Analysis for estimated percent sand in cores taken from San Francisco Bay, California, 1990-2016

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Frequently anticipated questions:

What does this data set describe?

Title:
Analysis for estimated percent sand in cores taken from San Francisco Bay, California, 1990-2016
Abstract:
Sediment analysis of cores collected in San Francisco Bay, San Pablo Bay, and the Carquinez Strait and Suisun Bay, California from 1990 to 2016 for percent sand. Handwritten core logs, x-radiographs, and the cores themselves, were examined for the presence of sand.
Supplemental_Information:
Additional information about the field activity or activities from which these data were derived is available online at:
https://cmgds.marine.usgs.gov/fan_info.php?fan=J190SF https://cmgds.marine.usgs.gov/fan_info.php?fan=J191SF https://cmgds.marine.usgs.gov/fan_info.php?fan=J200SF https://cmgds.marine.usgs.gov/fan_info.php?fan=2016-671-FA
The data presented here was originally in an excel spreadsheet with one tab per core. To make this data accessible to all, the analysis for each core has been combined into one flat file with headings for each type of data presented and records for the data listed by core. It is recommended that in working with the data, the record information be separated by core and by source.
Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government.
Although this Federal Geographic Data Committee-compliant metadata file is intended to document the dataset in nonproprietary form, as well as in Esri format, this metadata file may include some Esri-specific terminology.
  1. How might this data set be cited?
    Fregoso, Theresa A., Kharrazi, Bethany, and Jaffe, Bruce E., 20250723, Analysis for estimated percent sand in cores taken from San Francisco Bay, California, 1990-2016: data release DOI: 10.5066/P9Y7W1ZM, U.S. Geological Survey, Pacific Coastal and Marine Science Center, Santa Cruz, California.

    Online Links:

    This is part of the following larger work.

    Fregoso, Theresa A., Foxgrover, Amy C., Kharrazi, Bethany, and Jaffe, Bruce E., 2025, Estimates of percent sand in cores collected in San Francisco Bay,California.: Data Release DOI:10.5066/P9Y7W1ZM, U.S. Geological Survey, Pacific Coastal and Marine Science Center, Santa Cruz, CA.

    Online Links:

