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Delta smelt (Hypomesus transpacificus) life cycle model input data used in the article "Combining multiple data sources with different biases in state-space models for population dynamics" appearing in Ecology and Evolution Volume13, Issue6, June 2023, e10154 with DOI:10.1002/ece3.10154.

General Information
Data Package:
Local Identifier:edi.1433.2
Title:Delta smelt (Hypomesus transpacificus) life cycle model input data used in the article "Combining multiple data sources with different biases in state-space models for population dynamics" appearing in Ecology and Evolution Volume13, Issue6, June 2023, e10154 with DOI:10.1002/ece3.10154.
Alternate Identifier:DOI PLACE HOLDER
Abstract:

Synthesized data used for fitting delta smelt population dynamics models, essentially consisting of predictor variables (environmental conditions and indices of prey and predators) and response variables (abundance indices). Input data is sourced from a variety of both federal and California state government monitoring programs taking place within the San Francisco Estuary, California. These include California Department of Fish and Wildlife fish surveys, Interagency Ecological Program's Environmental Monitoring Program for zooplankton, California Department of Water Resources' Dayflow, and United States Geological Survey water monitoring data. The sourced data are recorded from sub-hourly to monthly time scales and at various spatial scales, aggregated at monthly or greater time scales using summary statistics (e.g. means) and are not spatially explicit but use spatial stratification approaches for statistic calculation as appropriate.

Publication Date:2024-04-15
For more information:
Visit: DOI PLACE HOLDER

Time Period
Begin:
1990
End:
2016

People and Organizations
Contact:Polansky, Leo (United States Fish and Wildlife Service) [  email ]
Contact:Mitchell, Lara (United States Fish and Wildlife Service) [  email ]
Organization:United States Fish and Wildlife Service
Creator:Polansky, Leo (United States Fish and Wildlife Service)
Creator:Mitchell, Lara (United States Fish and Wildlife Service)
Creator:Newman, Ken 

Data Entities
Data Table Name:
DSLCMinputsLCM2plus
Description:
Input data for delta smelt (Hyomesus transpacificus) case study of LCM2+.
Detailed Metadata

Data Entities

Data Table

Data:https://pasta-s.lternet.edu/package/data/eml/edi/1433/2/7a7ab648e9d49c60eccd48c317ef94e5
Name:DSLCMinputsLCM2plus
Description:Input data for delta smelt (Hyomesus transpacificus) case study of LCM2+.
Number of Records:26
Number of Columns:26

Table Structure
Object Name:DSLCMinputsforEDI.csv
Size:11095 byte
Authentication:de2e468bdee9c68bcaeaa1b84bab924f Calculated By MD5
Text Format:
Number of Header Lines:1
Record Delimiter:\r\n
Orientation:column
Simple Delimited:
Field Delimiter:,
Quote Character:"

