Data Package Metadata   View Summary

Daily water temperature (°C) in the Yolo Bypass and Sacramento River, 1998-2019

General Information
Data Package:
Local Identifier:edi.1178.1
Title:Daily water temperature (°C) in the Yolo Bypass and Sacramento River, 1998-2019
Alternate Identifier:DOI PLACE HOLDER
Abstract:
This data is an integration of raw logger data as well as relevant California Data Exchange Center (CDEC) data (Pien et al. 2020, hourly) and water quality data collected during the Yolo Bypass Fish Monitoring Program’s (YBFMP) fish collection (Pien and Kwan 2022) to produce a daily water temperature dataset for the Yolo Bypass and Sacramento River at Sherwood Harbor and Rio Vista Bridge. The raw YBFMP’s water temperature data was collected by loggers attached to the rotary screw trap (STTD) and Sherwood Harbor (SHR). Logger data ranged from daily means (1998) to a fifteen-minute collection interval (2013-2017 for the Yolo Bypass, 2009-2019 for Sherwood Harbor). A daily mean, maximum, minimum, standard deviation and coefficient of variation in water temperature was produced as well as columns for sample size (n, number of measurements per day), method (data collection or estimation), category, length (number of consecutive missing dates) and site. Daily water temperature data for the full extent of the YBFMP’s fish collection is valuable for a variety of purposes. For example, variation in water temperature during inundation and comparisons between temperatures in the Sacramento River and Yolo Bypass have been used as metrics of habitat complexity and linked to life history diversity in salmon (Goertler et al. 2017).
Publication Date:2022-07-23
For more information:
Visit: DOI PLACE HOLDER

Time Period
Begin:
1998-01-16
End:
2019-12-31

People and Organizations
Contact:Goertler, Pascale  (Senior Environmental Scientist) [  email ]
Creator:Goertler, Pascale  (Delta Stewardship Council – Delta Science Program, Senior Environmental Scientist)
Creator:Pien, Catarina (U.S. Bureau of Reclamation, Fish Biologist)
Associate:Kwan, Nicole (California Department of Water Resources , Senior Environmental Scientist, Data owner)
Associate:Ikemiyagi, Naoaki (California Department of Water Resources , Environmental Scientist, Data owner)
Associate:Frantzich, Jared (California Department of Water Resources , Senior Environmental Scientist, Data owner)

Data Entities
Data Table Name:
integrated_data
Description:
This data is an integration of raw logger data as well as relevant California Data Exchange Center (CDEC) data (Pien et al. 2020, hourly) and water quality data collected during the Yolo Bypass Fish Monitoring Program’s (YBFMP) fish collection (Pien and Kwan 2022) to produce a daily water temperature dataset for the Yolo Bypass and Sacramento River at Sherwood Harbor and Rio Vista Bridge.
Data Table Name:
methods_tbl
Description:
Summary table to clarify the methods used, by region, as well as the relationship between the method and category columns in the integrated data.
Data Table Name:
Frequency
Description:
Sampling frequency, date range, and notes from raw YBFMP logger data.
Data Table Name:
stations_tbl
Description:
site locations for data
Other Name:
missing_dates
Description:
This figure shows the missing dates that required imputation or estimate for each location and year.
Detailed Metadata

Data Entities


Data Table

Data:https://pasta-s.lternet.edu/package/data/eml/edi/1178/1/5055c89851653f175078378a6e8ba6eb
Name:integrated_data
Description:This data is an integration of raw logger data as well as relevant California Data Exchange Center (CDEC) data (Pien et al. 2020, hourly) and water quality data collected during the Yolo Bypass Fish Monitoring Program’s (YBFMP) fish collection (Pien and Kwan 2022) to produce a daily water temperature dataset for the Yolo Bypass and Sacramento River at Sherwood Harbor and Rio Vista Bridge.
Number of Records:23663
Number of Columns:13

