Data Package Metadata View Summary

Fish Restoration Program Tidal Wetland Restoration Monitoring in Upper San Francisco Estuary, 2015-ongoing

General Information

Data Package:

Local Identifier:

edi.269.10

Title:

Fish Restoration Program Tidal Wetland Restoration Monitoring in Upper San Francisco Estuary, 2015-ongoing

Alternate Identifier:

DOI PLACE HOLDER

Abstract:

The Fish Restoration Program Monitoring Team assesses the biological effectiveness of 8,000+ acres of tidal wetland restoration in the Upper San Francisco Estuary (Sacramento-San Joaquin Delta and Suisun Marsh) through a contract with the CA Department of Water Resources. The restoration is pursuant to requirements in the 2008 /2009 and 2019 Biological Opinions for state and federal water project operations. Data on fish and invertebrate abundance on or near these sites was collected as baseline monitoring data and to determine the most efficient methods for monitoring wetlands. Understanding how invertebrate and, fish, and phytoplankton communities change pre- to post-restoration is essential to evaluating the benefits of tidal wetlands to native fish species. Invertebrate data was collected using sweep nets, benthic cores, neuston nets, and zooplankton trawls. Fish data was collected using otter trawls, lampara nets, and beach seines. For each method, the team recorded the catch of fish or invertebratesorganisms, length of organisms, and a suite of environmental information, including: dissolved oxygen, temperature, pH, specific conductance, turbidity, chlorophyll a, phycocyanin, and dissolved organic carbon. Additional water quality samples, processed for Chlorophyll a, Dissolved Ammonia, Dissolved Nitrite + Nitrate, Dissolved Organic Carbon, Dissolved Organic Nitrogen, Dissolved Ortho-phosphate, Pheophytin a, Total Kjeldahl Nitrogen, Total Organic Carbon, Total Phosphorus, and Total Suspended Solids, were collected at a subset of sampling sites. Data are collected before and after restoration at project and reference sites (Before-After-Control-Impact-design), as well as at adjacent water bodies.

Publication Date:

2024-06-21

For more information:
Visit:	DOI PLACE HOLDER

Time Period

Begin:

2015

End:

2022

People and Organizations
Contact:	Bowles, Christy (California Department of Fish and Wildlife, Senior Environmental Scientist (Specialist)) [ email ]
Contact:	Sherman, Stacy (California Department of Fish and Wildlife, Environmental Program Manager) [ email ]
Creator:	Sherman, Stacy (California Department of Fish and Wildlife, Environmental Program Manager)
Creator:	Bowles, Christy (California Department of Fish and Wildlife, Senior Environmental Scientist (Specialist))
Creator:	Avila, Michelle (California Department of Fish and Wildlife, Environmental Scientist)
Creator:	Cox, Daniel (California Department of Fish and Wildlife, Environmental Scientist)
Creator:	Davidson, Emma (California Department of Fish and Wildlife, Environmental Scientist)
Creator:	Ng, Gabriel (California Department of Fish and Wildlife, Environmental Scientist)
Creator:	Hartman, Rosemary (California Department of Water Resources, Environmental Program Manager (Specialist))
Creator:	Ellis, Daniel (California Department of Fish and Wildlife, Senior Environmental Scientist (Specialist))
Creator:	Contreras, Dave (California Department of Fish and Wildlife, Environmental Scientist)

Data Entities
Data Table Name:	sitevisit_FRP2022
Description:	A site visit is a field data collection event. At each site visit, one or more samples may be collected. A site visit connects to samples in the macrozooplankton, zooplankton, or fish tables, via the VisitNo variable. Commonly, the site visit file will be merged with the macroinvert, zoops, or fish data files. This is a 1 to many merge, with VisitNo as the key variable. For example, in R, newdatafile<-merge(zoops_FRP2021, sitevisit_FRP2021, by=VisitNo). All samples are associated with a site visit, a site visit may have zero to many samples.
Data Table Name:	FRP_orglookup
Description:	Table of taxonomic information for organisms caught in mesozooplankton, macroinvertebrate, and fish samples.
Data Table Name:	phyto_FRP2022
Description:	Contains sample and catch data for phytoplankton samples. There is one observation (row) for each measured phytoplankton within a sample.
Data Table Name:	zoops_FRP2022
Description:	Mesozooplankton trawl data, including sample and catch data. CPUEs are reported for each taxon. To calculate the total CPUE for each sample, sum the CPUEs for individual taxa. Typically, there is one observation (row) for each taxonomic group within a sample, but occasionally, the subsampling was changed during processing and there are two observations (rows) for a single taxonomic group within the sample.
Data Table Name:	macroinvert_FRP2022
Description:	Contains sample and catch data for macroinvertebrate samples. Macroinvertebrate samples include all gear types with mesh size of 500 microns, including trawls, benthic samples, and samples taken in vegetation. Typically, there is one observation (row) for each taxonomic group within a sample, but occasionally, the subsampling was changed during processing and there are two observations (rows) for a single taxonomic group within the sample.
Data Table Name:	fish_FRP2022
Description:	Contains sample and catch data for fish samples. Total CPUE can be calculated by summing the individual catches, dividing by effort, and multiplying by 10,000 to get the number of fish per 10,000 m^3.
Other Name:	Monitoring SOPsv1.2
Description:	Contains detailed Standard Operating Procedures for field and lab data collection, including gear specifications.

Detailed Metadata

Data Entities

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/edi/269/10/564d8a6cd8ee2afaaf647957ef2f1892
Name:	sitevisit_FRP2022
Description:	A site visit is a field data collection event. At each site visit, one or more samples may be collected. A site visit connects to samples in the macrozooplankton, zooplankton, or fish tables, via the VisitNo variable. Commonly, the site visit file will be merged with the macroinvert, zoops, or fish data files. This is a 1 to many merge, with VisitNo as the key variable. For example, in R, newdatafile<-merge(zoops_FRP2021, sitevisit_FRP2021, by=VisitNo). All samples are associated with a site visit, a site visit may have zero to many samples.
Number of Records:	2784
Number of Columns:	17

Table Structure

Object Name:

sitevisit_FRP2022.csv

Size:

414958 byte

Authentication:

4bc3616dad94af0e5f36079a42a61dd0 Calculated By MD5

Text Format:

Number of Header Lines:

Record Delimiter:

\r\n

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	"

Table Column Descriptions

VisitNo

Location

Date

Temp

Turbidity

Chlorophyll

Phycocyanin

FDOM

Secchi

Microcystis

Tide

Weather

WindWaves

Flagged_Data

Column Name:

VisitNo

Location

Date

Temp

Turbidity

Chlorophyll

Phycocyanin

FDOM

Secchi

Microcystis

Tide

Weather

WindWaves

Flagged_Data

Definition:

Unique identifier for site visit. Each site visit represents a field sampling event and may contain zero or more samples.

Name of a restoration project, adjacent waterbody, or reference marsh.

Date of site visit and sample collection

Water temperature as measured by a YSI ProPlus, YSI 6600 sonde, or YSI EXO 2. Resolution 0.1 degrees C

Specific conductance as measured by a YSI ProPlus, YSI 6600, or YSI EXO 2 sonde

pH as measured by a YSI ProPlus, YSI 6600 sonde, or YSI EXO 2.

Dissolved oxygen as measured by a YSI ProPlus, YSI 6600, YSI EXO 2 sonde

Turbidity as measured with either a Micro TWP portable turbidity meter (HF Scientific, Inc, 0.1 NTU resolution), a YSI 6600 sonde, or YSI EXO 2.

Measure of chlorophyll pigment in water from YSI EXO 2

Measure of phycocyanin pigment in water by YSI EXO 2

Fluorescent Dissolved Organic Matter, measured by a YSI EXO 2

Depth at which the secchi disk can no longer be seen.

Amount of Microcystis (toxic cyanobacteria) present in the water.

Tidal current

Weather

Beaufort Wind Scale

Questionable data is flagged. 4 = data are not useable, 3 = data are questionable, 2= data are checked and good, 1 = good data with no flags. Comments are included in the Macrozooplankton, mesozooplankton, and fish data files.

Storage Type:

float

string

dateTime

float

string

Measurement Type:

ratio

nominal

dateTime

ratio

nominal

Measurement Values Domain:

Unit	Unique Identifier for a site visit
Type	real

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	Arnold Slough
Definition	Restoration project in Nurse-Denverton. Construction was completed October 2021.
Source

Code Definition

Code	Blacklock Marsh
Definition	Reference marsh for Arnold and Bradmoor restoration projects. Blacklock Marsh was an earlier restoration project that was completed in 2006.
Source

Code Definition

Code	Bradmoor Island
Definition	Restoration project in Nurse-Denverton. Construction was completed in November 2022.
Source

Code Definition

Code	Broad Slough
Definition	Adjacent water body for Winter Island restoration project.
Source

Code Definition

Code	Browns Island
Definition	Reference marsh for Winter Island and Chipps Island restoration projects
Source

Code Definition

Code	Cache Slough
Definition	The slough to the southwest of the Lookout Slough restoration project
Source

Code Definition

Code	Cache Slough South
Definition	South of Liberty Island
Source

Code Definition

Code	Chipps Island
Definition	Planned restoration project in the Sacramento-San Joaquin Confluence.
Source

Code Definition

Code	Decker Island
Definition	Restoration project in the lower Sacramento River. Construction was completed in October 2018.
Source

Code Definition

Code	Dow
Definition	Corteva Wetlands Preserve (formerly Dow Wetland Preserve) in the Sacramento-San Joaquin Confluence. Dow was sampled as a potential restoration project but is no longer sampled by FRP.
Source

Code Definition

Code	East Delta
Definition	Eastern portion of the Delta.
Source

Code Definition

Code	Grizzly Bay
Definition	Adjacent water body for Tule Red restoration project.
Source

Code Definition

Code	Honker-Spoonbill
Definition	Honker Bay and Spoonbill are the adjacent waterbodies for Chipps Island
Source

Code Definition

Code	Horseshoe Bend
Definition	Adjacent water body for Decker Island restoration project.
Source

Code Definition

Code	Liberty Island
Definition	Reference for restoration projects in Cache Slough Complex, North Delta. It is a former agricultural island, unintentionally breached and left to restore naturally in the late 1990s
Source

Code Definition

Code	Lindsey Slough
Definition	Lindsey Slough was sampled as a potential reference for projects in the Cache Slough Complex but is no longer sampled. It is a CDFW restoration project that was completed in 2014
Source

Code Definition

Code	Lookout Slough
Definition	Planned restoration project in Cache Slough Complex.
Source

Code Definition

Code	Lower Yolo Ranch
Definition	Restoration project in the Cache Slough Complex, North Delta. Construction was completed in August 2020.
Source

Code Definition

Code	Miner Slough
Definition	Adjacent water body for Prospect Island restoration project.
Source

Code Definition

Code	Montezuma
Definition	This is the section of the Montezuma Slough that is outside of Nurse-Denverton.
Source

Code Definition

Code	Nurse-Denverton
Definition	Adjacent water body for Arnold Slough and Bradmoor Island restoration projects.
Source

