Data Package Metadata   View Summary

Delta smelt (Hypomesus transpacificus) life cycle model input data.

General Information
Data Package:
Local Identifier:edi.1433.3
Title:Delta smelt (Hypomesus transpacificus) life cycle model input data.
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:2024-04-16
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 ]
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:
DSLCMinputs_2023
Description:
Synthesized data used for fitting delta smelt population dynamics models including the case study appearing Polansky, Mitchell, and Newman (2023), "Combining multiple data sources with different biases in state-space models for population dynamics", Ecology and Evolution, DOI: 10.1002/ece3.10154.
Data Table Name:
DSLCMinputs_2024
Description:
Synthesized data used for fitting delta smelt population dynamics models and includes the subset of data used in Polansky, Mitchell, and Nobriga (2024), "Identifying minimum freshwater habitat conditions for an endangered fish using life cycle analysis", Conservation Science and Practice, DOI: 10.1111/csp2.13124.
Detailed Metadata

Data Entities


Data Table

Data:https://pasta-s.lternet.edu/package/data/eml/edi/1433/3/365b76f25a5039ed6f84924a46b46c42
Name:DSLCMinputs_2023
Description:Synthesized data used for fitting delta smelt population dynamics models including the case study appearing Polansky, Mitchell, and Newman (2023), "Combining multiple data sources with different biases in state-space models for population dynamics", Ecology and Evolution, DOI: 10.1002/ece3.10154.
Number of Records:26
Number of Columns:26

Table Structure
Object Name:DSLCMinputs_2023.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:Calendar year earliest start month in data time interval used in constructing input data.Abundance index estimate for post-larval life stage based on 20mm survey data.Standard error of abundance index estimate of nHat_s1.Abundance index estimate for juvenile life stage based on STN survey data.Standard error of abundance index estimate of nHat_s2.Abundance index estimate for sub-adult life stage based on FMWT survey data.Standard error of abundance index estimate of nHat_s3.Abundance index estimate for adult life stage based on SpMWT and SKT survey data.Standard error of abundance index estimate of nHat_s4.Average length of adults in calendar year equal to the cohort_year.Total (summed daily) delta outflow from March to May of calendar year equal to the cohort_year.Average of monthly average Secchi depth recorded by the fish monitoring programs during March to May of the cohort_year entry.Average of monthly average temperature recorded by the fish monitoring programs during March to May of the cohort_year entry.Biomass index of adult copepods and mysids using data from March to May of the cohort_year entry.Biomass index of nauplii copepods using data from March to May of the cohort_year entry.Average daily X2 during September and October of the calendar year equal to the cohort_year minus 1.Total (summed daily) delta outflow from June to August of calendar year equal to the cohort_year.Average of monthly average Secchi depth recorded by the fish monitoring programs during June to August of the cohort_year entry.Average of monthly average temperature recorded by the fish monitoring programs during June to August of the cohort_year entry.Average low salinity zone habitat volume from September through November.Average of monthly average Secchi depth recorded by the fish monitoring programs during September through November of the cohort_year entry.Biomass index of adult copepods and mysids using data from September through November of the cohort_year entry.Average Old and Middle rivers daily flow from December of the calendar year equal to the cohort_year through March of the subsequent calendar year.Average of monthly averages of Secchi depth in South Delta stations during December of the calendar year equal to the cohort_year through March of the subsequent calendar year.Biomass index of adult copepods and mysids from December of the calendar year equal to the cohort_year through March of the subsequent calendar year.Abundance index of age-1 and older striped bass from December of the calendar 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:
UnitTime (year).
Typeinteger
UnitNumber of individuals.
Typereal
Min
Max
UnitNumber of individuals.
Typereal
Min
Max
UnitNumber of individuals.
Typereal
Min
Max
UnitNumber of individuals.
Typereal
Min
Max
UnitNumber of individuals.
Typereal
Min
Max
UnitNumber of individuals.
Typereal
Min
Max
UnitNumber of individuals.
Typereal
Min
Max
UnitNumber of individuals.
Typereal
Min
Max
Unitmillimeter
Typereal
Unitacre-feet
Typereal
Unitcentimeter
Typereal
Unitcelsius
Typereal
UnitBiomass per unit volume.
Typereal
UnitBiomass per unit volume.
Typereal
Unitkm
Typereal
Unitacre-feet
Typereal
Unitcentimeter
Typereal
Unitcelsius
Typereal
Unitcubic kilometers
Typereal
Unitcentimeter
Typereal
UnitBiomass per unit volume.
Typereal
UnitFlow in cubic feet per second.
Typereal
Unitcentimeter
Typereal
UnitBiomass per unit volume.
Typereal
UnitNumber of individuals.
Typereal
Missing Value Code:  
CodeNA
ExplNo estimate available.
CodeNA
ExplNo estimate available.
CodeNA
ExplNo estimate available.
CodeNA
ExplNo estimate available.
CodeNA
ExplNo estimate available.
CodeNA
ExplNo estimate available.
   