Table Structure
Object Name:integrated_data.csv
Size:2962630 byte
Authentication:729b358d1f74f4d14884dcec1180a928 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
 datemeanmaxminsdcvnsitecategorymethodlengthregionyear
Column Name:date  
mean  
max  
min  
sd  
cv  
n  
site  
category  
method  
length  
region  
year  
Definition:datedaily mean temperature (°C)daily maximum temperature (°C)daily minimum temperature (°C)daily standard deviation in water temperature (°C) daily coefficient of variation in water temperature (°C) number of data points per daysite of data collectiontype of estimate or datamethod used to estimate daily water temperature length of consecutive missing days of dataregion for which data belongsyear
Storage Type:dateTime  
float  
float  
float  
float  
float  
float  
string  
string  
string  
float  
string  
float  
Measurement Type:dateTimeratioratioratioratioratiorationominalnominalnominalrationominalratio
Measurement Values Domain:
FormatYYYY-MM-DD
Precision
Unitcelsius
Typereal
Unitcelsius
Typereal
Unitcelsius
Typereal
Unitcelsius
Typereal
Unitcelsius
Typereal
Unitcount
Typeinteger
Definitionsite of data collection
Allowed Values and Definitions
Enumerated Domain 
Code Definition
Codenan
Definitionno temperature data was available or estimated for this date
Source
Code Definition
Code7&Under
Definitionconsecutive missing dates is seven or less
Source
Code Definition
Codedata
Definitiondata was available for this date
Source
Code Definition
CodeOver7
Definitionconsecutive missing dates is more than seven
Source
Allowed Values and Definitions
Enumerated Domain 
Code Definition
Codenan
Definitionno temperature data was available or estimated for this date
Source
Code Definition
Codedaily_mean
Definitiondaily means only provided for this date
Source
Code Definition
CodeimputeTS
Definitionimputed in R using the package “imputeTS”, an exponential weighted moving average
Source
Code Definition
Codelm_lis
Definitiona linear model with the Lisbon Weir station data was used
Source
Code Definition
Codelm_rv
Definitiona linear model with the Rio Vista station data was used
Source
Code Definition
CodePien_2020
Definitiondata from Pien et al., 2020
Source
Code Definition
CodeWQ_w_fish
Definitiondata from Pien and Kwan 2022
Source
Code Definition
Codeybfmp_logger
DefinitionYBFMP logger data
Source
Unitcount
Typeinteger
Allowed Values and Definitions
Enumerated Domain 
Code Definition
Codefloodplain_bypass
DefinitionYolo Bypass
Source
Code Definition
Coderiver_downstream
DefinitionSacramento River at Rio Vista
Source
Code Definition
Coderiver_upstream
DefinitionSacramento River at Sherwood Harbor
Source
Unityear
Typeinteger
Missing Value Code:  
CodeNA
Explno data available to calculate or estimate a mean
CodeNA
Explno data available to calculate or estimate
CodeNA
Explno data available to calculate or estimate
CodeNA
Explno data available to calculate or estimate
CodeNA
Explno data available to calculate or estimate
CodeNA
Explno data available
CodeNA
Explno site
CodeNA
Explno category
CodeNA
Explno method
CodeNA
Explno missing dates estimated
   
Accuracy Report:                          
Accuracy Assessment:                          
Coverage:                          
Methods:                          

Data Table

Data:https://pasta-s.lternet.edu/package/data/eml/edi/1178/1/975a4dfb6658ce2d1bc6c53bc10b9533
Name:methods_tbl
Description:Summary table to clarify the methods used, by region, as well as the relationship between the method and category columns in the integrated data.
Number of Records:15
Number of Columns:4

Table Structure
Object Name:methods_tbl.csv
Size:574 byte
Authentication:452bd7452ed27665fbafa445b66c8967 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
 regionmethodcategorydate_n
Column Name:region  
method  
category  
date_n  
Definition:region for which data belongsmethod used to estimate daily water temperature type of estimate or datanumber of days
Storage Type:string  
string  
string  
float  
Measurement Type:nominalnominalnominalratio
Measurement Values Domain:
Allowed Values and Definitions
Enumerated Domain 
Code Definition
Codefloodplain_bypass
DefinitionYolo Bypass
Source
Code Definition
Coderiver_downstream
DefinitionSacramento River at Rio Vista
Source
Code Definition
Coderiver_upstream
DefinitionSacramento River at Sherwood Harbor
Source
Definitionmethod used to estimate daily water temperature
Allowed Values and Definitions
Enumerated Domain 
Code Definition
Codenan
Definitionmissing data
Source
Code Definition
Code7&Under
Definitionconsecutive missing dates is seven or less
Source
Code Definition
Codedata
Definitiondata was available for this date
Source
Code Definition
CodeOver7
Definitionconsecutive missing dates is more than seven
Source
Unitcount
Typeinteger
Missing Value Code:  
CodeNA
Explno method
CodeNA
Explno category
 
Accuracy Report:        
Accuracy Assessment:        
Coverage:        
Methods:        

Data Table

Data:https://pasta-s.lternet.edu/package/data/eml/edi/1178/1/7cf395303ce3665a9834721d4b748e4b
Name:Frequency
Description:Sampling frequency, date range, and notes from raw YBFMP logger data.
Number of Records:44
Number of Columns:6