Code Definition

Code	Peytonia-Suisun
Definition	Adjacent water body for Wings Landing restoration project.
Source

Code Definition

Code	Prospect Island
Definition	Planned restoration project in Cache Slough Complex.
Source

Code Definition

Code	Rush Ranch
Definition	Reference for Wings Landing restoration project. Part of the San Francisco Bay National Estuarine Research Reserve.
Source

Code Definition

Code	Ryer Island
Definition	Reference for Tule Red restoration project
Source

Code Definition

Code	San Joaquin
Definition	The lower San Joaquin River
Source

Code Definition

Code	Shag Slough
Definition	Adjacent water body for Lookout Slough restoration project.
Source

Code Definition

Code	Sherman Island
Definition	Sherman Island in the Sacramento-San Joaquin Confluence
Source

Code Definition

Code	Stairsteps-Liberty Cut
Definition	Adjacent water body for Lower Yolo Ranch.
Source

Code Definition

Code	Suisun Bay
Definition	Suisun Bay near Ryer Island
Source

Code Definition

Code	Toe Drain
Definition	Adjacent water body for Yolo Flyway Farms
Source

Code Definition

Code	Tule Red
Definition	Restoration project in Suisun Slough. Construction was completed in October 2019.
Source

Code Definition

Code	Tule Red_Adjacent
Definition	Ponded wetland adjacent to Tule Red restoration project. Sampled before restoration.
Source

Code Definition

Code	Webb Tract Island and Berm
Definition	Reference for Decker Island restoration project. A remnant marsh northeast of Webb Tract
Source

Code Definition

Code	Wildlands
Definition	Formally known as Liberty Island Conservation Bank. Restoration project in Cache Slough Complex. Not a FRP project.
Source

Code Definition

Code	Wings Landing
Definition	Restoration project in west Suisun Marsh. Construction was completed in September 2020.
Source

Code Definition

Code	Winter Island
Definition	Restoration project in the Sacramento-San Joaquin Confluence. Construction was completed in September 2019
Source

Code Definition

Code	Yolo Flyway Farms
Definition	Restoration project in Cache Slough Complex. Construction was completed in September 2018
Source

Format	YYYY-MM-DD
Precision

Unit	celsius
Precision	0.1
Type	real

Unit	MicrosiemensPerCm
Precision	1
Type	real

Unit	pH
Precision	0.1
Type	real

Unit	milligramPerLiter
Precision	0.1
Type	real

Unit	FNU
Type	real
Min	0
Max

Unit	RFU
Precision	0.1
Type	real

Unit	RFU
Precision	0.1
Type	real

Unit	RFU
Precision	0.1
Type	real

Unit	centimeter
Precision	1
Type	real

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	1=absent
Definition	absent
Source

Code Definition

Code	2=low
Definition	low
Source

Code Definition

Code	3=medium
Definition	medium
Source

Code Definition

Code	4=high
Definition	high
Source

Code Definition

Code	5=very high
Definition	very high
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	1=high slack
Definition	high slack
Source

Code Definition

Code	2=ebb
Definition	ebb
Source

Code Definition

Code	3=low slack
Definition	low slack
Source

Code Definition

Code	4=flood
Definition	flood
Source

Code Definition

Code	5=NA
Definition	NA
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	1=0-33% clouds
Definition	0-33% clouds
Source

Code Definition

Code	2=33-66% clouds
Definition	33-66% clouds
Source

Code Definition

Code	3=66-100% clouds
Definition	66-100% clouds
Source

Code Definition

Code	4=rain
Definition	rain
Source

Code Definition

Code	5=fog
Definition	fog
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	0=Calm; glassy
Definition	Calm; glassy
Source

Code Definition

Code	1=wind 1-3 mph; scaley ripples
Definition	wind 1-3 mph; scaley ripples
Source

Code Definition

Code	2= wind 4-7 mph; small wavelets
Definition	wind 4-7 mph; small wavelets
Source

Code Definition

Code	3= wind 8-12 mph; large wavelets
Definition	wind 8-12 mph; large wavelets
Source

Code Definition

Code	4= wind 13-18 mph; small waves
Definition	wind 13-18 mph; small waves
Source

Code Definition

Code	5= wind 19-24 mph; moderate waves; some spray
Definition	wind 19-24 mph; moderate waves; some spray
Source

Definition

text

Missing Value Code:

Code	NA
Expl	Data was not collected or instrument malfunctioned

Code	NA
Expl	Data was not collected or instrument malfunctioned

Code	NA
Expl	Data was not collected or instrument malfunctioned

Code	NA
Expl	Data was not collected or instrument malfunctioned

Code	NA
Expl	Data was not collected or instrument malfunctioned

Code	NA
Expl	Data was not collected or instrument malfunctioned

Code	NA
Expl	Data was not collected or instrument malfunctioned

Code	NA
Expl	Data was not collected or instrument malfunctioned

Code	NA
Expl	Data was not collected

Code	NA
Expl	Data was not collected

Code	NA
Expl	Data was not collected

Code	NA
Expl	Data was not collected

Code	NA
Expl	Data was not collected

Accuracy Report:

Accuracy Assessment:

Coverage:

Methods:

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/edi/269/10/731994de4b658f3fd12dceda58353f9e
Name:	FRP_orglookup
Description:	Table of taxonomic information for organisms caught in mesozooplankton, macroinvertebrate, and fish samples.
Number of Records:	690
Number of Columns:	9

Table Structure

Object Name:

FRP_orglookup2022.csv

Size:

60458 byte

Authentication:

54645dfddf3d9aec78fd9253a824c689 Calculated By MD5

Text Format:

Number of Header Lines:

Record Delimiter:

\r\n

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	"

Table Column Descriptions

CommonName

Phylum

Class

Order

Family

Genus

Species

LifeStage

Notes

Column Name:

CommonName

Phylum

Class

Order

Family

Genus

Species

LifeStage

Notes

Definition:

Lowest taxonomic level used to identify individual organisms.

Taxonomic phylum

Taxonomic class

Taxonomic order

Taxonomic family

Genus

Species

Life stage

Notes and comments, including changes from 2018 publication taxonomy.

Storage Type:

string

Measurement Type:

nominal

Measurement Values Domain:

Definition

text

Definition

text

Definition

text

Definition

text

Definition

text

Definition

text

Definition

text

Definition

text

Definition

text

Missing Value Code:

Code	NA
Expl	Missing data

Code	NA
Expl	Missing data or includes multiple taxonomic groups

Code	NA
Expl	Missing data or includes multiple taxonomic groups

Code	NA
Expl	Missing data or includes multiple taxonomic groups

Code	NA
Expl	Missing data or includes multiple taxonomic groups

Code	NA
Expl	Missing data or includes multiple taxonomic groups

Code	NA
Expl	Missing data or includes multiple life stages

Code	NA
Expl	No comments

Accuracy Report:

Accuracy Assessment:

Coverage:

Methods:

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/edi/269/10/6367f6f47590ee20036f56716a7b4212
Name:	phyto_FRP2022
Description:	Contains sample and catch data for phytoplankton samples. There is one observation (row) for each measured phytoplankton within a sample.
Number of Records:	6600
Number of Columns:	22

Table Structure

Object Name:

phyto_FRP2022.csv

Size:

2117320 byte

Authentication:

694e9119a1b7c778758bcc911756c1dd Calculated By MD5

Text Format:

Number of Header Lines:

Record Delimiter:

\r\n

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	"

Table Column Descriptions

VisitNo

SampleID_frp

Survey

Location

LatitudeStart

LongitudeStart

Date

StartTime

DepthOfSample

DepthOfWater

Substrate

LAB_NAME

OriginalTaxon

CommonName

Taxonomy_FRP

Taxonomy_TB

Units_permL

Cells_permL

Biov_permL

GALD

PhytoForm

QualityCheck

Column Name:

VisitNo

SampleID_frp

Survey

Location

LatitudeStart

LongitudeStart

Date

StartTime

DepthOfSample

DepthOfWater

Substrate

LAB_NAME

OriginalTaxon

CommonName

Taxonomy_FRP

Taxonomy_EMP

Units_permL

Cells_permL

Biov_permL

GALD

PhytoForm

QualityCheck

Definition:

Unique identifier for site visit. Each site visit represents a field sampling event and may contain one or more samples.

Unique identifier for a single sample

Project group that collected the data.

Name of a restoration project, adjacent waterbody, or reference marsh.

Latitude where sample collection started in decimal degrees, WGS1984 as measured by Garmin 72H GPS or Lowrance HDS-7 Gen2 sonar

Longitude where sampling begins in decimal degrees, WGS1984 as measured by Garmin 72H GPS or Lowrance HDS-7 Gen2 sonar

Date sampling occurred

Time at beginning of sample collection

Distance from water surface to depth of sample collection.

Depth of water

Microhabitat where sample was collected.

Name of the lab that processed the data

Taxon assigned by the contractor when the sample was originally processed.

Lowest taxonomic level used to identify individual organisms. See organism lookup table for more information.

Taxonomic classifications used by FRP

Taxonomic classifications used by the Interagency Ecological Program Environmental Monitoring Program

Number of organism units per mililiter

Number of cells per millilter

Biovolume of phytoplankton per mililiter water

Greatest axial linear dimension

Phytoplankton form code; shape

Notes about quality concerns

Storage Type:

float

string

float

dateTime

float

string

float

string

Measurement Type:

ratio

nominal

ratio

dateTime

ratio

nominal

ratio

nominal

Measurement Values Domain:

Unit	code for unique identifier
Type	integer

Definition

text

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	FRP
Definition	Fish Restoration Program
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	Arnold Slough
Definition	Restoration project in Nurse-Denverton. Construction was completed October 2021.
Source

Code Definition

Code	Blacklock Marsh
Definition	Reference marsh for Arnold and Bradmoor restoration projects. Blacklock Marsh was an earlier restoration project that was completed in 2006.
Source

Code Definition

Code	Bradmoor Island
Definition	Restoration project in Nurse-Denverton. Construction was completed in November 2022.
Source

Code Definition

Code	Broad Slough
Definition	Adjacent water body for Winter Island restoration project.
Source

Code Definition

Code	Browns Island
Definition	Reference marsh for Winter Island and Chipps Island restoration projects
Source

Code Definition

Code	Chipps Island
Definition	Planned restoration project in the Sacramento-San Joaquin Confluence.
Source

Code Definition

Code	Decker Island
Definition	Restoration project in the lower Sacramento River. Construction was completed in October 2018.
Source

Code Definition

Code	Dow
Definition	Corteva Wetlands Preserve (formerly Dow Wetland Preserve) in the Sacramento-San Joaquin Confluence. Dow was sampled as a potential restoration project but is no longer sampled by FRP.
Source

Code Definition

Code	Grizzly Bay
Definition	Adjacent water body for Tule Red restoration project.
Source

Code Definition

Code	Honker-Spoonbill
Definition	Honker Bay and Spoonbill are the adjacent waterbodies for Chipps Island.
Source

