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Monitoring adult Chinook salmon upstream passage on Yuba River

General Information
Data Package:
Local Identifier:edi.1707.1
Title:Monitoring adult Chinook salmon upstream passage on Yuba River
Alternate Identifier:DOI PLACE HOLDER
Abstract:

Adult salmonid data on the Yuba River is collected and managed by the Yuba Water Agency and the California Department of Water Resources. Upstream passage data is collected year-round at Daguerre Point Dam, 24 hours a day and 7 days a week. Data from this monitoring is modeled by Brian Poxon and Paul Bratovich to produce estimates of adult escapement (upstream passage) abundance. These data will also be used to inform the development of a juvenile production estimate (JPE) for spring-run Chinook salmon in the Sacramento River Watershed.

Short Name:Yuba River Chinook Upstream Passage
Publication Date:2024-07-11
For more information:
Visit: DOI PLACE HOLDER

Time Period
Begin:
2004-03-01
End:
2023-02-28

People and Organizations
Contact:Vander Meulen, Jacob (Yuba Water Agency) [  email ]
Creator:Vander Meulen, Jacob (Yuba Water Agency)
Associate:Poxon, Brian (HDR, Inc., principal investigator)
Associate:Campos, Casey (California Department of Water Resources, associate)
Associate:Kindopp, Jason (California Department of Water Resources, associate)

Data Entities
Data Table Name:
yuba_instantaneous_passage.csv
Description:
Instantaneous passage records - not to be used for modeling or analysis
Data Table Name:
yuba_daily_uncorrected_passage.csv
Description:
Uncorrected daily net passage counts - not to be used for modeling or analysis
Data Table Name:
yuba_daily_corrected_passage.csv
Description:
Corrected and run differentiated daily passage counts
Other Name:
Poxon_and_Bratovich_2023_LYR_Chinook_Passage_and_Run_Differentiation_Update_Summary_Table.pdf
Description:
Summary Table of Results for Lower Yuba River VAKI Riverwatcher™ Chinook Salmon Passage and Run Differentiation Analyses for Biological Years 2004-2022
Detailed Metadata

Data Entities

Data Table

Data:https://pasta-s.lternet.edu/package/data/eml/edi/1707/1/5bacc68cab273e943961dcc48f8e2499
Name:yuba_instantaneous_passage.csv
Description:Instantaneous passage records - not to be used for modeling or analysis
Number of Records:107557
Number of Columns:9

Table Structure
Object Name:yuba_instantaneous_passage.csv
Size:5688360 bytes
Authentication:b7cb71eb516ec601c8d6bc89d1c78f34 Calculated By MD5
Text Format:
Number of Header Lines:1
Record Delimiter:\n
Orientation:column
Simple Delimited:
Field Delimiter:,

Table Column Descriptions
 yuba_instantaneous_passageyuba_instantaneous_passageyuba_instantaneous_passageyuba_instantaneous_passageyuba_instantaneous_passageyuba_instantaneous_passageyuba_instantaneous_passageyuba_instantaneous_passageyuba_instantaneous_passage
Column Name:date  
time  
depth  
length  
ladder  
direction_of_passage  
adipose_clipped  
species  
count  
Definition:Date stamp of fish passage event.Time stamp of fish passage event.Fish body depth, as estimated by VAKI Winari software.Fish body length, as estimated by VAKI Winari software; see RMT VAKI Riverwatcher Protocol for additional information.Location of data collection. Levels = c("north", "south"). North refers to DPD North ladder (river right looking downstream); South refers to DPD South ladder (river left looking downstream).Direction of fish travel through VAKI chute. Levels = c("up", "down").Whether or not fish observed had a clipped adipose fin, determined by PSMFC staff review of VAKI imagery. Levels = c("TRUE", "FALSE", "undetermined").Species of fish observed. Levels = "chinook".Count of fish observed. Each observation in the dataset is for one fish.
Storage Type:                  
Measurement Type:dateTimedateTimeratiorationominalnominalnominalnominalratio
Measurement Values Domain:
FormatYYYY-MM-DD
Precision
FormatH:M:S
Precision
Unitmillimeter
Typereal
Min40 
Max255 
Unitcentimeter
Typereal
Min0 
Max189 
DefinitionLocation of data collection. Levels = c("north", "south"). North refers to DPD North ladder (river right looking downstream); South refers to DPD South ladder (river left looking downstream).
DefinitionDirection of fish travel through VAKI chute. Levels = c("up", "down").
DefinitionWhether or not fish observed had a clipped adipose fin, determined by PSMFC staff review of VAKI imagery. Levels = c("TRUE", "FALSE", "undetermined").
DefinitionSpecies of fish observed. Levels = "chinook".
Unitcount of fish
Typeinteger
Min1 
Max1 
Missing Value Code:                  
Accuracy Report:                  
Accuracy Assessment:                  
Coverage:                  
Methods:                  