Table Column Descriptions
 Cohort_YearnHat_s1nSE_s1nHat_s2nSE_s2nHat_s3nSE_s3nHat_s4nSE_s4FebAdultLength_for_SSBOutflow_Mar0May0Secchi_meanofmeans_Mar0May0Temperature_meanofmeans_Mar0May0ACM_BPUV_Mar0May0NJ_BPUV_Mar0May0X2_lagOutflow_Jun0Aug0Secchi_meanofmeans_Jun0Aug0Temperature_meanofmeans_Jun0Aug0LSZ_Sep0Nov0Secchi_meanofmeans_Sep0Nov0ACM_BPUV_Sep0Nov0OMR_Dec0Mar1SouthSecchi_meanofmeans_Dec0Mar1ACM_BPUV_Dec0Feb1SBAge1Plus_Dec0Dec0
Column Name:Cohort_Year  
nHat_s1  
nSE_s1  
nHat_s2  
nSE_s2  
nHat_s3  
nSE_s3  
nHat_s4  
nSE_s4  
FebAdultLength_for_SSB  
Outflow_Mar0May0  
Secchi_meanofmeans_Mar0May0  
Temperature_meanofmeans_Mar0May0  
ACM_BPUV_Mar0May0  
NJ_BPUV_Mar0May0  
X2_lag  
Outflow_Jun0Aug0  
Secchi_meanofmeans_Jun0Aug0  
Temperature_meanofmeans_Jun0Aug0  
LSZ_Sep0Nov0  
Secchi_meanofmeans_Sep0Nov0  
ACM_BPUV_Sep0Nov0  
OMR_Dec0Mar1  
SouthSecchi_meanofmeans_Dec0Mar1  
ACM_BPUV_Dec0Feb1  
SBAge1Plus_Dec0Dec0  
Definition:Birth year of a delta smelt cohort.Estimated stage 1 delta smelt abundance based on May samples from the 20mm survey's age0 catch. The calendar year of sampling is the cohort year.Standard error of estimated stage 1 delta smelt abundance based on May samples from the 20mm survey program's age0 catch.Estimated stage 2 delta smelt abundance based on July-August samples from the Summer Townet Survey's age0 catch. The calendar year of sampling is the cohort year.Standard error of estimated stage 2 delta smelt abundance based on July-August samples from the Summer Townet Survey program's age0 catch.Estimated stage 3 delta smelt abundance based on October-November samples from the Fall Midwater Trawl program's age0 catch. The calendar year of sampling is the cohort year.Standard error of estimated stage 3 delta smelt abundance based on October-November samples from the Fall Midwater Trawl's age0 catch. The calendar year of sampling is the cohort year.Estimated stage 4 delta smelt abundance based on February-March samples from the Spring Midwater Trawl (cohort years 1990-2000) and Spring Kodiak Trawl (cohort years 2001-2015) surveys' age1 catch. The calendar year of sampling is the cohort year plus one.Standard error of estimated stage 4 delta smelt abundance based on February-March samples from the Spring Midwater Trawl (cohort years 1990-2000) and Spring Kodiak Trawl (cohort years 2001-2015) surveys' age1 catch. The calendar year of sampling is the cohort year plus one.Average fork length (mm) of February age 1 delta smelt catch by the Spring Midwater Trawl (cohort years 1990-2000) and Spring Kodiak Trawl (cohort years 2001-2015) surveys. The calendar year of sampling is the cohort year.Total daily Delta outflow (acre-feet) during March-May with calendar year equal to the cohort year. Data are daily values from the Dayflow database summed over 92 days.Average Secchi depth (cm) across all samples taken from March through May of the calendar year equal to the cohort year. Samples are from CDFW fish monitoring programs and the value is the mean of the monthly means.Average temperature (deg C) across all samples taken from March through May by CDFW fish monitoring programs during the calendar year equal to the cohort year. Mean is the average of the monthly means.Average biomass per unit volume of adult cladocera (Bosmina, Daphnia, Diaphan and Othclado) and mysids (Hyperacanthomysis longirostris and Neomysis mercedis).Nauplii and juvenile zooplankton from the IEP zooplankton monitoring data. Nauplii field names are "COPNAUP", "EURYNAUP", "OTHCOPNAUP", "PDIAPNAUP", "SINONAUP", and juvenile field names are "CALJUV", "EURYJUV", "OTHCALJUV", "PDIAPJUV", "SINOCALJUV", "ASINEJUV", "ACARJUV", "DIAPTJUV", "TORTJUV".Average daily X2 location during September