Code Definition

Code	Horseshoe Bend
Definition	Adjacent water body for Decker Island restoration project.
Source

Code Definition

Code	Liberty Island
Definition	Reference for restoration projects in Cache Slough Complex, North Delta. It is a former agricultural island, unintentionally breached and left to restore naturally in the late 1990s
Source

Code Definition

Code	Lindsey Slough
Definition	Lindsey Slough was sampled as a potential reference for projects in the Cache Slough Complex but is no longer sampled. It is a CDFW restoration project that was completed in 2014
Source

Code Definition

Code	Lookout Slough
Definition	Planned restoration project in Cache Slough Complex.
Source

Code Definition

Code	Lower Yolo Ranch
Definition	Restoration project in the Cache Slough Complex, North Delta. Construction was completed in August 2020.
Source

Code Definition

Code	Miner Slough
Definition	Adjacent water body for Prospect Island restoration project.
Source

Code Definition

Code	Nurse-Denverton
Definition	Adjacent water body for Arnold Slough and Bradmoor Island restoration projects.
Source

Code Definition

Code	Peytonia-Suisun
Definition	Adjacent water body for Wings Landing restoration project.
Source

Code Definition

Code	Prospect Island
Definition	Planned restoration project in Cache Slough Complex.
Source

Code Definition

Code	Rush Ranch
Definition	Reference for Wings Landing restoration project. Part of the San Francisco Bay National Estuarine Research Reserve.
Source

Code Definition

Code	Ryer Island
Definition	Reference for Tule Red restoration project
Source

Code Definition

Code	Shag Slough
Definition	Adjacent water body for Lookout Slough restoration project.
Source

Code Definition

Code	Stairsteps-Liberty Cut
Definition	Adjacent water body for Lower Yolo Ranch.
Source

Code Definition

Code	Toe Drain
Definition	Adjacent water body for Yolo Flyway Farms
Source

Code Definition

Code	Tule Red
Definition	Restoration project in Suisun Slough. Construction was completed in October 2019.
Source

Code Definition

Code	Webb Tract Islands and Berms
Definition	Reference for Decker Island restoration project. A remnant marsh northeast of Webb Tract.
Source

Code Definition

Code	Wings Landing
Definition	Restoration project in west Suisun Marsh. Construction was completed in September 2020.
Source

Code Definition

Code	Winter Island
Definition	Restoration project in the Sacramento-San Joaquin Confluence. Construction was completed in September 2019
Source

Code Definition

Code	Yolo Flyway Farms
Definition	Restoration project in Cache Slough Complex. Construction was completed in September 2018
Source

Unit	degree
Type	real
Min	38
Max	38.2

Unit	degree
Type	real
Min	121.3
Max	122.1

Format	YYYY-MM-DD
Precision

Format	hh:mm
Precision	30

Unit	meter
Precision	0.1
Type	real

Unit	meter
Type	real

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	benthic
Definition	Sample was collected from the top 0.5cm of sediment.
Source

Code Definition

Code	epiphytic
Definition	Sample was collected by scraping vegetation.
Source

Code Definition

Code	pelagic
Definition	Sample was collected from water.
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	BSA
Definition	Data were processed by BSA Environmental Services, Inc.
Source

Code Definition

Code	EcoAnalyst
Definition	Data were processed by EcoAnalysts, Inc.
Source

Code Definition

Code	EcoAnalysts
Definition	Data were processed by EcoAnalysts, Inc.
Source

Code Definition

Code	FRP
Definition	Data were processed by Fish Restoration Program, Department of Fish and Wildlife, in Stockton, CA.
Source

Definition

text

Definition

text

Definition

text

Definition

text

Unit	organism units per mL
Type	real

Unit	Cells per mL
Type	real

Unit	Volume phytoplankton per mL water
Type	real

Unit	Liner dimension
Type	real

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	c
Definition	colony
Source

Code Definition

Code	f
Definition	filament
Source

Code Definition

Code	i
Definition	individual cell
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	BrokenDiatoms
Definition	Sample had broken phytoplankton.
Source

Code Definition

Code	Good
Definition	Data meet quality standards.
Source

Code Definition

Code	LessThan400cells
Definition	When the sample was processed, fewer than 400 cells were counted.
Source

Code Definition

Code	LessThan400cells PoorlyPreserved
Definition	Less than 400 cells were counted and the sample was poorly preserved.
Source

Code Definition

Code	PoorlyPreserved
Definition	Sample was poorly preserved.
Source

Missing Value Code:

Code	NA
Expl	Data was not collected or instrument malfunctioned

Code	NA
Expl	Data was not collected or instrument malfunctioned

Code	NA
Expl	Data was not collected

Code	NA
Expl	Data was not collected or instrument malfunctioned

Code	NA
Expl	Data not collected

Code	NA
Expl	Data not collected

Code	NA
Expl	Missing

Code	NA
Expl	Data not collected

Code	NA
Expl	Data not collected

Accuracy Report:

Accuracy Assessment:

Coverage:

Methods:

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/edi/269/10/0d4c07cd46fa3fc1464a0bcfdabb1176
Name:	zoops_FRP2022
Description:	Mesozooplankton trawl data, including sample and catch data. CPUEs are reported for each taxon. To calculate the total CPUE for each sample, sum the CPUEs for individual taxa. Typically, there is one observation (row) for each taxonomic group within a sample, but occasionally, the subsampling was changed during processing and there are two observations (rows) for a single taxonomic group within the sample.
Number of Records:	18950
Number of Columns:	25

Table Structure

Object Name:

zoops_FRP2022.csv

Size:

7379852 byte

Authentication:

9fec00590da0f3b11d384e2a1063014a Calculated By MD5

Text Format:

Number of Header Lines:

Record Delimiter:

\r\n

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	"

Table Column Descriptions

SampleID_key

SampleID_frp

CommonName

VisitNo

subsample

Count

AdjCount

CPUE

Flagged_Data

StartTime

EndTime

LatitudeStart

LatitudeEnd

LongitudeStart

LongitudeEnd

DepthOfWater

NetMeterEnd

TowDirection

NetMeterStart

GearTypeAbbreviation

effort

LAB_NAME

Location

Date

Comments

Column Name:

SampleID_key

SampleID_frp

CommonName

VisitNo

subsample

Count

AdjCount

CPUE

Flagged_Data

StartTime

EndTime

LatitudeStart

LatitudeEnd

LongitudeStart

LongitudeEnd

DepthOfWater

NetMeterEnd

TowDirection

NetMeterStart

GearTypeAbbreviation

effort

LAB_NAME

Location

Date

Comments

Definition:

Unique numeric identifier for a single sample

Unique identifier for a single sample

Lowest taxonomic level used to identify individual organisms. See organism lookup table for more information.

Unique identifier for site visit. Each site visit represents a field sampling event and may contain one or more samples.

Fraction of total sample processed for identification

Number of individual organisms of a specified taxon counted in sample

Number of individual organisms of a specified taxon in total sample when adjusted for subsampling

Catch per unit effort, calculated as number of individuals of a taxon/ effort. CPUE is reported for each CommonName in a sample and all CPUEs of an individual must be summed to find the total CPUE in a sample.

Questionable data is flagged with a comment

Time at beginning of sample collection

Time at end of sample collection

Latitude where sample collection started in decimal degrees, WGS1984 as measured by Garmin 72H GPS or Lowrance HDS-7 Gen2 sonar

Latitude where sample collection ends, in decimal degrees, WGS1984 as measured by Garmin 72H GPS or Lowrance HDS-7 Gen2 sonar

Longitude where sampling begins in decimal degrees, WGS1984 as measured by Garmin 72H GPS or Lowrance HDS-7 Gen2 sonar

Longitude where sampling ends, in decimal degrees, WGS1984 as measured by Garmin 72H GPS or Lowrance HDS-7 Gen2 sonar

Water depth

Reading on the flow meter after sample is collected. Used for mesozooplankton trawls

Direction of tow relative to tide

Reading on the flow meter before sample is collected. Used for mesozooplankton samples

Gear type used to collect sample.

In zooplankton trawls samples effort is the volume of water that went through the net (m^3)

Name of the lab that processed the data

Name of a restoration project, adjacent waterbody, or reference marsh.

Date sampling occurred

Notes and comments. Note comments include comments for the site visit, sample, and organisms caught.

Storage Type:

float

string

float

string

dateTime

float

string

float

string

float

string

dateTime

string

Measurement Type:

ratio

nominal

ratio

nominal

dateTime

ratio

nominal

ratio

nominal

ratio

nominal

dateTime

nominal

Measurement Values Domain:

Unit	unique numerical identifier
Type	real

Definition

text

Definition

text

Unit	code for unique identifier
Type	integer

Unit	fraction
Type	real
Min	0.01
Max	1

Unit	Number of individual organisms in a sample
Type	real

Unit	Number of individual organisms
Type	real

Unit	Number per m^3
Type	real

Definition

text

Format	hh:mm
Precision

Format	hh:mm
Precision

Unit	degree
Type	real
Min	38
Max	38.2

Unit	degree
Type	real
Min	38
Max	38.2

Unit	degree
Type	real
Min	121.3
Max	122.1

Unit	degree
Type	real
Min	121.3
Max	122.1

Unit	meter
Precision	0.1
Type	real

Unit	Number of rotations
Type	real

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	1= with flow
Definition	Tow went with flow of water current
Source

Code Definition

Code	2= against flow
Definition	Tow went against the flow of water current
Source

Code Definition

Code	3= unknown
Definition	Unknown how the tow was conducted relative to the water current flow
Source

Unit	Number of rotations
Type	real

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	ZOBL
Definition	Mesozooplankton net, deployment using a sled obliquely through the water column. Net is 75cm long, 14.6cm diameter mouth, and 150 micron mesh size
Source

Code Definition

Code	ZOOP
Definition	Mesozooplankton net towed just below the water surface. Net is 75cm long, 14.6cm diameter mouth, and 150 micron mesh size
Source

Code Definition

Code	ZBEN
Definition	Mesozooplankton net, deployment using a sled on the sediment surface. Net is 75cm long, 14.6cm diameter mouth, and 150 micron mesh size
Source

Unit	meterCubed
Type	real

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	BSA
Definition	Data were processed by BSA Environmental Services, Inc.
Source

Code Definition

Code	EcoAnalysts
Definition	Data were processed by EcoAnalysts, Inc.
Source

Code Definition

Code	FRP
Definition	Data were processed by Fish Restoration Program, Department of Fish and Wildlife, in Stockton, CA.
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	Arnold Slough
Definition	Restoration project in Nurse-Denverton. Construction was completed October 2021.
Source

Code Definition

Code	Blacklock Marsh
Definition	Reference marsh for Arnold and Bradmoor restoration projects. Blacklock Marsh was an earlier restoration project that was completed in 2006.
Source

Code Definition

Code	Bradmoor Island
Definition	Restoration project in Nurse-Denverton. Construction was completed in November 2022.
Source

Code Definition

Code	Broad Slough
Definition	Adjacent water body for Winter Island restoration project.
Source