Data Table

Data:https://pasta-s.lternet.edu/package/data/eml/edi/1707/1/011d012db656dcf36404b76da062f1d1
Name:yuba_daily_uncorrected_passage.csv
Description:Uncorrected daily net passage counts - not to be used for modeling or analysis
Number of Records:27756
Number of Columns:6

Table Structure
Object Name:yuba_daily_uncorrected_passage.csv
Size:882740 bytes
Authentication:afd2caa93f2495258d765ce9760b5177 Calculated By MD5
Text Format:
Number of Header Lines:1
Record Delimiter:\n
Orientation:column
Simple Delimited:
Field Delimiter:,

Table Column Descriptions
 yuba_daily_uncorrected_passageyuba_daily_uncorrected_passageyuba_daily_uncorrected_passageyuba_daily_uncorrected_passageyuba_daily_uncorrected_passageyuba_daily_uncorrected_passage
Column Name:date  
biological_year  
ladder  
count  
adipose_clipped  
vaki_operation  
Definition:Calendar date.Biological year for Yuba River Chinook salmon adult passage. Defined as extending from March 1 through February of the following year annually based on lifestage periodicities identified in RMT (2013).Ladder location of VAKI Riverwatcher. Levels = c("north", "south"). North refers to Dagurerre Point Dam North ladder (river right looking downstream), south refers to Daguerre Point Dam South ladder (river left looking downstream).Daily net upstream count of fish, uncorrected for periods of VAKI Riverwatcher non-operation.Whether or not the fish observed had a clipped adipose fin. Levels = c(TRUE, FALSE). If FALSE includes adipose fin intact and adipose fin unidentified; TRUE includes fish with adipose fin clipped.Daily proportion of hours during which the VAKI Riverwatcher at the associated ladder was operational; values range from 0 (indicating 0 hours of operation) to 1 (indicating 24 hours of operation); inclusive.
Storage Type:            
Measurement Type:dateTimedateTimenominalrationominalratio
Measurement Values Domain:
FormatYYYY-MM-DD
Precision
FormatYYYY
Precision
DefinitionLadder location of VAKI Riverwatcher. Levels = c("north", "south"). North refers to Dagurerre Point Dam North ladder (river right looking downstream), south refers to Daguerre Point Dam South ladder (river left looking downstream).
Unitcount of fish
Typeinteger
Min0 
Max539 
DefinitionWhether or not the fish observed had a clipped adipose fin. Levels = c(TRUE, FALSE). If FALSE includes adipose fin intact and adipose fin unidentified; TRUE includes fish with adipose fin clipped.
Unitproportion
Typereal
Min0 
Max1 
Missing Value Code:            
Accuracy Report:            
Accuracy Assessment:            
Coverage:            
Methods:            

Data Table

Data:https://pasta-s.lternet.edu/package/data/eml/edi/1707/1/ec152189411208baf0862a339d814887
Name:yuba_daily_corrected_passage.csv
Description:Corrected and run differentiated daily passage counts
Number of Records:37250
Number of Columns:5

Table Structure
Object Name:yuba_daily_corrected_passage.csv
Size:1651235 bytes
Authentication:254a77fec1f85cb22bed05cbd564f39d Calculated By MD5
Text Format:
Number of Header Lines:1
Record Delimiter:\n
Orientation:column
Simple Delimited:
Field Delimiter:,

