Data Package Metadata View Summary

Fish abundance in the San Francisco Estuary (1959-2021), an integration of 9 monitoring surveys.

General Information

Data Package:

Local Identifier:

edi.746.1

Title:

Fish abundance in the San Francisco Estuary (1959-2021), an integration of 9 monitoring surveys.

Alternate Identifier:

DOI PLACE HOLDER

Abstract:

The San Francisco Estuary (SFE) is simultaneously a central hub of water delivery in California and home to commercially important and endangered fishes, such as Chinook Salmon, Green Sturgeon, and Delta and Longfin Smelt. Extensive ecological monitoring has been conducted for over 50 years, mainly under the auspices of the Interagency Ecological Program for the San Francisco Estuary (https://iep.ca.gov/). We integrated fish catch and length data from 9 long-term monitoring surveys in the SFE. The integrated database contains survey-level data such as environmental variables and sampling effort in addition to the fish-level species, lengths, and counts. Zero catches have been filled in for any species not caught in a sample. The geographic scope includes San Francisco Bay through the upper estuary, and the timeseries spans 1959 to 2021. Sampling methods, gear, fish length metric, and other factors differ among the component surveys. Sampling designs (locations and temporal frequency) have also changed over time. Thus, it is highly recommended to inspect the documentation of the component surveys for more information on their methods.

Publication Date:

2022-02-03

For more information:
Visit:	DOI PLACE HOLDER

Time Period

Begin:

1959-06-13

End:

2021-09-23

People and Organizations
Contact:	Bashevkin, Samuel M (Delta Science Program, Delta Stewardship Council) [ email ]
Creator:	Bashevkin, Samuel M (Delta Science Program, Delta Stewardship Council)
Creator:	Gaeta, Jereme W (California Department of Fish and Wildlife and the Interagency Ecological Program)
Creator:	Nguyen, Trinh X (California Department of Fish and Wildlife and the Interagency Ecological Program)
Creator:	Mitchell, Lara (U.S. Fish and Wildlife Service)
Creator:	Khanna, Shruti (California Department of Fish and Wildlife and the Interagency Ecological Program)

Data Entities
Data Table Name:	Sample-level table
Description:	Sample-level environmental and effort data. Can be joined to the fish table with the SampleID column.
Data Table Name:	Fish-level data
Description:	Fish-level length and abundance data. Can be joined to the survey table with the SampleID column.
Data Table Name:	Length conversion equations
Description:	Length conversion equations for 20 fishes, of the form fork or total length = intercept + slope * standard length.
Other Name:	Compressed fish and survey data.
Description:	The fish and survey tables compressed into an rda file (compressed file format for the R programming language). These data are exactly identical to their csv analogs. They are provided to reduce download time for R-users.

Detailed Metadata

Data Entities

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/edi/746/1/79240c490fe74543da6b86a1c7c751b9
Name:	Sample-level table
Description:	Sample-level environmental and effort data. Can be joined to the fish table with the SampleID column.
Number of Records:	374221
Number of Columns:	23

Table Structure

Object Name:

survey.csv

Size:

78748370 bytes

Authentication:

c8f47fba852b64258834e5e53c9326ce Calculated By MD5

Text Format:

Number of Header Lines:

Record Delimiter:

\r\n

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	"

Table Column Descriptions

Column Name:

Source

Station

Latitude

Longitude

Date

Datetime

Survey

Depth

SampleID

Method

Tide

Sal_surf

Sal_bot

Temp_surf

Secchi

Secchi_estimated

Tow_duration

Tow_area

Tow_volume

Cable_length

Tow_direction

Notes_tow

Notes_flowmeter

Definition:

Name of the source survey

Unique name of each sampling location

Latitude of the sampling location

Longitude of the sampling location

Date sample was collected

Date and time sample was collected

Cumulative survey number in the source dataset

Bottom depth. Sometimes this is recorded at the time of the tow, and sometimes it's an average depth for the sampling location.

Unique identifier for each sample (i.e. tow). This is the key to join the fish and sample tables together.

Gear type

Tidal stage

Surface salinity

Bottom salinity

Surface temperature

Secchi depth

Was Secchi depth estimated? This is only used for FMWT data.

Duration of tow

Area sampled by tow

Volume sampled by tow

Length of cable released when net deployed

Direction of tow, this has not been standardized among surveys.

Notes recorded about the tow

Notes recorded about the flowmeter used to calculate tow_area or tow_volume

Storage Type:

string

float

date

float

string

float

string

float

string

Measurement Type:

nominal

ratio

dateTime

ratio

nominal

ratio

nominal

ratio

nominal

Measurement Values Domain:

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	20mm
Definition	CDFW 20mm Survey
Source