Code Definition

Code	Browns Island
Definition	Reference marsh for Winter Island and Chipps Island restoration projects
Source

Code Definition

Code	Cache Slough
Definition	The slough to the southwest of the Lookout Slough restoration project
Source

Code Definition

Code	Chipps Island
Definition	Planned restoration project in the Sacramento-San Joaquin Confluence.
Source

Code Definition

Code	Decker Island
Definition	Restoration project in the lower Sacramento River. Construction was completed in October 2018.
Source

Code Definition

Code	Dow
Definition	Corteva Wetlands Preserve (formerly Dow Wetland Preserve) in the Sacramento-San Joaquin Confluence. Dow was sampled as a potential restoration project but is no longer sampled by FRP.
Source

Code Definition

Code	Grizzly Bay
Definition	Adjacent water body for Tule Red restoration project.
Source

Code Definition

Code	Honker-Spoonbill
Definition	Honker Bay and Spoonbill are the adjacent waterbodies for Chipps Island.
Source

Code Definition

Code	Horseshoe Bend
Definition	Adjacent water body for Decker Island restoration project.
Source

Code Definition

Code	Liberty Island
Definition	Reference for restoration projects in Cache Slough Complex, North Delta. It is a former agricultural island, unintentionally breached and left to restore naturally in the late 1990s
Source

Code Definition

Code	Lindsey Slough
Definition	Lindsey Slough was sampled as a potential reference for projects in the Cache Slough Complex but is no longer sampled. It is a CDFW restoration project that was completed in 2014
Source

Code Definition

Code	Lookout Slough
Definition	Planned restoration project in Cache Slough Complex.
Source

Code Definition

Code	Lower Yolo Ranch
Definition	Restoration project in the Cache Slough Complex, North Delta. Construction was completed in August 2020.
Source

Code Definition

Code	Miner Slough
Definition	Adjacent water body for Prospect Island restoration project.
Source

Code Definition

Code	Montezuma
Definition	This is the section of the Montezuma Slough that is outside of Nurse-Denverton.
Source

Code Definition

Code	Nurse-Denverton
Definition	Adjacent water body for Arnold Slough and Bradmoor Island restoration projects.
Source

Code Definition

Code	Peytonia-Suisun
Definition	Adjacent water body for Wings Landing restoration project.
Source

Code Definition

Code	Prospect Island
Definition	Planned restoration project in Cache Slough Complex.
Source

Code Definition

Code	Rush Ranch
Definition	Reference for Wings Landing restoration project. Part of the San Francisco Bay National Estuarine Research Reserve.
Source

Code Definition

Code	Ryer Island
Definition	Reference for Tule Red restoration project
Source

Code Definition

Code	Shag Slough
Definition	Adjacent water body for Lookout Slough restoration project.
Source

Code Definition

Code	Sherman Island
Definition	Sherman Island in the Sacramento-San Joaquin Confluence
Source

Code Definition

Code	Stairsteps-Liberty Cut
Definition	Adjacent water body for Lower Yolo Ranch.
Source

Code Definition

Code	Suisun Bay
Definition	Suisun Bay near Ryer Island
Source

Code Definition

Code	Toe Drain
Definition	Adjacent water body for Yolo Flyway Farms
Source

Code Definition

Code	Tule Red
Definition	Restoration project in Suisun Slough. Construction was completed in October 2019.
Source

Code Definition

Code	Tule Red_Adjacent
Definition	Ponded wetland adjacent to Tule Red restoration project. Sampled before restoration.
Source

Code Definition

Code	Webb Tract Islands and Berms
Definition	Reference for Decker Island restoration project. A remnant marsh northeast of Webb Tract. Was incorrectly spelled in EDI2021 data as "Webb Tract Island and Berm".
Source

Code Definition

Code	Wings Landing
Definition	Restoration project in west Suisun Marsh. Construction was completed in September 2020.
Source

Code Definition

Code	Winter Island
Definition	Restoration project in the Sacramento-San Joaquin Confluence. Construction was completed in September 2019
Source

Code Definition

Code	Yolo Flyway Farms
Definition	Restoration project in Cache Slough Complex. Construction was completed in September 2018
Source

Format	YYYY-MM-DD
Precision

Definition

text

Missing Value Code:

Code	NA
Expl	Data was not collected

Code	NA
Expl	Data was not collected

Code	NA
Expl	Data was not collected or instrument malfunctioned

Code	NA
Expl	Data was not collected or instrument malfunctioned

Code	NA
Expl	Data was not collected or instrument malfunctioned

Code	NA
Expl	Data was not collected or instrument malfunctioned

Code	NA
Expl	Data was not collected or instrument malfunctioned

Code	NA
Expl	Data was not collected or instrument malfunctioned

Code	NA
Expl	Data was not collected

Code	NA
Expl	Data was not collected or instrument malfunctioned

Accuracy Report:

Accuracy Assessment:

Coverage:

Methods:

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/edi/269/10/461d09b7fb1693bfa65d57bbde0dd545
Name:	macroinvert_FRP2022
Description:	Contains sample and catch data for macroinvertebrate samples. Macroinvertebrate samples include all gear types with mesh size of 500 microns, including trawls, benthic samples, and samples taken in vegetation. Typically, there is one observation (row) for each taxonomic group within a sample, but occasionally, the subsampling was changed during processing and there are two observations (rows) for a single taxonomic group within the sample.
Number of Records:	27283
Number of Columns:	33

Table Structure

Object Name:

macroinvert_FRP2022.csv

Size:

9262529 byte

Authentication:

4a076fcbb57bc6c4ad84a04f9f25c8fc Calculated By MD5

Text Format:

Number of Header Lines:

Record Delimiter:

\r\n

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	"

Table Column Descriptions

SampleID_key

SampleID_frp

CommonName

VisitNo

subsample

Count

AdjCount

Flagged_Data

StartTime

EndTime

Location

Date

Column Name:

SampleID_key

SampleID_frp

CommonName

VisitNo

subsample

Count

AdjCount

Flagged_Data

StartTime

EndTime

LatitudeStart

LatitudeEnd

LongitudeStart

LongitudeEnd

DepthOfSample

DepthOfWater

NetMeterEnd

TowDirection

NetMeterStart

Boulder

Cobble

Gravel

Organics

Sand

Silt

DetritalVolume

GearTypeAbbreviation

LAB_NAME

Location

Date

Comments

effort

CPUE

Definition:

Unique numeric identifier for a single sample

Unique identifier for a single sample

Lowest taxonomic level used to identify individual organisms. See organism lookup table for more information.

Unique identifier for site visit. Each site visit represents a field sampling event and may contain zero or more samples.

Fraction of total sample processed for identification

Number of individual organisms of a specified taxon counted in sample

Number of individual organisms of a specified taxon in total sample when adjusted for subsampling

Questionable data is flagged with a comment

Time at beginning of sample collection

Time at end of sample collection

Latitude where sample collection starts in decimal degree WGS1984 as measured by Garmin 72H GPS or Lowrance HDS-7 Gen2 sonar

Latitude where sample collection ends in decimal degrees, WGS1984 as measured by Garmin 72H GPS or Lowrance HDS-7 Gen2 sonar

Longitude where sample collection starts, in decimal degrees, WGS1984 as measured by Garmin 72H GPS or Lowrance HDS-7 Gen2 sonar

Longitude where sampling ends in decimal degrees, WGS1984 as measured by Garmin 72H GPS or Lowrance HDS-7 Gen2 sonar

Distance from water surface to depth of sample collection.

Water depth

Reading on the flowmeter after sample is collected. Used for macrozooplankton trawls

Direction of tow relative to tide

Reading on the flowmeter before sample is collected. Used for macrozooplankton trawls

Approximate percentage of boulders in a benthic sample.

Approximate percentage of cobble in a benthic sample.

Approximate percentage of gravel in a benthic sample.

Approximate percentage of organics in a benthic sample.

Approximate percentage of sand in a benthic sample.

Approximate percentage of silt in a benthic sample.

Volume of detritus in sample, used for invertebrate samples.

Gear type used to collect sample.

Name of the lab that processed the data

Name of a restoration project, adjacent waterbody, or reference marsh.

Date sampling occurred.

Notes and comments including site visits, samples, and organisms caught.

The volume or surface area or unit of habitat sampled.

Storage Type:

float

string

float

string

dateTime

float

string

float

string

dateTime

string

float

Measurement Type:

ratio

nominal

ratio

nominal

dateTime

ratio

nominal

ratio

nominal

dateTime

nominal

ratio

Measurement Values Domain:

Unit	Unique identifier
Type	integer

Definition

text

Definition

text

Unit	Unique identifier
Type	integer

Unit	Proportion
Type	real
Min	0.01
Max	1

Unit	Count
Type	real

Unit	Count
Type	real

Definition

text

Format	hh:mm
Precision

Format	hh:mm
Precision

Unit	Decimal degree
Type	real

Unit	Decimal degree
Type	real
Min	38
Max	38.2

Unit	Decimal degree
Type	real
Min	38
Max	38.2

Unit	Decimal degree
Type	real
Min	121.3
Max	122.1

Unit	meter
Type	real
Min	121.3
Max	122.1

Unit	meter
Precision	0.1
Type	real

Unit	Number of rotations
Precision	0.1
Type	real

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	1= with flow
Definition	Tow with flow
Source

Code Definition

Code	2= against flow
Definition	Tow against flow
Source

Code Definition

Code	3= unknown
Definition	Tow direction unknown
Source

Unit	Number of rotations
Type	real

Unit	percent
Type	real

Unit	percent
Type	real

Unit	percent
Type	real
Min	0
Max	100

Unit	percent
Type	real
Min	0
Max	100

Unit	percent
Type	real
Min	0
Max	100

Unit	percent
Type	real
Min	0
Max	100

Unit	milliliter
Type	real

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	EAV
Definition	Vegetation-associated invertebrates in emergent aquatic vegetation taken with a 0.3m x 0.25m sweep net (d-frame net) with 500 micron mesh, mouth opening= 0.075m^2
Source

Code Definition

Code	FAV
Definition	Vegetation-associated invertebrates in floating aquatic vegetation taken with a 0.3m x 0.25m sweep net (d-frame net) with 500 micron mesh, mouth opening= 0.075m^2
Source

Code Definition

Code	MAC
Definition	Macrozooplankton net deployed just below the water surface, 2m long with 500 micron mesh, mouth opening = 0.5m diameter, tapers to 6.7cm cod end
Source

Code Definition

Code	MACBEN
Definition	Macrozooplankton net deployed along the sediment surface with a sled, 500 micron mesh x 2m long, mouth opening = 0.4m x 0.4m, mouth area = 0.16m^2
Source

Code Definition

Code	MACOBL
Definition	Macroinvertebrate net oblique trawl with a sled, 500 micron mesh x 2m long, mouth opening = 0.4m x 0.4m, mouth area = 0.16m^2
Source

Code Definition

Code	NT
Definition	Neuston net targets macroinvertebrate, 0.3 m x 0.45 m rectangular net, 1 m long with 500 micron mesh, pulled along the surface, half-way out of the water, mouth area = 0.135 m^2
Source