and October during the prior calendar year relative to the cohort year. Data sourced from the Dayflow database.Total daily Delta outflow (acre-feet) during June-August with calendar year equal to the cohort year. Data are daily values from the Dayflow database summed over 92 days.Average Secchi depth (cm) across all samples taken from June-August by CDFW fish monitoring programs during the calendar year equal to the cohort year.Average temperature (deg C) across all samples taken from June-August by CDFW fish monitoring programs during the calendar year equal to the cohort year. Mean is the mean of the three monthly means.Average daily low salinity zone habitat volume during September through November of the calendar year that is equal to the cohort year. Values based on a model relating LSZ habitat volume to X2 location based on relationships derived by MacWilliams et al. (2015, https://escholarship.org/uc/item/7x65r0tf).Average Secchi depth (cm) across all samples taken from September through November by CDFW fish monitoring programs during the calendar year equal to the cohort year.Average biomass per unit volume of adult cladocera (Bosmina, Daphnia, Diaphan and Othclado) and mysids (Hyperacanthomysis longirostris and Neomysis mercedis) caught during September to November of the calendar year equal to the cohort year.Average daily Old and Middle rivers flows from December of the calendar year equal to the cohort year through March of the calendar year equal to the cohort year plus 1. Data sourced from daily USGS tidally filtered flow measurements.Average Secchi depth (cm) across all samples taken from December of the calendar year equal to the cohort year through March of the calendar year equal to the cohort year plus 1 within a southern portion of the Delta. Samples are from the CDFW fish monitoring programs and the value is the mean of the monthly means.Average biomass per unit volume of adult cladocera (Bosmina, Daphnia, Diaphan and Othclado) and mysids (Hyperacanthomysis longirostris and Neomysis mercedis) caught during December of the calendar year equal to the cohort year though February of the calendar year equal to the cohort year plus 1. Data are from the IEP EMP's zooplankton survey.Age 1 and older striped bass abundance index. Abundance calculated from FMWT catch during December of the calendar year equal to the cohort year.
Storage Type:float  
float  
float  
float  
float  
float  
float  
float  
float  
float  
float  
float  
float  
float  
float  
float  
float  
float  
float  
float  
float  
float  
float  
float  
float  
float  
Measurement Type:ratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratio
Measurement Values Domain:
UnitYear (time).
Typeinteger
Unitabundance index
Typereal
Unitabundance index
Typereal
Unitabundance index
Typereal
Unitabundance index
Typereal
Unitabundance index
Typereal
Unitabundance index
Typereal
Unitabundance index
Typereal
Unitabundance index
Typereal
Unitmillimeter
Typereal
Unitacre-feet
Typereal
Unitcentimeter
Typereal
Unitcelsius
Typereal
Unitmicrograms of Carbon per cubic meter water sampled
Typereal
Unitmicrograms of Carbon per cubic meter water sampled
Typereal
Unitkm from the Golden Gate Bridge.
Typereal
Unitacre-feet
Typereal
Unitcentimeter
Typereal
Unitcelsius
Typereal
Unitthousands of cubic meters.
Typereal
Unitcentimeter
Typereal
Unitmicrograms of Carbon per cubic meter water sampled
Typereal
Unitcubic feet per second
Typereal
Unitcentimeter
Typereal
Unitmicrograms of Carbon per cubic meter water sampled
Typereal
Unittotal abundance up to an unknown gear efficiency scaler
Typereal
Missing Value Code:  
CodeNA
ExplNo survey data available.
CodeNA
ExplNo survey data available.
            