Table Column Descriptions
 yuba_daily_corrected_passageyuba_daily_corrected_passageyuba_daily_corrected_passageyuba_daily_corrected_passageyuba_daily_corrected_passage
Column Name:date  
biological_year  
count  
run  
adipose_clipped  
Definition:Calendar date.Biological year for Yuba River Chinook salmon adult passage. Defined as extending from March 1 through February of the following year annually based on lifestage periodicities identified in RMT (2013).Daily net upstream passage estimate of Chinook salmon, reflecting application of the analyses and methodologies presented in Poxon and Bratovich (2020) to correct net upstream counts for periods of VAKI system non-operation and differentiate between run types.Run type as differentiated by methods outlined in Poxon and Bratovich (2020). Levels = c("early spring", "late spring", "fall", and "no run differentiated"). "Early spring" are those individuals passing upstream of Daguerre Point Dam from March 1 through July 14; “late spring” are the portion of those individuals passing upstream of Daguerre Point Dam from July 15 through September 30 that are attributed to the spring-run Chinook salmon run type; “fall” are the portion of those individuals passing upstream of Daguerre Point Dam from July 15 through September 30 that are attributed to the spring-run Chinook salmon run type, as well as those individuals passing upstream of Daguerre Point Dam from October 1 through the end of February; “no run differentiated” refers to dates where no run differentiation analysis could be completed. See methods for details on time series from 2016, 2017, and biological year 2019.Whether or not an individual fish's adipose fin was clipped. Levels = c(TRUE, FALSE). If TRUE, the adipose fin was clipped; if FALSE, the adipose fin was either intact or unidentified.
Storage Type:          
Measurement Type:dateTimedateTimerationominalnominal
Measurement Values Domain:
FormatYYYY-MM-DD
Precision
FormatYYYY
Precision
Unitcount of fish
Typeinteger
Min0 
Max538 
DefinitionRun type as differentiated by methods outlined in Poxon and Bratovich (2020). Levels = c("early spring", "late spring", "fall", and "no run differentiated"). "Early spring" are those individuals passing upstream of Daguerre Point Dam from March 1 through July 14; “late spring” are the portion of those individuals passing upstream of Daguerre Point Dam from July 15 through September 30 that are attributed to the spring-run Chinook salmon run type; “fall” are the portion of those individuals passing upstream of Daguerre Point Dam from July 15 through September 30 that are attributed to the spring-run Chinook salmon run type, as well as those individuals passing upstream of Daguerre Point Dam from October 1 through the end of February; “no run differentiated” refers to dates where no run differentiation analysis could be completed. See methods for details on time series from 2016, 2017, and biological year 2019.
DefinitionWhether or not an individual fish's adipose fin was clipped. Levels = c(TRUE, FALSE). If TRUE, the adipose fin was clipped; if FALSE, the adipose fin was either intact or unidentified.
Missing Value Code:          
Accuracy Report:          
Accuracy Assessment:          
Coverage:          
Methods:          

Non-Categorized Data Resource

Name:Poxon_and_Bratovich_2023_LYR_Chinook_Passage_and_Run_Differentiation_Update_Summary_Table.pdf
Entity Type:PDF
Description:Summary Table of Results for Lower Yuba River VAKI Riverwatcher™ Chinook Salmon Passage and Run Differentiation Analyses for Biological Years 2004-2022
Physical Structure Description:
Object Name:Poxon_and_Bratovich_2023_LYR_Chinook_Passage_and_Run_Differentiation_Update_Summary_Table.pdf
Size:184682 bytes
Authentication:5a1de94858a11c972d7c970348392af3 Calculated By MD5
Externally Defined Format:
Format Name:PDF
Data:https://pasta-s.lternet.edu/package/data/eml/edi/1707/1/f288a6cf9f9dc3f8c59a33add5e3953c

Data Package Usage Rights

This information is released under the Creative Commons license - Attribution - CC BY (https://creativecommons.org/licenses/by/4.0/). The consumer of these data ("Data User" herein) is required to cite it appropriately in any publication that results from its use. The Data User should realize that these data may be actively used by others for ongoing research and that coordination may be necessary to prevent duplicate publication. The Data User is urged to contact the authors of these data if any questions about methodology or results occur. Where appropriate, the Data User is encouraged to consider collaboration or co-authorship with the authors. The Data User should realize that misinterpretation of data may occur if used out of context of the original study. While substantial efforts are made to ensure the accuracy of data and associated documentation, complete accuracy of data sets cannot be guaranteed. All data are made available "as is." The Data User should be aware, however, that data are updated periodically and it is the responsibility of the Data User to check for new versions of the data. The data authors and the repository where these data were obtained shall not be liable for damages resulting from any use or misinterpretation of the data. Thank you.