Code Definition

Code	Bay Study
Definition	CDFW Bay Study
Source

Code Definition

Code	DJFMP
Definition	USFWS Delta Juvenile Fish Monitoring Program
Source

Code Definition

Code	EDSM
Definition	USFWS Enhanced Delta Smelt Monitoring
Source

Code Definition

Code	FMWT
Definition	CDFW Fall Midwater Trawl
Source

Code Definition

Code	SKT
Definition	CDFW Spring Kodiak Trawl
Source

Code Definition

Code	SLS
Definition	CDFW Smelt Larva Survey
Source

Code Definition

Code	STN
Definition	CDFW Summer Townet
Source

Code Definition

Code	Suisun
Definition	UC Davis Suisun Marsh Fish Study
Source

Definition

Unique name of each sampling location

Unit	degree
Type	real
Min	37.50185
Max	39.21999207

Unit	degree
Type	real
Min	-122.4984841
Max	-121.164823

Format	YYYY-MM-DD
Precision

Format	YYYY-MM-DD hh:mm:ss
Precision

Unit	dimensionless
Type	natural
Min	1
Max	61

Unit	meter
Type	real
Min	0
Max	41.1

Definition

Unique identifier for each sample (i.e. tow). This is the key to join the fish and sample tables together.

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	20mm net
Definition	20mm net
Source

Code Definition

Code	Beach seine
Definition	Beach seine
Source

Code Definition

Code	Kodiak trawl
Definition	Kodiak trawl
Source

Code Definition

Code	Midwater trawl
Definition	Midwater trawl
Source

Code Definition

Code	Oblique tow
Definition	Oblique tow
Source

Code Definition

Code	Otter trawl
Definition	Otter trawl
Source

Code Definition

Code	STN net
Definition	Summer townet
Source

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	Ebb
Definition	Ebb tide
Source

Code Definition

Code	Flood
Definition	Flood tide
Source

Code Definition

Code	High Slack
Definition	High slack tide
Source

Code Definition

Code	Low Slack
Definition	Low slack tide
Source

Unit	dimensionless
Type	real
Min	0.000358201267026534
Max	162.076718289885

Unit	dimensionless
Type	real
Min	0.031814021671517
Max	23.0656442081952

Unit	celsius
Type	real
Min	3
Max	32.1

Unit	centimeter
Type	real
Min	0
Max	5000

Allowed Values and Definitions

Enumerated Domain

Code Definition

Code	TRUE
Definition	The Secchi value is estimated
Source

Code Definition

Code	FALSE
Definition	The Secchi value is not estimated
Source

Unit	minute
Type	real
Min	1
Max	26

Unit	squareMeter
Type	real
Min	126.6768
Max	5217.33333333333

Unit	meterCubed
Type	real
Min	-370199.865262681
Max	336969.55966674

Unit	meter
Type	real
Min	0
Max	91.44

Definition

Direction of tow, this has not been standardized among surveys.

Definition

Notes recorded about the tow

Definition

Notes recorded about the flowmeter used to calculate tow_area or tow_volume

Missing Value Code:

Code	NA
Expl	No coordinates available

Code	NA
Expl	No coordinates available

Code	NA
Expl	Not recorded

Code	NA
Expl	The source dataset does not record survey numbers

Code	NA
Expl	Not recorded

Code	NA
Expl	Not recorded

Code	NA
Expl	Not recorded

Code	NA
Expl	Not recorded

Code	NA
Expl	Not recorded

Code	NA
Expl	Not recorded

Code	NA
Expl	Not recorded (only used for FMWT data)

Code	NA
Expl	Not recorded

Code	NA
Expl	Not recorded or this effort metric not used for this gear type

Code	NA
Expl	Not recorded or this effort metric not used for this gear type

Code	NA
Expl	Not recorded

Code	NA
Expl	Not recorded

Code	NA
Expl	Not recorded

Code	NA
Expl	Not recorded

Accuracy Report:

Accuracy Assessment:

Coverage:

Methods:

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/edi/746/1/5429d3e82b1671e7454c7b5d7a15c6ef
Name:	Fish-level data
Description:	Fish-level length and abundance data. Can be joined to the survey table with the SampleID column.
Number of Records:	45846708
Number of Columns:	5

Table Structure

Object Name:

fish.csv

Size:

3275553630 bytes

Authentication:

509b5516430ece2730060597eafde902 Calculated By MD5

Text Format:

Number of Header Lines:

Record Delimiter:

\r\n

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	"

Table Column Descriptions

Column Name:

SampleID

Taxa

Length

Count

Notes_catch

Definition:

Unique identifier for each sample (i.e. tow). This is the key to join the fish and sample tables together.

Scientific name for the sampled taxa

Fish length in fork length or total length for species with no fork for all studies except Suisun study, for which lengths are recorded as standard length. See the Length_conversion table for equations to convert standard length to fork/total length.

Adjusted length frequency (see methods) of fish for each sample, taxa, and measured length

Notes recorded about the fish catch

Storage Type:

string

float

string

Measurement Type:

nominal

ratio

nominal

Measurement Values Domain:

Definition

Unique identifier for each sample (i.e. tow). This is the key to join the fish and sample tables together.