    Other_Citation_Details:
    Suggested Citation: Fregoso, T.A., Foxgrover, A.C., Kharrazi, B., and Jaffe, B.E., 2025, Estimates of percent sand in cores collected in San Francisco Bay, California: U.S. Geological Survey data release, https://doi.org/10.5066/P9Y7W1ZM.
  2. What geographic area does the data set cover?
    West_Bounding_Coordinate: -122.507046
    East_Bounding_Coordinate: -121.863877
    North_Bounding_Coordinate: 38.133552
    South_Bounding_Coordinate: 37.448070
  3. What does it look like?
    SFBayCoreLocations.png (PNG)
    Map depicting the location and source of cores included in this study
  4. Does the data set describe conditions during a particular time period?
    Beginning_Date: 23-Jan-1990
    Ending_Date: 21-Oct-2016
    Currentness_Reference:
    ground condition at time data were collected
  5. What is the general form of this data set?
    Geospatial_Data_Presentation_Form: comma-delimited text
  6. How does the data set represent geographic features?
    1. How are geographic features stored in the data set?
      This is a Point data set. It contains the following vector data types (SDTS terminology):
      • Point (186)
    2. What coordinate system is used to represent geographic features?
      Horizontal positions are specified in geographic coordinates, that is, latitude and longitude. Latitudes are given to the nearest 0.00001. Longitudes are given to the nearest 0.00001. Latitude and longitude values are specified in Decimal degrees. The horizontal datum used is World Geodetic System 1984 (WGS84).
      The ellipsoid used is WGS84.
      The semi-major axis of the ellipsoid used is 6378137.0.
      The flattening of the ellipsoid used is 1/298.257223563.
  7. How does the data set describe geographic features?
    Attribute Table
    Table containing attribute information associated with the dataset (Source: Producer defined)
    Core
    The core ID (Source: producer defined) For A/C cores, the core IDs begin with of the last two numbers of the year collected, followed by a dash and sequential numbers assigned on day of collection. For Jaffe cores, cores begin with BC for box cores, or GC or GCC for gravity cores, followed by a dash and sequential numbers assigned on day of collection. Watt cores begin with SPB followed by sequential numbers assigned on day of collection. Yee cores begin with initials representing subembayment (SB – south bay, LSB – lower south bay, SU – Suisun, CB – Central Bay, SPB – San Pablo Bay), followed either by sequential numbers assigned on day of collection or more descriptive place name.
    Source
    The sources of the information for the rest of the attribute values (Source: producer defined)
    ValueDefinition
    paper logdata taken from a handwritten core log
    noteSpecific detail about record
    core length,recorded length of core
    graphic logdigital representation of a core log
    Date_logged
    Date core was logged, day/month/year, or year only. -9999 used when date not known. (Source: producer defined)
    Range of values
    Minimum:2/10/2003
    Maximum:11/4/2020
    Units:Date in month/day/year format or year
    Interval_top_cm
    the location of the top of current interval in the specified core. -9999 represents data records where core interval does not apply. (Source: producer defined)
    Range of values
    Minimum:1
    Maximum:368
    Units:cm
    Resolution:0.1
    Interval_bottom_cm
    the location of the bottom of current interval in the specified core. -9999 represents data records where core interval does not apply. (Source: producer defined)
    Range of values
    Minimum:1
    Maximum:372
    Units:cm
    Resolution:0.1
    Interval_length
    Length of interval in the specified core. -9999 represents data records where core length does not apply. (Source: producer defined)
    Range of values
    Minimum:1
    Maximum:372
    Units:cm
    Resolution:0.1
    Sand_pct
    the measured percent of sand by volume as a decimal for the interval record, -9999 indicates that this value does not apply to record column. (Source: producer defined)
    Range of values
    Minimum:0.00
    Maximum:1
    Units:decimal percent
    Resolution:0.0001
    Min_pct
    the minimum percent by volume as a decimal of sand for the interval record, -9999 indicates that this value does not apply to record column. (Source: producer defined)
    Range of values
    Minimum:0.0000
    Maximum:1.0000
    Units:decimal percent
    Resolution:0.0001
    Max_pct
    the maximum percent by volume as a decimal of sand for the interval record, -9999 indicates that this value does not apply to record column. (Source: producer defined)
    Range of values
    Minimum:0.0000
    Maximum:1.0000
    Units:decimal percent
    Resolution:0.0001
    Notes
    Notes on sediment type for the specific interval. (Source: producer defined) Notes on sediment type for the specific interval, na represents no applicable data.
    Comments
    Any relevant notes to interval (Source: producer defined) Any relevant notes, na represents no applicable data
    cm_sand
    The thickness of the sand layer in the interval. This value divided by the length of the interval in which it appears, is the calculated percent sand for the interval. -9999 was used for records where data were not relevant. (Source: producer defined)
    Range of values
    Minimum:0
    Maximum:64
    Units:cm
    Resolution:0.1
    XWGS84
    longitude, No data values -9999 (Source: producer defined)
    Range of values
    Minimum:-122.47317
    Maximum:-122.030 90
    Units:degree
    YWGS84
    latitude, No data values -9999 (Source: producer defined)
    Range of values
    Minimum:37.45950
    Maximum:38.10355
    Units:degree
    XUTM83
    X UTM NAD83 zone 10 north. No data values -9999 (Source: producer defined)
    Range of values
    Minimum:546303.6232
    Maximum:585012.344
    Units:meters
    YUTM83
    y UTM NAD83 zone 10 north. No data values -9999 (Source: producer defined)
    Range of values
    Minimum:4146268.693
    Maximum:4217483.725
    Units:meters
    Bay
    Subembayment where core is located (Source: producer defined)
    ValueDefinition
    SuisunSubembayment
    San PabloSubembayment
    CentralSubembayment
    SouthSubembayment
    Lower SouthSubembayment
    nano applicable data
    Year
    Year of core collection (Source: producer defined)
    Range of values
    Minimum:1990
    Maximum:2016
    Units:year
    Equipment
    Coring method (Source: producer defined)
    ValueDefinition
    BoxCoring method
    GravityCoring method
    VibracoreCoring method
    nano applicable data
    Survey
    survey reference (Source: producer defined)
    ValueDefinition
    Anima/Clifton1990 and 1991 Anima and Clifton survey cruises
    Jaffe2000 Jaffe survey cruise
    Watt2016 Watt survey cruise
    Yee2006 Yee survey cruise
    nano applicable data
    Entity_and_Attribute_Overview: The first line of the csv file is a header line.
    Entity_and_Attribute_Detail_Citation: U.S. Geological Survey