CodeNA
ExplNo estimate available.
         
CodeNA
ExplNo estimate available.
                   
Accuracy Report:                                                    
Accuracy Assessment:                                                    
Coverage:                                                    
Methods:                                                    

Data Table

Data:https://pasta-s.lternet.edu/package/data/eml/edi/1433/3/87fd99e287f5f08250a507bbe94d56c0
Name:DSLCMinputs_2024
Description:Synthesized data used for fitting delta smelt population dynamics models and includes the subset of data used in Polansky, Mitchell, and Nobriga (2024), "Identifying minimum freshwater habitat conditions for an endangered fish using life cycle analysis", Conservation Science and Practice, DOI: 10.1111/csp2.13124.
Number of Records:30
Number of Columns:30

Table Structure
Object Name:DSLCMinputs_2024.csv
Size:15181 byte
Authentication:0f87202c090259ba1a6bd15fefc4be14 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_s4Outflow_Mar0May0Secchi_meanofmeans_Mar0May0Temperature_meanofmeans_Mar0May0ACM_BPUV_Mar0May0_rescaledEI.ratio_Mar0May0X2_Mar0May0NJ_BPUV_Mar0May0Outflow_Jun0Aug0_dailySecchi_meanofmeans_Jun0Aug0SBAge0_Jun0Aug0NJACM_BPUV_Jun0Aug0LSZ_Sep0Nov0X2_Sep0Nov0Outflow_Sep0Nov0_dailySecchi_meanofmeans_Sep0Nov0NJACM_BPUV_Sep0Nov0SBAge0_Sep0Nov0OMR_Dec0Mar1_metricSouthSecchi_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  
Outflow_Mar0May0  
Secchi_meanofmeans_Mar0May0  
Temperature_meanofmeans_Mar0May0  
ACM_BPUV_Mar0May0_rescaled  
EI.ratio_Mar0May0  
X2_Mar0May0  
NJ_BPUV_Mar0May0  
Outflow_Jun0Aug0_daily  
Secchi_meanofmeans_Jun0Aug0  
SBAge0_Jun0Aug0  
NJACM_BPUV_Jun0Aug0  
LSZ_Sep0Nov0  
X2_Sep0Nov0  
Outflow_Sep0Nov0_daily  
Secchi_meanofmeans_Sep0Nov0  
NJACM_BPUV_Sep0Nov0  
SBAge0_Sep0Nov0  
OMR_Dec0Mar1_metric  
SouthSecchi_meanofmeans_Dec0Mar1  
ACM_BPUV_Dec0Feb1  
SBAge1Plus_Dec0Dec0  
Definition:Birth year of cohort.Abundance index of post-larval life stage.Standard error of the nHat_s1 abundance index.Abundance index of juvenile life stage.Standard error of the nHat_s2 abundance index.Abundance index of sub-adult life stage.Standard error of the nHat_s3 abundance index.Abundance index of adult life stage.Standard error of the nHat_s4 abundance index.Total freshwater flow out of the Delta during March through May.Average Secchi depths of monthly averaged samples during March through May.Average water temperature of monthly averaged samples during March through May.Biomass index of adult copepods and mysids, divided by 100, based on surveys from March through May.Ratio of total Delta freshwater exports to total Delta freshwater inflow during March through May.Average daily X2 during March through May.Biomass index of nauplii and juvenile copepods based on March to May surveys.Daily average freshwater flow out of the Delta during June through August.Average Secchi depths of monthly averaged samples during June through August.Abundance index of juvenile striped bass based on June through August surveys.Biomass index of nauplii, juvenile, and adult copepods, and mysids, based on June through August surveys.Average daily low salinity zone habitat volume from September through November.Average daily X2 during September through November.Daily average freshwater flow out of the Delta during September through November.Average Secchi depths of monthly averaged samples during September and November.Biomass index of nauplii, juvenile, and adult copepods, and mysids, based on September and November surveys.Abundance index of age-0 striped bass based on September and November surveys.Average Old and Middle rivers flow rate based on daily measurements from December of cohort_year through the subsequent March.Average Secchi depth of monthly averaged samples taken in the southern Delta from December of the calendar year equal to the cohort_year through the subsequent February.Biomass index of adult copepods and mysids, based on surveys from December of the calendar year equal to the cohort_year through the subsequent February.Abundance index of age-1 and older striped bass based on December surveys.
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  
float  
float  
float  
float  
Measurement Type:ratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratio
Measurement Values Domain:
UnitYear
Typeinteger
UnitNumber of individuals.
Typereal
UnitNumber of individuals.
Typereal
UnitNumber of individuals.
Typereal
UnitNumber of individuals.
Typereal
UnitNumber of individuals.
Typereal
UnitNumber of individuals.
Typereal
UnitNumber of individuals.
Typereal
UnitNumber of individuals.
Typereal
Unitacre-feet
Typereal
Unitcentimeter
Typereal
Unitcelsius
Typereal
UnitBiomass per unit volume.
Typereal
UnitUnitless number (acre-feet divided by acre-feet).
Typereal
Unitkm
Typereal
UnitBiomass per unit volume.
Typereal
UnitMillion cubic meters per day.
Typereal
Unitcentimeter
Typereal
UnitNumber of individuals.
Typereal
UnitBiomass per unit volume.
Typereal
Unitcubic kilometers
Typereal
Unitkm
Typereal
UnitMillion cubic meters per day.
Typereal
Unitcentimeter
Typereal
UnitBiomass per unit volume.
Typereal
UnitNumber of individuals.
Typereal
UnitCubic meters per day.
Typereal
Unitcentimeter
Typereal
UnitBiomass per unit volume.
Typereal
UnitNumber of individuals.
Typereal
Missing Value Code:  
CodeNA
ExplRelative population abundance index.
CodeNA
ExplStandard error of the estimated relative population abundance index.
CodeNA
ExplRelative population abundance index.
CodeNA
ExplStandard error of the estimated relative population abundance index.
CodeNA
ExplRelative population abundance index.
CodeNA
ExplStandard error of the estimated relative population abundance index.
                                             