Definition

Scientific name for the sampled taxa

Unit	millimeter
Type	real
Min	1
Max	1945

Unit	number
Type	real
Min	0
Max	90550

Definition

Notes recorded about the fish catch

Missing Value Code:

Code	NA
Expl	The length is unknown

Accuracy Report:

Accuracy Assessment:

Coverage:

Methods:

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/edi/746/1/2933237df1902243b4307f082bdc7d18
Name:	Length conversion equations
Description:	Length conversion equations for 20 fishes, of the form fork or total length = intercept + slope * standard length.
Number of Records:	20
Number of Columns:	3

Table Structure

Object Name:

Length_conversions.csv

Size:

745 bytes

Authentication:

ce31df715ae888e4610565139b57add5 Calculated By MD5

Text Format:

Number of Header Lines:

Record Delimiter:

\r\n

Orientation:

column

Simple Delimited:

Field Delimiter:	,
Quote Character:	"

Table Column Descriptions

Column Name:

Species

Intercept

Slope

Definition:

Species name

Intercept of the equation: fork or total length = intercept + slope * standard length

Storage Type:

string

float

Measurement Type:

nominal

ratio

Measurement Values Domain:

Definition

Species name

Unit	millimeter
Type	real
Min	-1.166
Max	3.362

Unit	dimensionless
Type	real
Min	0.926
Max	1.24

Missing Value Code:

Accuracy Report:

Accuracy Assessment:

Coverage:

Methods:

Non-Categorized Data Resource

Name:

Compressed fish and survey data.

Entity Type:

unknown

Description:

The fish and survey tables compressed into an rda file (compressed file format for the R programming language). These data are exactly identical to their csv analogs. They are provided to reduce download time for R-users.

Physical Structure Description:

Object Name:

fishsurvey_compressed.rds

Size:

19099556 bytes

Authentication:

7d8f8497779941140cfc300bea7cc1ca Calculated By MD5

Externally Defined Format:

Format Name:

Unknown

Data:

https://pasta-s.lternet.edu/package/data/eml/edi/746/1/926f4aa8484f185b69bc1827fa67d40c

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:
https://vocab.lternet.edu/	estuaries, fishes, species abundance, community composition, long term monitoring, endangered species, invasive species

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:

1. Data integration

Data integration was performed in the statistical programming language R (R Core Team 2021) using the ‘tidyverse’ family of packages (Wickham et al. 2019), and packaged into the R package LTMRdata v1.x.x (Bashevkin 2022). The latest version of the R package is available at https://github.com/sbashevkin/LTMRdata. Source datasets were either pulled in flat format from data publications, or ingested from the raw Access databases. When pulled from Access databases, the individual data tables were exported to csv format to facilitate import into R. The data tables from each survey were then joined together following the relationships diagram in their respective Access databases. Data from the primary sampling gear(s) of each survey were retained. Columns and categorical data (e.g., species names) were then renamed and units converted for consistency across surveys.

To standardize catch across trawls, we calculated metrics of effort for each trawl. Effort was calculated following methods from the FMWT, Bay Study, and Suisun Study metadata and personal communications from the PIs. Sampling effort was quantified following the methods of the component surveys, as either a tow area (for the otter trawls) or a tow volume (for all other gear types).

Generally, a subset of the total catch of a given species is measured from each trawl. To estimate the frequency of each size class of fish, we calculated the adjusted length frequencies for each species in each trawl after the methods of FMWT (James White, personal communication):

$$F_{a,l} = \ T_{c}(\frac{F_{m,l}}{T_{m}})$$

where F_a,l = adjusted frequency of each recorded length, T_c = total catch, F_m,l = measured frequency of each recorded length, and T_m = total number of fish measured. Some surveys occasionally subsampled for measurement separately on different groups within a species (generally based on size classes, age, or Salmon races). In these cases, we calculated the adjusted frequencies separately for each group. In the Suisun Study database, these groups were identified with unstandardized comments describing the size or age class. When possible, these comments were converted into a fish size range that could then be assigned a group. However, not all comments could be translated into a fish size range, leaving some fish sizes unknown in the Suisun Study data. Fish sizes are occasionally unknown in many of the surveys when no individuals of a species were measured in a sample.

The datasets were then combined by simply binding them together by their now-standardized column names. The last step in data integration was to fill in zeros. The surveys did not commonly record when a species was not present in a trawl, but these absences are critically important for statistical analysis. For any trawls in which a species was not recorded, we added a record of that species with an adjusted frequency of 0.

2. Fish lengths

While 8 of the surveys recorded fish lengths as fork length (or total length if no fork), the Suisun Study recorded standard length. We thus compiled conversion equations for 20 species (<emphasis role="strong">Table 3.1</emphasis>) to convert Suisun Study lengths (for those 20 species) to fork length (or total length if no fork). The equations are of the form:

F L = a + b × S L

where FL = fork length (or total length for species with no fork) in mm, a = intercept, b = slope, and SL = standard length in mm.

Lengths are especially important for the data integration because each survey would discard (not count nor measure) fish below a size cutoff, but those cutoffs have differed among surveys and over time. While the equations are provided, lengths are not converted in this dataset, so Suisun Study lengths are not comparable to the other surveys unless converted.

3. Final format

Before publication, the joined dataset was split into separate tables for the fish-level data (taxa, length, count, etc.) and the sample-level data (environmental variables, sampling effort, etc.). The fish length conversion equations are published in a separate table.

Description:

This method step describes provenance-based metadata as specified in the LTER EML Best Practices.