Table Structure
Object Name:Frequency.csv
Size:2768 byte
Authentication:3c4bb8a59ed106b0d3e9eec21c9f813f 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
 LocationYearStart DateEnd DateSampling frequencyNotes from DWR’s YBFMP
Column Name:Location  
Year  
Start Date  
End Date  
Sampling frequency  
Notes from DWR’s YBFMP  
Definition:YBFMP logger locationsyearbeginning of sampling, dateend of sampling, datesampling frequency based on number of measurements per dayNotes included in excel spreadsheets from original data
Storage Type:string  
float  
dateTime  
dateTime  
string  
string  
Measurement Type:nominalratiodateTimedateTimenominalnominal
Measurement Values Domain:
Allowed Values and Definitions
Enumerated Domain 
Code Definition
CodeSHR
DefinitionSherwood Harbor
Source
Code Definition
CodeSTDD
Definitionscrew trap at the Toe Drain
Source
Unityear
Typeinteger
Formatmm/dd/yyyy
Precision
Formatmm/dd/yyyy
Precision
Allowed Values and Definitions
Enumerated Domain 
Code Definition
Code15-minute
Definitionfifteen-minute collection interval
Source
Code Definition
Code30-minute
Definitionthirty-minute collection interval
Source
Code Definition
CodeDaily
Definitiondaily means only provided for this date
Source
Code Definition
Codedaily
Definitiondaily means only provided for this date
Source
Code Definition
CodeHourly
Definitionhourly collection interval
Source
Code Definition
Codehourly
Definitionhourly collection interval
Source
Allowed Values and Definitions
Enumerated Domain 
Code Definition
Codenan
Definitionno information provided
Source
Code Definition
Code1/1/2017 - 4/5/2017 - Data is from YSI sonde near RSTR - hobo DATA was lost during downloading process
Definitionnotes
Source
Code Definition
CodeBattery in HOBO died 9/12/2016 and was removed and replaced with new HOBO logger 9/15/16, Inserted Water Temperature Data from CDEC site SRH due to missing data - missing data was mostly due to downloading errors onto the HOBO shuttle
Definitionnotes
Source
Code Definition
CodeData file from 1/10/2017 11:15 - 4/4/2017 9:30 was lost during download - data was replaced w/ FPT CDEC temp data (text in blue), Data files 12/14/17-1/18/18 had date and time error that had to be corrected - due to HOBO shuttle low battery and incorrect internal date and time
Definitionnotes
Source
Code Definition
CodeData from 9/20 12:00 thru 12/31 23:45 inserted from data collected with YSI sonde installed at STTD site
Definitionnotes
Source
Code Definition
Codenew data loggers were deployed (spring)
Definitionnotes
Source
Code Definition
Codeonly daily average temperature is available
Definitiondaily means only provided for this date
Source
Code Definition
CodeRSTR data collected year-round
Definitionnotes
Source
Code Definition
CodeRSTR was destroyed during inundation event - Large data gap (3/17/11 - 5/4/2011)
Definitionnotes
Source
Missing Value Code:            
Accuracy Report:            
Accuracy Assessment:            
Coverage:            
Methods:            

Data Table

Data:https://pasta-s.lternet.edu/package/data/eml/edi/1178/1/09e7587cf2b2fde6136f1d50762bd6e0
Name:stations_tbl
Description:site locations for data
Number of Records:24
Number of Columns:6

Table Structure
Object Name:stations_tbl.csv
Size:1930 byte
Authentication:1d71ceaa6005ee617d47cfb91a50df55 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
 StationCodeStationNameStationNumberLatitudeLongitudeSource
Column Name:StationCode  
StationName  
StationNumber  
Latitude  
Longitude  
Source  
Definition:station name from YBFMP or CDECname/description of locationstation name from YBFMP or CDEClatitudelongitudesource of additional data
Storage Type:string  
string  
string  
float  
float  
string  
Measurement Type:nominalnominalnominalratiorationominal
Measurement Values Domain:
Definitionstation name from YBFMP or CDEC
Definitionname/description of location
Definitionstation name from YBFMP or CDEC
Unitdecimal degrees
Typereal
Unitdecimal degrees
Typereal
Allowed Values and Definitions
Enumerated Domain 
Code Definition
Codenan
Definitionnot yet published, YBFMP logger data
Source
Code Definition
CodePien and Kwan 2022
Definitionhttps://portal.edirepository.org/nis/mapbrowse?packageid=edi.233.3
Source
Code Definition
CodePien et al. 2020
Definitionhttps://portal.edirepository.org/nis/mapbrowse?packageid=edi.591.2
Source
Missing Value Code:            
Accuracy Report:            
Accuracy Assessment:            
Coverage:            
Methods:            