Keywords

By Thesaurus:
(No thesaurus)spring run, juvenile production estimate, Oncorhynchus tshawytscha, California, Central Valley, SRJPE, Chinook salmon, VAKI Riverwatcher, Escapement, Upstream Passage

Methods and Protocols

These methods, instrumentation and/or protocols apply to all data in this dataset:

Methods and protocols used in the collection of this data package
Description:

Data Types

Upstream passage

Adult Upstream

Objective: Estimate spring-run spawning population

Type: VAKI Riverwatcher

Location: Daguerre Point Dam

Times of operation: Year-round

In the Yuba River, a VAKI Riverwatcher™ video monitoring system is operated within the two fish ladders (North and South) at Daguerre Point Dam. This dataset is considered to be a census for spring run chinook because mostly all spawn upstream of Daguerre Point Dam. Passage estimates using the adult upstream data have been modeled for 2004 – 2023. The modeling approach involves determining the run and interpolating for missing data.

Data is available in tables following sequential QA/QC processes and modeling:

Instantaneous passage records: data in this file form the base dataset for analyses and methodologies identified in Poxon and Bratovich (2020). These data are provided for transparency and are not intended to be used for modeling purposes.

Uncorrected daily passage: data in this file represent the aggregation of the instantaneous records in instantaneous passage records to net upstream daily passage counts. These data undergo the count correction and run differentiation analyses presented in Poxon & Bratovich (2020). These data are provided for transparency and are not intended to be used for modeling purposes.

Corrected and run-differentiated daily passage: data in this file are corrected for VAKI operational outages and contain run differentiated daily net Chinook salmon passage estimates. Data in this file represent the output (results) from the count correction and run differentiation analyses presented in Poxon and Bratovich (2020). Please see below for important notes regarding biological years 2016, 2017, and 2019.

Interpolation of missing data (i.e., when the video system was not working) is performed by application of a Generalized Additive Model (GAM). Run differentiation is performed by splitting the dataset into three temporal components (an early component of early migrating spring run, a middle component comprised of late migrating spring run and fall run, and a late component of fall run) and conducting an iterative analysis to find the best-supported ratio of spring run to fall run in the middle component, as outlined in Poxon and Bratovich (2020).

The 2016 and 2017 annual time series were deemed inappropriate for count correction and run separation analyses due to long periods of VAKI Riverwatcher™ system outages that resulted in incomplete datasets for both years. No estimates (run-differentiated or overall) are possible for these years. The total number of Chinook salmon for these years represent raw counts as affected by VAKI Riverwatcher™ system outages, and do not represent estimated annual abundances.

Additionally, run-type differentiation was not possible for biological year 2019 due to an extended closure (February 13, 2019 through September 10, 2019) of the DPD North Ladder, which fundamentally altered the temporal patterns of passage at DPD on which the run differentiation analysis is based. As a result, the only possible annual abundance estimate for the 2019 annual time series is Total Chinook Salmon. Table 1 in Poxon and Bratovich (2020), which did not acknowledge the limitations of 2019 data precluding run differentiation, has been superseded by Table 1 in Poxon and Bratovich (2023). Table 1 in Poxon and Bratovich (2023) is also expanded to include results of count correction and run differentiation analyses for biological years 2020 through 2022.

Resources

Poxon, B. and Bratovich, P. 2020. Lower Yuba River VAKI Riverwatcher™ Chinook Salmon Passage and Run Differentiation Analyses – 2020 Update. Prepared by HDR for Yuba Water Agency.