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. design based) 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:
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.

Maintenance

Maintenance:
Description:

2024-Apr-15: Updated data package to add table with additional inputs covering more years and more types of data.

Frequency:notPlanned
Other Metadata

Additional Metadata

additionalMetadata
        |___text '\n      '
        |___element 'metadata'
        |     |___text '\n         '
        |     |___element 'unitList'
        |     |     |___text '\n            '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'Number of individuals.'
        |     |     |     |  \___attribute 'name' = 'Number of individuals.'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description'
        |     |     |     |___text '\n            '
        |     |     |___text '\n            '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'Flow in cubic feet per second.'
        |     |     |     |  \___attribute 'name' = 'Flow in cubic feet per second.'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description'
        |     |     |     |___text '\n            '
        |     |     |___text '\n            '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'Time (year).'
        |     |     |     |  \___attribute 'name' = 'Time (year).'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description'
        |     |     |     |___text '\n            '
        |     |     |___text '\n            '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'Biomass per unit volume.'
        |     |     |     |  \___attribute 'name' = 'Biomass per unit volume.'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description'
        |     |     |     |___text '\n            '
        |     |     |___text '\n            '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'Year'
        |     |     |     |  \___attribute 'name' = 'Year'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description'
        |     |     |     |     |___text 'Time (year).'
        |     |     |     |___text '\n            '
        |     |     |___text '\n            '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'Cubic meters per day.'
        |     |     |     |  \___attribute 'name' = 'Cubic meters per day.'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description'
        |     |     |     |___text '\n            '
        |     |     |___text '\n            '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'Unitless number (acre-feet divided by acre-feet).'
        |     |     |     |  \___attribute 'name' = 'Unitless number (acre-feet divided by acre-feet).'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description'
        |     |     |     |___text '\n            '
        |     |     |___text '\n            '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'Million cubic meters per day.'
        |     |     |     |  \___attribute 'name' = 'Million cubic meters per day.'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description'
        |     |     |     |___text '\n            '
        |     |     |___text '\n            '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'cubic kilometers'
        |     |     |     |  \___attribute 'name' = 'cubic kilometers'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description'
        |     |     |     |     |___text 'Obtained from Figure 12 of MacWilliams et al. 2015, Three-Dimensional Modeling of Hydrodynamics and Salinity in the San Francisco Estuary: An Evaluation of Model Accuracy, X2, and the Low–Salinity Zone, San Francisco Estuary and Watershed Science, https://escholarship.org/uc/item/7x65r0tf.'
        |     |     |     |___text '\n            '
        |     |     |___text '\n            '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'km'
        |     |     |     |  \___attribute 'name' = 'km'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description'
        |     |     |     |     |___text 'The distance from where water salt concentration is 2psu to the Golden Gate Bridge.'
        |     |     |     |___text '\n            '
        |     |     |___text '\n            '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'acre-feet'
        |     |     |     |  \___attribute 'name' = 'acre-feet'
        |     |     |     |___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   '

EDI is a collaboration between the University of New Mexico and the University of Wisconsin – Madison, Center for Limnology:

UNM logo UW-M logo