Code Definition

Code	PPG
Definition	Petite ponar targets benthic macroinvertebrates, mouth area = 0.0231 m^2
Source

Code Definition

Code	PVC
Definition	PVC core targets macroinvertebrates, 10.16cm (4'') PVC pipe, mouth (surface area) 0.00811 m^2
Source

Code Definition

Code	SAV
Definition	Vegetation-associated invertebrates in submersed aquatic vegetation taken with a 0.3m x 0.25m sweep net (D-frame net) with 500 micron mesh, mouth opening= 0.075m^2
Source

Code Definition

Code	SN
Definition	Vegetation-associated invertebrates taken with a 0.3m x 0.25m sweep net (D-frame net) with 500 micron mesh, mouth opening= 0.075m^2
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	EcoAnalysts
Definition	Data were processed by EcoAnalysts, Inc.
Source

Code Definition

Code	FRP
Definition	Data were processed by Fish Restoration Program, Department of Fish and Wildlife, in Stockton, CA.
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	Arnold Slough
Definition	Restoration project in Nurse-Denverton. Construction was completed October 2021.
Source

Code Definition

Code	Blacklock Marsh
Definition	Reference marsh for Arnold and Bradmoor restoration projects. Blacklock Marsh was an earlier restoration project that was completed in 2006.
Source

Code Definition

Code	Bradmoor Island
Definition	Restoration project in Nurse-Denverton. Construction was completed in November 2022.
Source

Code Definition

Code	Broad Slough
Definition	Adjacent water body for Winter Island restoration project.
Source

Code Definition

Code	Browns Island
Definition	Reference marsh for Winter Island and Chipps Island restoration projects
Source

Code Definition

Code	Cache Slough
Definition	The slough to the southwest of the Lookout Slough restoration project
Source

Code Definition

Code	Chipps Island
Definition	Planned restoration project in the Sacramento-San Joaquin Confluence.
Source

Code Definition

Code	Decker Island
Definition	Restoration project in the lower Sacramento River. Construction was completed in October 2018.
Source

Code Definition

Code	Dow
Definition	Corteva Wetlands Preserve (formerly Dow Wetland Preserve) in the Sacramento-San Joaquin Confluence. Dow was sampled as a potential restoration project but is no longer sampled by FRP.
Source

Code Definition

Code	Grizzly Bay
Definition	Adjacent water body for Tule Red restoration project.
Source

Code Definition

Code	Honker-Spoonbill
Definition	Honker Bay and Spoonbill are the adjacent waterbodies for Chipps Island.
Source

Code Definition

Code	Horseshoe Bend
Definition	Adjacent water body for Decker Island restoration project.
Source

Code Definition

Code	Liberty Island
Definition	Reference for restoration projects in Cache Slough Complex, North Delta. It is a former agricultural island, unintentionally breached and left to restore naturally in the late 1990s
Source

Code Definition

Code	Lindsey Slough
Definition	Lindsey Slough was sampled as a potential reference for projects in the Cache Slough Complex but is no longer sampled. It is a CDFW restoration project that was completed in 2014
Source

Code Definition

Code	Lookout Slough
Definition	Planned restoration project in Cache Slough Complex.
Source

Code Definition

Code	Lower Yolo Ranch
Definition	Restoration project in the Cache Slough Complex, North Delta. Construction was completed in August 2020.
Source

Code Definition

Code	Miner Slough
Definition	Adjacent water body for Prospect Island restoration project.
Source

Code Definition

Code	Montezuma
Definition	This is the section of the Montezuma Slough that is outside of Nurse-Denverton.
Source

Code Definition

Code	Nurse-Denverton
Definition	Adjacent water body for Arnold Slough and Bradmoor Island restoration projects.
Source

Code Definition

Code	Peytonia-Suisun
Definition	Adjacent water body for Wings Landing restoration project.
Source

Code Definition

Code	Prospect Island
Definition	Planned restoration project in Cache Slough Complex.
Source

Code Definition

Code	Rush Ranch
Definition	Reference for Wings Landing restoration project. Part of the San Francisco Bay National Estuarine Research Reserve.
Source

Code Definition

Code	Ryer Island
Definition	Reference for Tule Red restoration project
Source

Code Definition

Code	Shag Slough
Definition	Adjacent water body for Lookout Slough restoration project.
Source

Code Definition

Code	Sherman Island
Definition	Sherman Island in the Sacramento-San Joaquin Confluence
Source

Code Definition

Code	Stairsteps-Liberty Cut
Definition	Adjacent water body for Lower Yolo Ranch.
Source

Code Definition

Code	Suisun Bay
Definition	Suisun Bay near Ryer Island
Source

Code Definition

Code	Toe Drain
Definition	Adjacent water body for Yolo Flyway Farms
Source

Code Definition

Code	Tule Red
Definition	Restoration project in Suisun Slough. Construction was completed in October 2019.
Source

Code Definition

Code	Tule Red_Adjacent
Definition	Ponded wetland adjacent to Tule Red restoration project. Sampled before restoration.
Source

Code Definition

Code	Webb Tract Islands and Berms
Definition	Reference for Decker Island restoration project. A remnant marsh northeast of Webb Tract. Was incorrectly spelled in EDI2021 data as "Webb Tract Island and Berm".
Source

Code Definition

Code	Wings Landing
Definition	Restoration project in west Suisun Marsh. Construction was completed in September 2020.
Source

Code Definition

Code	Winter Island
Definition	Restoration project in the Sacramento-San Joaquin Confluence. Construction was completed in September 2019
Source

Code Definition

Code	Yolo Flyway Farms
Definition	Restoration project in Cache Slough Complex. Construction was completed in September 2018
Source

Format	YYYY-MM-DD
Precision

Definition

text

Unit	area or volume sampled
Type	real

Unit	Catch per Unit Effort
Type	real

Missing Value Code:

Code	NA
Expl	Not recorded

Code	NA
Expl	Data was not collected

Code	NA
Expl	Data was not collected

Code	NA
Expl	Data was not collected or instrument malfunctioned

Code	NA
Expl	Data was not collected or instrument malfunctioned

Code	NA
Expl	Data was not collected or instrument malfunctioned

Code	NA
Expl	Data was not collected or instrument malfunctioned

Code	NA
Expl	Data was not collected or instrument malfunctioned

Code	NA
Expl	Data was not collected or instrument malfunctioned

Code	NA
Expl	Data was not collected or instrument malfunctioned

Code	NA
Expl	Data was not collected

Code	NA
Expl	Data was not collected or instrument malfunctioned

Code	NA
Expl	Data was not collected

Code	NA
Expl	Data was not collected

Code	NA
Expl	Data was not collected

Code	NA
Expl	Data was not collected

Code	NA
Expl	Data was not collected

Code	NA
Expl	Data was not collected

Code	NA
Expl	Data was not collected or no data was recorded

Code	NA
Expl	Data was not collected

Accuracy Report:

Accuracy Assessment:

Coverage:

Methods:

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/edi/269/10/06feaacf0bdb3f42cf9fd68b57ecff61
Name:	fish_FRP2022
Description:	Contains sample and catch data for fish samples. Total CPUE can be calculated by summing the individual catches, dividing by effort, and multiplying by 10,000 to get the number of fish per 10,000 m^3.
Number of Records:	16459
Number of Columns:	27

Table Structure

Object Name:

fish_FRP2022.csv

Size:

4413300 byte

Authentication:

58b00378ef713444b4fbde56632cb46b Calculated By MD5

Text Format:

Number of Header Lines:

Record Delimiter:

\r\n

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	"

Table Column Descriptions

VisitNo

SampleID_key

SampleID_frp

CommonName

Length

Count

StartTime

LatitudeStart

LatitudeEnd

LongitudeStart

LongitudeEnd

DepthOfWater

NetMeterEnd

TowDirection

NetMeterStart

SeineCode

SeineDeploymentType

LengthOfTrawl

Width

PercentOpen

GearTypeAbbreviation

effort

LAB_NAME

Location

Date

Comments

FishCatchNotes

Column Name:

VisitNo

SampleID_key

SampleID_frp

CommonName

Length

Count

StartTime

LatitudeStart

LatitudeEnd

LongitudeStart

LongitudeEnd

DepthOfWater

NetMeterEnd

TowDirection

NetMeterStart

SeineCode

SeineDeploymentType

LengthOfTrawl

Width

PercentOpen

GearTypeAbbreviation

effort

LAB_NAME

Location

Date

Comments

FishCatchNotes

Definition:

Unique identifier for site visit. Each site visit represents a field sampling event and may contain zero or more samples.

Unique numeric identifier for a single sample

Unique identifier for a single sample

Lowest taxonomic level used to identify individual organisms. See organism lookup table for more information.

Fish length measured as fork length

Number of individual organisms of a specified taxon counted in sample

Time at beginning of sample collection

Latitude where sample collection started in decimal degrees, WGS1984 as measured by Garmin 72H GPS or Lowrance HDS-7 Gen2 sonar

Latitude where sample collection ends, in decimal degrees, WGS1984 as measured by Garmin 72H GPS or Lowrance HDS-7 Gen2 sonar

Longitude where sampling begins in decimal degrees, WGS1984 as measured by Garmin 72H GPS or Lowrance HDS-7 Gen2 sonar

Longitude where sampling ends, in decimal degrees, WGS1984 as measured by Garmin 72H GPS or Lowrance HDS-7 Gen2 sonar

Water depth

Reading on the flow meter after sample is collected. Used for otter trawls

Direction of tow relative to tide

Reading on the flow meter before sample is collected. Used for otter trawls.

Used for fish samples to describe net deployment. Code 3 (major snag or tear) and Code 4 (not deployed) are not reported here, but are available upon request.

Describes how fish net was deployed.

LengthOfTrawl varies depending on gear type. In otter trawls, it’s the amount of line out. For beach seines it is the distance from shore.

Width of deployed net

For cast net samples, it is the percent of net that is opened during a cast

Gear type used to collect sample.

Volume of water sampled

Name of the lab that processed the data

Name of a restoration project, adjacent waterbody, or reference marsh.

Date sampling occurred

Notes and comments for site visits, samples, and organisms caught.