Non-Categorized Data Resource

Name:missing_dates
Entity Type:tiff
Description:This figure shows the missing dates that required imputation or estimate for each location and year.
Physical Structure Description:
Object Name:missing_dates.tiff
Size:10800192 byte
Authentication:e8f3442f12d63fd0cba597d2072b0d31 Calculated By MD5
Externally Defined Format:
Format Name:tiff
Data:https://pasta-s.lternet.edu/package/data/eml/edi/1178/1/0b2a93672810a06cd7f200e40a358aee

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)water temperature , estuary, Yolo Bypass, California, Interagency Ecological Program for the San Francisco Bay Delta Estuary, California Data Exchange Center, California Department of Water Resources, Delta Stewardship Council - Delta Science Program, National Center for Ecological Analysis and Synthesis
LTER Controlled Vocabularyfloodplain

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:
Daily water temperature (°C) was estimated for each of the three locations (Yolo Bypass, and Sacramento River at Sherwood Harbor and Rio Vista) from a variety of sources. Data integration code can be found at https://github.com/Delta-Stewardship-Council/ybfmp_temperature. The f_get functions bring in the raw data from the data_raw folder and relevant EDI publications. The f_get_hourly and f_gert_WQ_w_fish scripts incorporate Pien et al., 2020 (hourly QC’ed California Data Exchange Center data for Lisbon Weir, LIS, and Rio Vista, RVB and RIV) and Pien and Kwan 2022 (water quality data collected during the Yolo Bypass Fish Monitoring Program’s fish collection). The f_get_RSTR (Yolo Bypass at the rotary screw trap) and f_get_SHWharbor (Sacramento River at Sherwood Harbor) organize and QC the Yolo Bypass Fish Monitoring Program’s (YBFMP) logger data, which are then made into daily summaries in f_make_daily. The imputation and linear regression estimation to fill missing dates was conducted in the f_make_(site name) scripts. The data in the data_raw folder is continuous water temperature collected by the YBFMP between 1998 and 2019. Data were collected in the Yolo Bypass at the Screw Trap in the Toe Drain (STTD) and at the Sacramento River at Sherwood Harbor (SHR) using a HOBO loggers (Onset Computer Corp "Optic StowAway Temp" loggers). Logger data ranged from daily means (1998) to a fifteen-minute collection interval (2013-2017 for the Yolo Bypass, 2009-2019 for Sherwood Harbor). Missing data occurred regularly due to malfunctions in equipment, shortages of staff, and inability to access sites (see frequency table). A daily mean, maximum, minimum, standard deviation and coefficient of variation in water temperature was produced as well as columns for sample size (n, number of measurements per day), method (data collection or estimation), category, length (number of consecutive missing dates) and site. Method and category refer to the source or type of estimate used to produce the daily values (see methods table). Within our period of interest (1998-2019) consecutive missing days of data ranged from 693 days (2018/01/31- 2019/12/25 in the Yolo Bypass) to one day. In the Yolo Bypass, when possible missing data was substituted with water temperature measured during fish sampling (method = WQ_w_fish, category = data). Remaining gaps of missing data that were less than or equal to seven consecutive days were imputed in R using the package “imputeTS”, an exponential weighted moving average (method = imputeTS, category = 7&under). When seven or more consecutive days were missing in the Yolo Bypass, first a linear model with the Lisbon Weir station data (Adjusted R-squared = 0.7967) and then a linear model with Rio Vista station data (Adjusted R-squared = 0.8106) was used to estimate water temperature (method = lm_lis and lm_rv, respectively). At Sherwood Harbor a linear model with Rio Vista station data (Adjusted R-squared = 0.9745) was used to estimate Sacramento River water temperature in cases with greater than seven days of consecutive missing dates (method = lm_rv, category = Over7). Despite our best efforts, missing days of data remain for the Yolo Bypass (n = 188) and Sherwood Harbor (n = 310) locations (NA). ==================== Data Sources ========================= DWR-6-SOP-016_v1.1_BeachSeineSampling (https://github.com/AEU-DISE/publish_fish/tree/main/metadata/methods_references), DWR-6-SOP-017_v1.1_FykeTrapSampling (https://github.com/AEU-DISE/publish_fish/tree/main/metadata/methods_references), DWR-6-SOP-018_v1.1_RotaryScrewTrapSampling (https://github.com/AEU-DISE/publish_fish/tree/main/metadata/methods_references), Fish_Publication_QAQC_Workflow_v1.0 (https://github.com/AEU-DISE/publish_fish/tree/main/metadata/methods_references) ===========================================================

