
Modified probability for using the Sacramento River migration route.
Producer Defined
0.348
0.474
chksum.1
Checks that sum of all migration route probabilities = 1
Producer Defined
1
1
Baseline
Baseline survival for all migration routes from the starting location to Chipps Island.
Producer Defined
0.298
0.665
Modified
Modified survival for all migration routes from the starting location to Chipps Island.
Producer Defined
0.298
0.665
Difference
Difference in survival between baseline and modified
Producer Defined
0
0
Understanding how routing modifications influence survival of juvenile salmon is complex because reach-specific survival and routing at key river junctions in the North Delta each have a different relationship with river flow. Therefore, to facilitate understanding of how routing modifications at key river junctions influence through-Delta survival, we developed this spreadsheet model to allow managers to explore the potential effects of modifying routing. The purpose is to provide a screening tool that allows managers to quickly run many different scenarios to understand how both routing and route-specific survival interact to affect overall survival through the Delta. In addition, this tool allows managers to evaluate the sensitivity of through-Delta survival to different routing management actions at multiple locations in the North Delta. This tool may be useful in narrowing the range of potential scenarios that might be investigated using more complex modeling techniques (e.g., agent-based models) and eventually evaluated with field studies.
Perry, R.W., Pope, A.C., Romine, J.G., Brandes, P.L., Burau, J.R., Blake, A.R., Ammann, A.J. and Michel, C.J., 2018. Flow-mediated effects on travel time, routing, and survival of juvenile Chinook salmon in a spatially complex, tidally forced river delta. Canadian Journal of Fisheries and Aquatic Sciences, 75(11), pp.1886-1901. https://doi.org/10.1139/cjfas-2017-0310
Perry, R.W., Brandes, P.L., Burau, J.R., Klimley, A.P., MacFarlane, B., Michel, C. and Skalski, J.R., 2013. Sensitivity of survival to migration routes used by juvenile Chinook salmon to negotiate the Sacramento-San Joaquin River Delta. Environmental Biology of Fishes, 96(2), pp.381-392. https://doi.org/10.1007/s10641-012-9984-6
GS ScienceBase
U.S. Geological Survey
mailing address
Denver Federal Center, Building 810, Mail Stop 302
Denver
CO
80225
United States
1-888-275-8747
sciencebase@usgs.gov
Unless otherwise stated, all data, metadata and related materials are considered to satisfy the quality standards relative to the purpose for which the data were collected. Although these data and associated metadata have been reviewed for accuracy and completeness and approved for release by the U.S. Geological Survey (USGS), no warranty expressed or implied is made regarding the display or utility of the data for other purposes, nor on all computer systems, nor shall the act of distribution constitute any such warranty.
Digital Data
https://doi.org/10.5066/P9OG5NX7.
None
20260522
Russell W Perry
U.S. Geological Survey, NW-PACIFIC ISLAND REG
RESEARCH FISHERY BIOLOGIST
mailing address
5501 Cook Underwood Road
Cook
WA
98605
US
509-538-2942
509-538-2843
rperry@usgs.gov
FGDC Biological Data Profile of the Content Standard for Digital Geospatial Metadata
FGDC-STD-001.1-1999