Notes and comments

Storage Type:

float

string

float

dateTime

float

string

float

string

float

string

float

string

dateTime

string

Measurement Type:

ratio

nominal

ratio

dateTime

ratio

nominal

ratio

nominal

ratio

nominal

ratio

nominal

dateTime

nominal

Measurement Values Domain:

Unit	Unique numerical identifier for a site visit
Type	integer

Unit	Unique numerical identifier for a sample
Type	real

Definition

text

Definition

text

Unit	millimeter
Type	real

Unit	Number of individual organisms in a sample
Type	real

Format	hh:mm
Precision

Unit	Decimal degree
Type	real
Min	38
Max	38.2

Unit	Decimal degree
Type	real
Min	38
Max	38.2

Unit	Decimal degree
Type	real
Min	121.3
Max	122.1

Unit	Decimal degree
Type	real
Min	121.3
Max	122.1

Unit	meter
Precision	0.1
Type	real

Unit	Number of rotations
Type	real

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	1= with flow
Definition	Tow with flow
Source

Code Definition

Code	2= against flow
Definition	Tow against flow
Source

Code Definition

Code	3= unknown
Definition	Tow direction unknown
Source

Unit	Number of rotations
Type	real

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	1. No twists; snags; or tears
Definition	No twists; snags; or tears
Source

Code Definition

Code	2. Partial twist; snag; or tear
Definition	Partial twist; snag; or tear
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	Boat
Definition	Net deployed by boat
Source

Code Definition

Code	Crew Members
Definition	Net deployed by crew members
Source

Code Definition

Code	Crew Members and Boat
Definition	Net deployed by crew members and boat
Source

Code Definition

Code	Drag & Drop End
Definition	Net is deployed at the end of a channel by crewmembers and cod end is released by boat
Source

Code Definition

Code	Drag & Drop Middle
Definition	Net is deployed in the middle of a channel by crewmembers and cod end is released by boat
Source

Code Definition

Code	Drag and Drop
Definition	Net is deployed in a channel by crewmembers and cod end is released by boat
Source

Unit	meter
Type	real

Unit	meter
Type	real

Unit	percent
Type	real

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	BEASEI
Definition	Beach seine
Source

Code Definition

Code	BIGLAM
Definition	Large lampara net
Source

Code Definition

Code	LAMBE
Definition	Lampara net, deployed wading and brought to boat
Source

Code Definition

Code	LAMBEA
Definition	Lampara net, deployed wading and brought to beach
Source

Code Definition

Code	LAMOPE
Definition	Lampara net, deployed in open water
Source

Code Definition

Code	OTTTRA
Definition	Otter trawl
Source

Unit	meterCubed
Type	real

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	EcoAnalysts
Definition	Data were processed by EcoAnalysts, Inc.
Source

Code Definition

Code	FRP
Definition	Data were processed by Fish Restoration Program, Department of Fish and Wildlife, in Stockton, CA.
Source

Code Definition

Code	BSA
Definition	Data were processed by BSA Environmental Services, Inc.
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	Arnold Slough
Definition	Restoration project in Nurse-Denverton. Construction was completed October 2021.
Source

Code Definition

Code	Blacklock Marsh
Definition	Reference marsh for Arnold and Bradmoor restoration projects. Blacklock Marsh was an earlier restoration project that was completed in 2006.
Source

Code Definition

Code	Broad Slough
Definition	Adjacent water body for Winter Island restoration project.
Source

Code Definition

Code	Browns Island
Definition	Reference marsh for Winter Island and Chipps Island restoration projects
Source

Code Definition

Code	Cache Slough
Definition	The slough to the southwest of the Lookout Slough restoration project
Source

Code Definition

Code	Chipps Island
Definition	Planned restoration project in the Sacramento-San Joaquin Confluence.
Source

Code Definition

Code	Decker Island
Definition	Restoration project in the lower Sacramento River. Construction was completed in October 2018.
Source

Code Definition

Code	Grizzly Bay
Definition	Adjacent water body for Tule Red restoration project.
Source

Code Definition

Code	Honker-Spoonbill
Definition	Honker Bay and Spoonbill are the adjacent waterbodies for Chipps Island.
Source

Code Definition

Code	Horseshoe Bend
Definition	Adjacent water body for Decker Island restoration project.
Source

Code Definition

Code	Liberty Island
Definition	Reference for restoration projects in Cache Slough Complex, North Delta. It is a former agricultural island, unintentionally breached and left to restore naturally in the late 1990s
Source

Code Definition

Code	Lindsey Slough
Definition	Lindsey Slough was sampled as a potential reference for projects in the Cache Slough Complex but is no longer sampled. It is a CDFW restoration project that was completed in 2014
Source

Code Definition

Code	Lookout Slough
Definition	Planned restoration project in Cache Slough Complex.
Source

Code Definition

Code	Lower Yolo Ranch
Definition	Restoration project in the Cache Slough Complex, North Delta. Construction was completed in August 2020.
Source

Code Definition

Code	Miner Slough
Definition	Adjacent water body for Prospect Island restoration project.
Source

Code Definition

Code	Nurse-Denverton
Definition	Adjacent water body for Arnold Slough and Bradmoor Island restoration projects.
Source

Code Definition

Code	Peytonia-Suisun
Definition	Adjacent water body for Wings Landing restoration project.
Source

Code Definition

Code	Ryer Island
Definition	Reference for Tule Red restoration project
Source

Code Definition

Code	San Joaquin
Definition	The lower San Joaquin River
Source

Code Definition

Code	Shag Slough
Definition	Adjacent water body for Lookout Slough restoration project.
Source

Code Definition

Code	Stairsteps-Liberty Cut
Definition	Adjacent water body for Lower Yolo Ranch.
Source

Code Definition

Code	Toe Drain
Definition	Adjacent water body for Yolo Flyway Farms
Source

Code Definition

Code	Tule Red
Definition	Restoration project in Suisun Slough. Construction was completed in October 2019.
Source

Code Definition

Code	Tule Red_Adjacent
Definition	Ponded wetland adjacent to Tule Red restoration project. Sampled before restoration.
Source

Code Definition

Code	Webb Tract Islands and Berms
Definition	Reference for Decker Island restoration project. A remnant marsh northeast of Webb Tract. Was incorrectly spelled in EDI2021 data as "Webb Tract Island and Berm".
Source

Code Definition

Code	Wings Landing
Definition	Restoration project in west Suisun Marsh. Construction was completed in September 2020.
Source

Code Definition

Code	Winter Island
Definition	Restoration project in the Sacramento-San Joaquin Confluence. Construction was completed in September 2019
Source

Code Definition

Code	Yolo Flyway Farms
Definition	Restoration project in Cache Slough Complex. Construction was completed in September 2018
Source

Format	YYYY-MM-DD
Precision

Definition

text

Definition

text

Missing Value Code:

Code	NA
Expl	Data was not collected

Code	NA
Expl	Data was not collected

Code	NA
Expl	Data was not collected

Code	NA
Expl	Data was not collected or instrument malfunctioned

Code	NA
Expl	Data was not collected or instrument malfunctioned

Code	NA
Expl	Data was not collected or instrument malfunctioned

Code	NA
Expl	Data was not collected or instrument malfunctioned

Code	NA
Expl	Data was not collected or instrument malfunctioned

Code	NA
Expl	Data was not collected or instrument malfunctioned

Code	NA
Expl	Data was not collected or instrument malfunctioned

Code	NA
Expl	Data was not collected or instrument malfunctioned

Code	NA
Expl	Data was not collected

Code	NA
Expl	Data was not collected

Code	NA
Expl	Data was not collected

Code	NA
Expl	Data was not collected

Code	NA
Expl	Data was not collected

Code	NA
Expl	Data was not collected

Code	NA
Expl	Data was not collected

Code	NA
Expl	No comments

Code	NA
Expl	No comments

Accuracy Report:

Accuracy Assessment:

Coverage:

Methods:

Non-Categorized Data Resource

Name:

Monitoring SOPsv1.2

Entity Type:

application/pdf

Description:

Contains detailed Standard Operating Procedures for field and lab data collection, including gear specifications.

Physical Structure Description:

Object Name:

Monitoring SOPsv1.2.pdf

Size:

7822000 byte

Authentication:

38f3fc0957df5152aefb93e17be3298a Calculated By MD5

Externally Defined Format:

Format Name:

application/pdf

Data:

https://pasta-s.lternet.edu/package/data/eml/edi/269/10/8f389ef54992eaf94cb7aac4b98d4201

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)	Delta Smelt, Splittail, Tule Perch, tidal wetland, emergent aquatic vegetation, salmon rearing, floating aquatic vegetation, Longfin Smelt, benthic invertebrates, submersed aquatic vegetation, submerged aquatic vegetation, diatom, cyanobacteria, Chinook Salmon
LTER Controlled Vocabulary	restoration, phytoplankton, zooplankton, food webs, estuaries, nutrients, water quality, chlorophyll

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:

All sampling methods used to collect this data are consistent with the standard operating procedures developed by the Interagency Ecological Program (IEP) Tidal Wetlands Monitoring Project Workteam. The Standard Operating Procedures (SOPs) are included. For more detailed information on project background, sampling design, and analysis, see FRP annual reports:

Contreras, D., R. Hartman, S. Sherman, A. Furler, and A. Low. 2016. Pilot study phase I: Results from 2015 gear methodology trials in the North Delta. California Department of Fish and Wildlife, Fish Restoration Program, Stockton, CA.

Contreras, D., R. Hartman, and S. Sherman. 2017. Pilot Study Phase II: Results from 2016 gear evaluation in the North Delta. California Department of Fish and Wildlife, Fish Restoration Program, Stockton, CA. http://www.water.ca.gov/environmentalservices/docs/frpa/pilot_phase_II_report_FINAL_3MAY2017.pdf. Contreras, D., R. Hartman, and S. Sherman. 2018. Sampling fish and invertebrate resources in tidal wetlands of the Sacramento-San Joaquin Delta: Report on Phase III Pilot Monitoring, 2017. California Department of Fish and Wildlife, Stockton, CA.

Hartman R, Avila M, Barros A, Bowles C, Ellis D, Tempel T, Sherman S. 2022. I’m Not that Shallow – Different Zooplankton Abundance but Similar Community Composition Between Habitats in the San Francisco Estuary. San Francisco Estuary and Watershed Science. 20(3) doi:https://doi.org/10.15447/sfews.2022v20iss3art1.

Hartman R, Sherman S, Contreras D, Furler A, Kok R. 2019. Characterizing macroinvertebrate community composition and abundance in freshwater tidal wetlands of the Sacramento-San Joaquin Delta. PLOS ONE. 14(11):e0215421.[accessed 2021 09 07] doi: https://doi.org/10.1371/journal.pone.0215421.

Description:

Environmental Parameters: Water quality (pH, DO, temperature, conductivity, and turbidity) was collected for each fish or invertebrate sample using a YSI 6600, YSI Exo2, or YSI Proplus and portable turbidity meter. Other environmental observations, including tidal stage, water depth, weather, wind speed, and habitat type were also collected (see SOPs for gear specifications). Most water quality data was taken at the Start Latitude and Longitude. Deviations are typically noted in the comments.

Description:

Fish: FRP sampled fish in shallow water habitat near planned tidal wetland projects. Sampling occurred concurrently with the UC Davis Arc Survey and US Fish and Wildlife Service (USFWS) Liberty Island Survey in 2015-2016. Sampling occurred concurrently with mid-channel sampling by the IEP Summer Townet (STN) and Fall Midwater Trawl (FMWT) surveys, June-December, 2017. Based on the STN and FMWT sampling schedule, sites were surveyed twice a month from June-August and once a month from September-December. In 2018-2019, sampling occurred in and adjacent to restoration projects, reference marshes, and adjacent water bodies from summer to winter. No targeted fish sampling occurred in 2020. In 2021, sampling occurred during the spring and fall.