Who produced the data set?

  1. Who are the originators of the data set? (may include formal authors, digital compilers, and editors)
    • Theresa A. Fregoso
    • Bethany Kharrazi
    • Bruce E. Jaffe
  2. Who also contributed to the data set?
  3. To whom should users address questions about the data?
    U.S. Geological Survey, Pacific Coastal and Marine Science Center
    Attn: PCMSC Science Data Coordinator
    2885 Mission Street
    Santa Cruz, CA

    831-427-4747 (voice)
    pcmsc_data@usgs.gov

Why was the data set created?

Estimating the amount of sand made available to the estuary through erosion of the San Francisco Bay floor and sand sequestered within the system through deposition from the 1980s to 2010s for use in constructing a sand sediment budget. We utilized the bathymetric change analysis of Fregoso and others (2023) that documents sediment volume change from a 1980s bathymetric surface to a 2010s bathymetric surface, in combination with information on the sand content of the bed sediment derived from sediment cores and surface samples from six different sediment studies, to estimate the net change in sand volume in the bed of San Francisco Bay.

How was the data set created?

  1. From what previous works were the data drawn?
    A/C cores (source 1 of 6)
    Anima, R.J., Clifton, H. E., Reiss, Carol, and Wong, Florence L., 2005, Locations and descriptions of gravity, box, and push cores collected in San Francisco Bay between January and February, 1990 and 1991: U.S. Geological Survey, online.

    Online Links:

    Type_of_Source_Media: online report
    Source_Contribution: Core data for analysis of sand
    A/C and Jaffe logs 1 (source 2 of 6)
    Woodrow, Donald L., Chin, John L., Wong, Florence L., Fregoso, Theresa A., and Jaffe, Bruce E., 2017, Description of gravity cores from San Pablo Bay and Carquinez Strait, San Francisco Bay, California: U.S. Geological Survey, online.

    Online Links:

    Type_of_Source_Media: online report
    Source_Contribution: Core logs for analysis of sand
    A/C and Jaffe logs 2 (source 3 of 6)
    Fregoso, Theresa A., Woodrow, Donald L., and Orzech, Kevin, 2024, Gravity and Box cores San Francisco Bay, California: U.S. Geological Survey, online.

    Online Links:

    Type_of_Source_Media: online report
    Source_Contribution: Core logs for analysis of sand
    Jaffe cores (source 4 of 6)
    Allison, Dan, Hampton, Margaret, and Jaffe, Bruce E., 2003, Preliminary Analysis of Cores from North San Francisco Bay, California: U.S. Geological Survey, online.

    Online Links:

    Type_of_Source_Media: online report
    Source_Contribution: Core data for analysis of sand
    Watt cores (source 5 of 6)
    Takesue, Rene K., McGann, Mary L., Lorenson, Thomas D., and Watt, Janet T., 2021, Geophysical properties, geochronologic, and geochemical data of sediment cores collected from San Pablo Bay, California: U.S. Geological Survey, online.

    Online Links:

    Type_of_Source_Media: online resources
    Source_Contribution: Core data for analysis of sand
    Yee cores (source 6 of 6)
    Yee, Donald, Bemis, Bryan, Hammond, Douglas, Heim, Wes, Jaffe, Bruce E., Rattonetti, Anthony, and Bergen, Saskia. van, 2011, Age Estimates and Pollutant Concentrations of Sediment Cores from San Francisco Bay and Wetlands.: San Francisco Estuary Institute, online.