Poxon, B. and Bratovich, P. 2023. Summary Table of Results for Lower Yuba River VAKI Riverwatcher™ Chinook Salmon Passage and Run Differentiation Analyses for Biological Years 2004-2022. Prepared by HDR for Yuba Water Agency.

People and Organizations

Publishers:
Organization:Environmental Data Initiative
Email Address:
info@edirepository.org
Web Address:
https://edirepository.org
Id:https://ror.org/0330j0z60
Creators:
Individual: Jacob Vander Meulen
Organization:Yuba Water Agency
Email Address:
JVanderMeulen@yubawater.org
Contacts:
Individual: Jacob Vander Meulen
Organization:Yuba Water Agency
Email Address:
JVanderMeulen@yubawater.org
Associated Parties:
Individual: Brian Poxon
Organization:HDR, Inc.
Email Address:
Brian.Poxon@hdrinc.com
Role:principal investigator
Individual: Casey Campos
Organization:California Department of Water Resources
Email Address:
Casey.Campos@water.ca.gov
Role:associate
Individual: Jason Kindopp
Organization:California Department of Water Resources
Email Address:
jason.kindopp@water.ca.gov
Role:associate

Temporal, Geographic and Taxonomic Coverage

Temporal, Geographic and/or Taxonomic information that applies to all data in this dataset:

Time Period
Begin:
2004-03-01
End:
2023-02-28
Geographic Region:
Description:Yuba River Chinook Upstream Passage
Bounding Coordinates:
Northern:  39.217Southern:  39.1735
Western:  -121.5136Eastern:  -121.4039
Taxonomic Range:
Classification:
Rank Name:kingdom
Rank Value:Animalia
Classification:
Rank Name:phylum
Rank Value:Chordata
Classification:
Rank Name:class
Rank Value:Teleostei
Classification:
Rank Name:order
Rank Value:Salmoniformes
Classification:
Rank Name:family
Rank Value:Salmonidae
Classification:
Rank Name:genus
Rank Value:Oncorhynchus
Classification:
Rank Name:species
Rank Value:Oncorhynchus tshawytscha
Common Name:Chinook Salmon
Identifer:Integrated Taxonomic Information Service (ITIS)
Info for ID: 161980 (Oncorhynchus tshawytscha)
Taxonomic Range:
Classification:
Rank Name:kingdom
Rank Value:Animalia
Classification:
Rank Name:phylum
Rank Value:Chordata
Classification:
Rank Name:class
Rank Value:Teleostei
Classification:
Rank Name:order
Rank Value:Salmoniformes
Classification:
Rank Name:family
Rank Value:Salmonidae
Classification:
Rank Name:genus
Rank Value:Oncorhynchus
Classification:
Rank Name:species
Rank Value:Oncorhynchus mykiss
Common Name:Steelhead Trout
Identifer:Integrated Taxonomic Information Service (ITIS)
Info for ID: 161989 (Oncorhynchus mykiss)

Project

Parent Project Information:

Title:Monitoring adult Chinook salmon upstream passage on Yuba River
Personnel:
Individual: Jacob Vander Meulen
Organization:Yuba Water Agency
Email Address:
JVanderMeulen@yubawater.org
Role:Project Lead

Maintenance

Maintenance:
Description:ongoing
Frequency:annually
Other Metadata

Additional Metadata

additionalMetadata
        |___text '\n      '
        |___element 'metadata'
        |     |___text '\n         '
        |     |___element 'unitList'
        |     |     |___text '\n            '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'count of fish'
        |     |     |     |  \___attribute 'name' = 'count of fish'
        |     |     |     |  \___attribute 'unitType' = 'dimensionless'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description'
        |     |     |     |     |___text 'number of fish counted'
        |     |     |     |___text '\n            '
        |     |     |___text '\n            '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'proportion'
        |     |     |     |  \___attribute 'name' = 'proportion'
        |     |     |     |  \___attribute 'unitType' = 'dimensionless'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description'
        |     |     |     |     |___text 'proportion of day operational'
        |     |     |     |___text '\n            '
        |     |     |___text '\n         '
        |     |___text '\n      '
        |___text '\n   '

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