Sampling sites were typically void of vegetation and composed of sand and mud substrate mixtures. In 2015 and 2016, lampara nets were deployed concurrently with USFWS and UC Davis once per month. In 2017, Beach seines and lampara nets were deployed concurrently with the STN during the summer (June-August) and with FMWT during the fall (September-December).

Before sampling began, the crew scouted all the tidal wetland restoration locations for areas where a beach seine could be deployed. These recurring sites were recorded as waypoints and repeatedly sampled throughout the study. In addition, two lampara sites were fixed in a side channel off Miner Slough because this will be the location of the southern breach of Prospect Island when it is restored as a tidal wetland. All other lampara sampling sites were randomly selected using the sampling design tool in ArcMap (ESRI Inc. Redlands, CA).

Beach Seine: The beach seine is a shallow water gear type that is deployed from shore by crewmembers. It measures 15 m long x 1.2 m high and is composed of 3.2 mm delta square mesh. One crewmember walked perpendicular from shore into the water holding one end of the net until a depth appropriate for proper seining was reached. A second crewmember followed the path of the first crewmember to minimize site disturbance and positioned their seine pole upon reaching the first crewmember. The first crewmember then turned parallel with the shore and continued walking until the seine was fully opened. Water depth and seine lengths were recorded before both crewmembers pulled the seine towards the beach at a similar speed until only the cod end bag remained in the water. The crew filled a tub with water and placed the cod end in the tub along with any fish caught in the wings of the seine.

Lampara Net: The lampara net is a tapered net measuring 36.5 m long x 3.7 m high. The cod end is composed of 9.5 mm stretch mesh and connects to two wings composed of variable stretched mesh (69.9, 146.1, and 88.9 mm). This net was deployed in shallow and channel habitat from a boat where the tip of the wing was tossed into the water attached to a buoy and sea anchor. Crew members deployed the net from the bow of the boat as the boat moved in a circular fashion back to the buoy and sea anchor. One crew member then brought the buoy and sea anchor onboard and hooked both ends of the net onto the front cleat. The boat then went backwards and caused the net to impinge on itself to prevent fish from escaping through the bottom of the net. Once the net was "folded in half", each crew member grabbed one side of the net and brought it onboard. Once the cod end was reached, it was placed in a tub filled with water. Some lamparas targeted vegetation, and this is noted in the comments.

Description:

Invertebrates: We sampled at restoration sites, existing reference wetlands, and adjacent open-water areas across the North Delta Arc and Suisun Marsh to incorporate varying salinity and surrounding land use. We sampled most sites intensely during a single spring sampling event in late March and early April, 2017 (4-10 samples per habitat type, depending on wetland size), with less intense sampling monthly March-June, 2017. In 2018-2021, sites were sampled more intensely during the spring, and a subset of sites were sampled during the summer and fall.

FRP macrozooplankton and mesozooplankton tows: For benthic and oblique macrozooplankton tows, a 2m net with a 0.4 m x 0.4 m mouth (500 microns mesh size is attached to a steel sled and pulled either at the bottom or obliquely through the water column for five minutes. Benthic and oblique mesozooplankton were sampled with a 0.75m long (150 microns mesh size) zooplankton net with a circular mouth of 0.146m diameter attached to the macrozooplankton net frame (similar to EMP methods, Hennessy 2009).

For surface macrozooplankton tows, a 2m long, 500 micron mesh size net with a circular mouth diameter of 0.5m is towed 0.15m below the surface of the water. Surface mesozooplankton tows use the same nets as benthic and oblique mesozooplankton tows and are also towed 0.15m below the water surface, A flowmeter was mounted in each net to measure sample volume. If the tidal channels or accessible near-shore habitat were too short to take a full tow (10 minutes for macrozooplankton tows and 5 minutes for mesozooplankton tows), the tow time was reduced. In some cases, gear was held in the mouth of a tidal channel to sample water flowing out of the channel on an ebb tide instead of being trawled. After retrieval, the nets were rinsed from the outside to wash down the sample into the cod end. All content collected in a cod end was preserved in 70% ethanol with rose bengal for later identification.

Neuston tow: Emerging insects and Collembola found at the surface of the water are an important feature in salmonid diets and are commonly sampled using neuston tows and drift nets (Sommer et al. 2001, Howe et al. 2014). The neuston net is a 45 cm x 30 cm rectangular net, 1 m long with 500 micron mesh towed half-way out of the water to sample invertebrates on the surface of the water. We towed the neuston net at the surface of the water from the side of the boat via a boat-hook. In narrow channels, we pulled the net along the edge of emergent vegetation by hand (as in Howe et al. 2014). We standardized effort by using the flowmeter readings from a concurrent mesozooplankton tow or calculating distance by GPS track multiplied by width of net multiplied by 1/2 of the height of the net to calculate volume of water sampled. After retrieval, all content collected in a cod end was preserved in 70% ethanol with rose bengal for later ID.

Our invertebrate tows were distributed in a stratified random manner across all open water and channels > 1.5 m across while avoiding aquatic vegetation where possible. We combined open-water sampling with fish sampling where possible to reduce disturbance and increase efficiency. Methods used in open-water have a long history of use in monitoring in the Delta, and allowed us to compare our measurements in vegetated wetlands to conditions in channels and make comparisons to long-term data sets.

Vegetated habitats: We used a 25 cm x 30 cm d-frame net with 500 micron mesh for all sweep net samples. We adapted the sweep net technique slightly for different habitat types.

Emergent Aquatic Vegetation (EAV): Five 1 m sweeps, scraping the vegetation as much as possible to knock invertebrates off the stems. All samples were taken within 1 m of the edge, since most of the emergent aquatic vegetation grows within that boundary. This is also the area where salmonids have been shown to forage most effectively (Simenstad and Cordell 2000). Samples were taken proportionately to be representative of the vegetation community composition at the site.

Submerged Aquatic Vegetation (SAV): Five 1 m sweeps through the thickest growth, collecting vegetation remaining within the frame of the net at the end of the sweep. Samples were taken proportionately to be representative of the vegetation community composition at the site.

Floating Aquatic Vegetation (FAV): The net was lifted from beneath a clump of FAV. Plant material outside of the net frame and any leaves above the surface of the water were severed from the sample with shears (similar to Donley Marineau et al. 2017). Samples were taken proportionately to be representative of the vegetation community composition.

All vegetated sample catch per unit efforts (CPUE) were calculated as number of invertebrates per sample.

Benthic core: Benthic cores have been used extensively to quantify chironomid and amphipod populations, as well as bivalves and other infauna in tidal wetlands (Howe et al. 2014; Wells 2015). In shallow water (< 1.5 m), we took a 10 cm diameter benthic core, hand-deployed to a depth of 20 cm. In deep water > 1.5 m, we used a 22.9x 22.9 cm ponar grab modified for use in hard substrates (as per USFWS Liberty Island Monitoring, L. Smith pers. comm). The sample was washed and sieved on board the boat to remove the sand/mud and preserve any organic detritus and invertebrates. Two crew members estimated % silt, sand, and gravel in the field, and averaged the values. Effort was calculated as catch per surface area of substrate sampled.

All instruments will have periodic calibrations and maintenance as per manufacturer's instructions.

Organisms in samples are identified and enumerated. Starting with 2019 samples, mesozooplankton taxa are not counted in macroinvertebrate samples. In benthic samples, only bivalves are counted. A count of zero indicates a taxa is present, but was not counted.

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:

Dr. Stacy Sherman

Organization:

California Department of Fish and Wildlife

Position:

Environmental Program Manager

Address:

2109 Arch Airport Rd,

Suite 100,

Stockton, CA 95206 US

Phone:

209-470-2906 (voice)

Email Address:

stacy.sherman@wildlife.ca.gov

Id:

https://orcid.org/0000-0002-8392-7287

Individual:

Dr. Christy Bowles

Organization:

California Department of Fish and Wildlife

Position:

Senior Environmental Scientist (Specialist)

Address:

2109 Arch Airport Rd,

Suite 100,

Stockton, CA 95206 US

Phone:

209-279-4913 (voice)

Email Address:

christy.bowles@wildlife.ca.gov

Id:

https://orcid.org/0000-0001-7154-3262

Individual:

Michelle Avila

Organization:

California Department of Fish and Wildlife

Position:

Environmental Scientist

Address:

2109 Arch Airport Rd,

Suite 100,

Stockton, CA 95206 US

Email Address:

michelle.avila@wildlife.ca.gov

Id:

https://orcid.org/0000-0003-1770-9078

Individual:

Daniel Cox

Organization:

California Department of Fish and Wildlife

Position:

Environmental Scientist

Address:

2109 Arch Airport Rd,

Suite 100,

Stockton, CA 95206 US

Email Address:

daniel.cox@wildlife.ca.gov

Id:

https://orcid.org/0000-0001-5251-5469

Individual:

Emma Davidson

Organization:

California Department of Fish and Wildlife

Position:

Environmental Scientist

Address:

2109 Arch Airport Rd,

Suite 100,

Stockton, CA 95206 US

Email Address:

emma.davidson@wildlife.ca.gov

Id:

https://orcid.org/0000-0002-1855-1746

Individual:

Dr. Gabriel Ng

Organization:

California Department of Fish and Wildlife

Position:

Environmental Scientist

Address:

2109 Arch Airport Rd,

Suite 100,

Stockton, CA 95206 US

Email Address:

gabriel.ng@wildlife.ca.gov

Id:

https://orcid.org/0000-0001-6481-1249

Individual:

Dr. Rosemary Hartman

Organization:

California Department of Water Resources

Position:

Environmental Program Manager (Specialist)

Email Address:

rosemary.hartman@water.ca.gov

Id:

https://orcid.org/0000-0002-0642-183x

Individual:

Daniel Ellis

Organization:

California Department of Fish and Wildlife

Position:

Senior Environmental Scientist (Specialist)

Email Address:

daniel.ellis@wildlife.ca.gov

Id:

https://orcid.org/0000-0002-5900-2962

Individual:

Dave Contreras

Organization:

California Department of Fish and Wildlife

Position:

Environmental Scientist

Address:

United States

Email Address:

dave.contreras@wildlife.ca.gov

Id:

https://orcid.org/0000-0002-8692-3185

Contacts:

Individual:

Dr. Christy Bowles

Organization:

California Department of Fish and Wildlife

Position:

Senior Environmental Scientist (Specialist)

Address:

2109 Arch Airport Rd,

Suite 100,

Stockton, CA 95206 US

Email Address:

christy.bowles@wildlife.ca.gov

Id:

https://orcid.org/0000-0001-7154-3262

Individual:

Dr. Stacy Sherman

Organization:

California Department of Fish and Wildlife

Position:

Environmental Program Manager

Address:

2109 Arch Airport Rd,

Suite 100,

Stockton, CA 95206 US

Email Address:

stacy.sherman@wildlife.ca.gov

Id:

https://orcid.org/0000-0002-8392-7287

Temporal, Geographic and Taxonomic Coverage

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

Time Period

Begin:

2015

End:

2022

Geographic Region:

Description:

All sampling was done in the San Francisco Estuary wetlands and adjacent channels. Samples were taken from the Cache Slough Complex, including: Yolo Flyway Farms, Lower Yolo Ranch, Liberty Island, Lookout Slough, Prospect Island, the Toe Drain, Shag Slough, Cache Slough, and Miner Slough. Samples were taken from the lower Sacramento and San Joaquin Rivers and their confluence, including: Decker Island, Webb Tract Islands and Berms, Winter Island, Browns Island, Chipps Island, Broad Slough, and Horseshoe Bend. Samples were taken from Grizzly Bay and Suisun Marsh, including: Wings Landing, Rush Ranch, Bradmoor Island, Arnold Slough, Blacklock, Tule Red, Ryer Island, Little Honker Bay, and Peytonia Slough.