CodeNA
ExplNo catch data available.
          
CodeNA
ExplNo data provided.
                    
Accuracy Report:                                                    
Accuracy Assessment:                                                    
Coverage:                                                    
Methods:                                                    

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)Hypomesus transpacificus, delta smelt, San Francisco Estuary, population data, pelagic fish
LTER Controlled Vocabularywater

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 are based on summary statistics (e.g. means) and applications of abundance estimate methods (e.g. abundance indices) using a wide variety of raw data sets provided by federal and California government agencies. Contact a data creator to obtain R code and raw input data.

People and Organizations

Publishers:
Organization:Environmental Data Initiative
Email Address:
info@edirepository.org
Web Address:
https://edirepository.org
Id:https://ror.org/0330j0z60
Creators:
Organization:United States Fish and Wildlife Service
Individual: Leo Polansky
Organization:United States Fish and Wildlife Service
Email Address:
leo_polansky@fws.gov
Id:https://orcid.org/0000-0003-2738-8079
Individual: Lara Mitchell
Organization:United States Fish and Wildlife Service
Email Address:
lara_mitchell@fws.gov
Id:https://orcid.org/0000-0002-8439-8508
Individual: Ken Newman
Email Address:
kbnewman2@gmail.com
Id:https://orcid.org/0000-0003-1734-5833
Contacts:
Individual: Leo Polansky
Organization:United States Fish and Wildlife Service
Email Address:
leo_polansky@fws.gov
Id:https://orcid.org/0000-0003-2738-8079
Individual: Lara Mitchell
Organization:United States Fish and Wildlife Service
Email Address:
lara_mitchell@fws.gov
Id:https://orcid.org/0000-0002-8439-8508

Temporal, Geographic and Taxonomic Coverage

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

Time Period
Begin:
1990
End:
2016
Geographic Region:
Description:San Francisco Estuary open water habitat, lower Sacramento and San Joaquin rivers and confluence.
Bounding Coordinates:
Northern:  38.601Southern:  37.775
Western:  -122.423Eastern:  -121.289

Project

Parent Project Information:

Title:Delta smelt life cycle modeling.
Personnel:
Individual: Leo Polansky
Email Address:
leo_polansky@fws.gov
Id:https://orcid.org/0000-0003-2738-8079
Role:Conceptual, mathematical, and statistical modeling of delta smelt population dynamics.
Individual: Lara Mitchell
Email Address:
lara_mitchell@fws.gov
Id:https://orcid.org/0000-0003-2738-8079
Role:Conceptual, mathematical, and statistical modeling of delta smelt population dynamics.
Individual: Ken Newman
Email Address:
kbnewman2@gmail.com
Id:https://orcid.org/0000-0003-1734-5833
Role:Conceptual, mathematical, and statistical modeling of delta smelt population dynamics.
Other Metadata

Additional Metadata

additionalMetadata
        |___text '\n      '
        |___element 'metadata'
        |     |___text '\n         '
        |     |___element 'unitList'
        |     |     |___text '\n            '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'acre-feet'
        |     |     |     |  \___attribute 'name' = 'acre-feet'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description'
        |     |     |     |___text '\n            '
        |     |     |___text '\n            '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'total abundance up to an unknown gear efficiency scaler'
        |     |     |     |  \___attribute 'name' = 'total abundance up to an unknown gear efficiency scaler'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description'
        |     |     |     |___text '\n            '
        |     |     |___text '\n            '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'km from the Golden Gate Bridge.'
        |     |     |     |  \___attribute 'name' = 'km from the Golden Gate Bridge.'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description'
        |     |     |     |___text '\n            '
        |     |     |___text '\n            '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'thousands of cubic meters.'
        |     |     |     |  \___attribute 'name' = 'thousands of cubic meters.'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description'
        |     |     |     |___text '\n            '
        |     |     |___text '\n            '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'cubic feet per second'
        |     |     |     |  \___attribute 'name' = 'cubic feet per second'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description'
        |     |     |     |___text '\n            '
        |     |     |___text '\n            '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'Year (time).'
        |     |     |     |  \___attribute 'name' = 'Year (time).'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description'
        |     |     |     |___text '\n            '
        |     |     |___text '\n            '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'abundance index'
        |     |     |     |  \___attribute 'name' = 'abundance index'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description'
        |     |     |     |___text '\n            '
        |     |     |___text '\n            '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'micrograms of Carbon per cubic meter water sampled'
        |     |     |     |  \___attribute 'name' = 'micrograms of Carbon per cubic meter water sampled'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description'
        |     |     |     |___text '\n            '
        |     |     |___text '\n         '
        |     |___text '\n      '
        |___text '\n   '

Additional Metadata

additionalMetadata
        |___text '\n      '
        |___element 'metadata'
        |     |___text '\n         '
        |     |___element 'emlEditor'
        |     |        \___attribute 'app' = 'ezEML'
        |     |        \___attribute 'release' = '2024.04.10'
        |     |___text '\n      '
        |___text '\n   '

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