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: Pascale Goertler
Organization:Delta Stewardship Council – Delta Science Program
Position:Senior Environmental Scientist
Email Address:
pascale.goertler@deltacouncil.ca.gov
Id:https://orcid.org/0000-0001-6259-5108
Individual: Catarina Pien
Organization:U.S. Bureau of Reclamation
Position:Fish Biologist
Email Address:
cpien@usbr.gov
Id:https://orcid.org/0000-0003-4427-6300
Contacts:
Individual: Pascale Goertler
Position:Senior Environmental Scientist
Email Address:
pascale.goertler@deltacouncil.ca.gov
Id:https://orcid.org/0000-0001-6259-5108
Associated Parties:
Individual: Nicole Kwan
Organization:California Department of Water Resources
Position:Senior Environmental Scientist
Email Address:
Nicole.Kwan@water.ca.gov
Id:https://orcid.org/0000-0003-1178-7788
Role:Data owner
Individual: Naoaki Ikemiyagi
Organization:California Department of Water Resources
Position:Environmental Scientist
Email Address:
Naoaki.Ikemiyagi@water.ca.gov
Role:Data owner
Individual: Jared Frantzich
Organization:California Department of Water Resources
Position:Senior Environmental Scientist
Email Address:
Jared.Frantzich@water.ca.gov
Role:Data owner
Metadata Providers:
Individual: Catarina Pien
Organization:U.S. Bureau of Reclamation
Position:Fish Biologist
Email Address:
cpien@usbr.gov
Id:https://orcid.org/0000-0003-4427-6300

Temporal, Geographic and Taxonomic Coverage

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

Time Period
Begin:
1998-01-16
End:
2019-12-31
Geographic Region:
Description:Yolo Bypass, a seasonal floodplain-tidal slough, and the Sacramento River at Sherwood Harbor and Rio Vista Bridge in California, USA.
Bounding Coordinates:
Northern:  38.74979Southern:  38.1592
Western:  -121.686Eastern:  -121.528

Project

Parent Project Information:

Title:DSP-NCEAS synthesis working group
Personnel:
Individual: Pascale Goertler
Organization:Delta Stewardship Council – Delta Science Program
Position:Senior Environmental Scientist
Email Address:
pascale.goertler@deltacouncil.ca.gov
Id:https://orcid.org/0000-0001-6259-5108
Role:creator
Individual: Catarina Pien
Organization:U.S. Bureau of Reclamation
Position:Fish Biologist
Email Address:
cpien@usbr.gov
Id:https://orcid.org/0000-0003-4427-6300
Role:Data and metadata provider
Abstract:Ecological synthesis is a critical component of ecosystem-based management and informed decision-making, both of which are tools for achieving the coequal goals. The need for increased capacity, dedicated time, and coordinated synthesis in the San Francisco Estuary (SFE) is widely recognized and included as an action in the Delta Science Plan, Science Action Agenda, and Interagency Ecological Program Science Strategy. This effort, led by the Delta Science Program (DSP) in partnership with the National Center for Ecological Analysis and Synthesis (NCEAS), provided high-quality training in data science and statistics and an opportunity for enhanced collaboration among agency and academic scientists in a focused working group. This is one of many products from this working group which can be used to offer strong scientific support to inform decision-making for restoration, protection of endangered species, and management of flow actions in the SFE.

Maintenance

Maintenance:
Description:This data is complete. However the California Department of Water Resources, Yolo Bypass Fish Monitoring Program (and member of the Interagency Ecological Program for the San Francisco Bay Delta Estuary) intends to QC and publish the raw temperature logger data (at the fifteen-minute interval), which was used to estimate daily mean, maximum, minimum, standard deviation and coefficient of variation water temperature in the Yolo Bypass and Sacramento River at Sherwood Harbor. Those data are currently available by request, those interested can contact the Aquatic Ecology Unit (Nicole.Kwan@water.ca.gov and Naoaki.Ikemiyagi@water.ca.gov).
Frequency:
Other Metadata

Additional Metadata

additionalMetadata
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        |     |     |     |  \___attribute 'id' = 'decimal degrees'
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Additional Metadata

additionalMetadata
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        |     |___element 'emlEditor'
        |     |        \___attribute 'app' = 'ezEML'
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