Bounding Coordinates:

Northern:	38.37159	Southern:	38.02852
Western:	-122.04542	Eastern:	-121.58102

Project

Parent Project Information:

Title:

Fish Restoration Program

Personnel:

Individual:

Dr. Stacy Sherman

Organization:

California Department of Fish and Wildlife

Position:

Environmental Program Manager

Address:

2109 Arch Airport Rd,

Stockton, CA 95206 US

Phone:

9165312339 (voice)

Email Address:

christy.bowles@wildlife.ca.gov

Id:

https://orcid.org/0000-0002-8392-7287

Role:

principalInvestigator, owner, contact

Individual:

Dr. Christy Bowles

Organization:

California Department of Fish and Wildlife

Position:

Senior Environmental Scientist (Specialist)

Address:

2109 Arch Airport Rd,

Stockton, CA 95206 US

Phone:

209-279-4913 (voice)

Email Address:

christy.bowles@wildlife.ca.gov

Id:

https://orcid.org/0000-0001-7154-3262

Role:

author, owner, contact

Individual:

Michelle Avila

Organization:

California Department of Fish and Wildlife

Position:

Environmental Scientist

Address:

2109 Arch Airport Rd,

Stockton, CA 95206 US

Email Address:

michelle.avila@wildlife.ca.gov

Id:

https://orcid.org/0000-0003-1770-9078

Role:

author

Individual:

Daniel Cox

Organization:

California Department of Fish and Wildlife

Position:

Environmental Scientist

Address:

2109 Arch Airport Rd,

Stockton, CA 95206 US

Email Address:

daniel.cox@wildlife.ca.gov

Id:

https://orcid.org/0000-0001-5251-5469

Role:

author

Individual:

Emma Davidson

Organization:

California Department of Fish and Wildlife

Position:

Environmental Scientist

Address:

2109 Arch Airport Rd,

Stockton, CA 95206 US

Email Address:

emma.davidson@wildlife.ca.gov

Id:

https://orcid.org/0000-0002-1855-1746

Role:

author

Individual:

Gabriel Ng

Organization:

California Department of Fish and Wildlife

Position:

Environmental Scientist

Address:

2109 Arch Airport Rd,

Stockton, CA 95206 US

Email Address:

gabriel.ng@wildlife.ca.gov

Id:

https://orcid.org/0000-0001-6481-1249

Role:

author

Additional Award Information:

Funder:

Department of Water Resources

Funder ID:

Fish Restoration Program

Title:

Contract

Maintenance

Maintenance:

Description:

Data collection is ongoing.

Changes have been made from the edi.269.3 to 269.4 versions:

Data through 2022 have been added. Phytoplankton and nutrient data were added with the 2022 EDI publication.

Changes have been made from the edi.269.2 to 269.3 versions:

Data through 2021 was added as well as additional variables. The data formatting changed. Previously, data was merged into separate files for macroinvertebrates (bugs), zooplankton, and fish sampling gears. Newer data has one file for site visit, with environmental data and separate files for macroinvertebrates, zooplankton, and fish sampling gears. Some samples were reprocessed to increase the percent subsampled.

Taxonomy has been updated in the orglookup_FRP data table, with notes on changes. Changes are primarily observations of new taxa and identification to a lower taxonomic resolution where possible, not changes in methodology such as counting organisms that were previously ignored. Starting with 2019 samples, mesozooplankton taxa are not counted in macroinvertebrate samples. In benthic samples, only bivalves are counted. A count of zero indicates a taxa is present, but was not counted.

Frequency:

annually

Other Metadata

Additional Metadata

additionalMetadata
        |___text '\n      '
        |___element 'metadata'
        |     |___text '\n         '
        |     |___element 'unitList'
        |     |     |___text '\n            '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'Unique identifier'
        |     |     |     |  \___attribute 'name' = 'Unique identifier'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description'
        |     |     |     |     |___text 'Unique numerical code assigned to each site visit.'
        |     |     |     |___text '\n            '
        |     |     |___text '\n            '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'pH'
        |     |     |     |  \___attribute 'name' = 'pH'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description'
        |     |     |     |___text '\n            '
        |     |     |___text '\n            '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'MicrosiemensPerCm'
        |     |     |     |  \___attribute 'name' = 'MicrosiemensPerCm'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description'
        |     |     |     |___text '\n            '
        |     |     |___text '\n            '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'RFU'
        |     |     |     |  \___attribute 'name' = 'RFU'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description'
        |     |     |     |___text '\n            '
        |     |     |___text '\n            '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'Proportion'
        |     |     |     |  \___attribute 'name' = 'Proportion'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description'
        |     |     |     |___text '\n            '
        |     |     |___text '\n            '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'Count'
        |     |     |     |  \___attribute 'name' = 'Count'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description'
        |     |     |     |___text '\n            '
        |     |     |___text '\n            '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'Number of rotations'
        |     |     |     |  \___attribute 'name' = 'Number of rotations'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description'
        |     |     |     |___text '\n            '
        |     |     |___text '\n            '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'code for unique identifier'
        |     |     |     |  \___attribute 'name' = 'code for unique identifier'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description'
        |     |     |     |___text '\n            '
        |     |     |___text '\n            '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'fraction'
        |     |     |     |  \___attribute 'name' = 'fraction'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description'
        |     |     |     |     |___text '0-1'
        |     |     |     |___text '\n            '
        |     |     |___text '\n            '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'unique numerical identifier'
        |     |     |     |  \___attribute 'name' = 'unique numerical identifier'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description'
        |     |     |     |___text '\n            '
        |     |     |___text '\n            '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'Number of individual organisms'
        |     |     |     |  \___attribute 'name' = 'Number of individual organisms'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description'
        |     |     |     |___text '\n            '
        |     |     |___text '\n            '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'Number per m^3'
        |     |     |     |  \___attribute 'name' = 'Number per m^3'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description'
        |     |     |     |___text '\n            '
        |     |     |___text '\n            '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'Catch per Unit Effort'
        |     |     |     |  \___attribute 'name' = 'Catch per Unit Effort'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description'
        |     |     |     |     |___text 'mac, zoop, neuston: individuals/m^3 sweep nets (EAV, FAV, SAV): individuals per 1 sweep benthic: individuals/m^2'
        |     |     |     |___text '\n            '
        |     |     |___text '\n            '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'area or volume sampled'
        |     |     |     |  \___attribute 'name' = 'area or volume sampled'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description'
        |     |     |     |     |___text 'mac, zoop, neuston: volume m^3 sweep nets (EAV, FAV, SAV): 1 sweep benthic (PVC, PPG): surface area m^2'
        |     |     |     |___text '\n            '
        |     |     |___text '\n            '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'Decimal degree'
        |     |     |     |  \___attribute 'name' = 'Decimal degree'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description'
        |     |     |     |___text '\n            '
        |     |     |___text '\n            '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'FNU'
        |     |     |     |  \___attribute 'name' = 'FNU'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description'
        |     |     |     |___text '\n            '
        |     |     |___text '\n            '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'organism units per mL'
        |     |     |     |  \___attribute 'name' = 'organism units per mL'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description'
        |     |     |     |___text '\n            '
        |     |     |___text '\n            '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'Cells per mL'
        |     |     |     |  \___attribute 'name' = 'Cells per mL'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description'
        |     |     |     |___text '\n            '
        |     |     |___text '\n            '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'Volume phytoplankton per mL water'
        |     |     |     |  \___attribute 'name' = 'Volume phytoplankton per mL water'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description'
        |     |     |     |___text '\n            '
        |     |     |___text '\n            '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'Liner dimension'
        |     |     |     |  \___attribute 'name' = 'Liner dimension'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description'
        |     |     |     |___text '\n            '
        |     |     |___text '\n            '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'Unique Identifier for a site visit'
        |     |     |     |  \___attribute 'name' = 'Unique Identifier for a site visit'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description'
        |     |     |     |___text '\n            '
        |     |     |___text '\n            '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'Unique numerical identifier for a site visit'
        |     |     |     |  \___attribute 'name' = 'Unique numerical identifier for a site visit'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description'
        |     |     |     |___text '\n            '
        |     |     |___text '\n            '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'Unique numerical identifier for a sample'
        |     |     |     |  \___attribute 'name' = 'Unique numerical identifier for a sample'
        |     |     |     |___text '\n               '
        |     |     |     |___element 'description'
        |     |     |     |___text '\n            '
        |     |     |___text '\n            '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'Number of individual organisms in a sample'
        |     |     |     |  \___attribute 'name' = 'Number of individual organisms in a sample'
        |     |     |     |___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' = '2024.05.22'
        |     |___text '\n      '
        |___text '\n   '

Copyright 2024 Environmental Data Initiative. This material is based upon work supported by the National Science Foundation under grants #2223103 and #2223104. Any opinions, findings, conclusions, or recommendations expressed in the material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. Please contact us with questions, comments, or for technical assistance regarding this web site or the Environmental Data Initiative. Please read our privacy policy to know what information we collect about you and to understand your privacy rights.

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

Data Package Metadata View Summary

Fish Restoration Program Tidal Wetland Restoration Monitoring in Upper San Francisco Estuary, 2015-ongoing

Data Entities

Data Table

Data Table

Data Table

Data Table

Data Table

Data Table

Non-Categorized Data Resource

Data Package Usage Rights

Keywords

Methods and Protocols

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

People and Organizations

Temporal, Geographic and Taxonomic Coverage

Project

Parent Project Information:

Maintenance

Additional Metadata

Additional Metadata

Recently Added

Recently Updated

Data Package Metadata View Summary

Fish Restoration Program Tidal Wetland Restoration Monitoring in Upper San Francisco Estuary, 2015-ongoing

+/- Data Entities

Data Table

Data Table

Data Table

Data Table

Data Table

Data Table

Non-Categorized Data Resource

+/- Data Package Usage Rights

+/- Keywords

+/- Methods and Protocols

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

+/- People and Organizations

+/- Temporal, Geographic and Taxonomic Coverage

+/- Project

Parent Project Information:

+/- Maintenance

+/- Additional Metadata

+/- Additional Metadata

Data Entities

Data Package Usage Rights

Keywords

Methods and Protocols

People and Organizations

Temporal, Geographic and Taxonomic Coverage

Project

Maintenance

Additional Metadata

Additional Metadata