    Online Links:

    Type_of_Source_Media: online resources
    Source_Contribution: Core data for analysis of sand
  2. How were the data generated, processed, and modified?
    Date: 26-Jun-2021 (process 1 of 1)
    Cores taken in San Francisco Bay were divided into the following bays: South Bay, Central Bay, San Pablo Bay and Suisun Bay. Each core was logged in one or several of the following ways prior to this effort: paper logs based on observations of the working/archived core, graphic illustrated logs included in various reports, and grain size tables included in reports and open file reports. The intervals chosen and qualitative findings of sand reported are drawn directly from the paper logs, as they have the most detail in describing units and illustrating sand presence. The paper logs were obtained electronically (some were included in open file reports) or physically in labeled binders at USGS Menlo Park. The other logging methods were used as secondary confirmations of the paper log content. For just a few cores, the secondary logs did not line up with the paper log. These cores were visited in person to confirm the mismatch. Where sand was described in the written portion of the paper logs and/or drawn in the visual depiction of the core, percent sand was estimated. The illustration of the core helped contextualize the distribution and thickness of sand in the units. Several paper logs included a written percent sand estimate, which was then reported in the spreadsheet for this effort. Where there was not a percent sand estimate, various methods were used to estimate sand presence in the units. If a unit contained sand laminae, then they were counted and estimated for thickness from the visual depiction of the core and associated descriptions to determine the amount of sand in the unit. If a unit contained sand interbeds or lenticular bedding, a similar process was used depending on the thickness of each bed. Where there were sand-filled burrows, an estimation was made based on the frequency and distribution of the burrows and their apparent thickness drawn on the paper log. If a unit was described at “Muddy Sand”, “Sandy Mud”, or any other description in which sand was either a matrix or a secondary grain size in any unit and not clearly distinguished visually on the paper log (i.e., sand was noted in the description but not visually marked in any identifiable way on the drawn core), a best estimation was made based on the description. Percent sand for intervals was calculated by dividing the total amount of sand in centimeters from the length of the unit in centimeters and multiplying by 100. Percent sand was estimated for the entire core when at least one unit contained sand. This was calculated by adding up the amount of sand in every unit and then dividing the sum by the length of the core. If a core had any gaps, these were subtracted from the overall length of the core. Data sources used in this process:
    • A/C cores
    • A/C and Jaffe logs 1
    • A/C and Jaffe logs 2
    • Jaffe cores
    • Watt cores
    • Yee cores
  3. What similar or related data should the user be aware of?
    Fregoso, Theresa A., Jaffe, Bruce E., Foxgrover, Amy C., Woodrow, Donald, Kharrazi, Bethany, and Orzech, Kevin, 2025, Contributions of erosion, deposition, and human activities to a change in sand storage in the bed of San Francisco Bay, California.

    Online Links:

    Other_Citation_Details:
    Fregoso, T.A., Jaffe, B.E., Foxgrover, A.C., Woodrow, D.L., Kharrazi, B., and Orzech, K., 2025, Contributions of erosion, deposition, and human activities to a change in sand storage in the bed of San Francisco Bay, California, 1980s to 2010s: U.S. Geological Survey Open-File Report 2025–1022, 30 p., https://doi.org/10.3133/ofr20251022.
    Fregoso, Theresa A., Jaffe, Bruce E., and Foxgrover, Amy C., 2023, Bathymetric change analyses in San Francisco Bay, California, from 1971 to 2020.

    Online Links:

    Other_Citation_Details:
    Fregoso, T.A., Jaffe, B.E., and Foxgrover, A.C., 2023, Bathymetric change analysis in San Francisco Bay, California, from 1971 to 2020: U.S. Geological Survey data release, https://doi.org/10.5066/P9Y5PEV0

How reliable are the data; what problems remain in the data set?

  1. How well have the observations been checked?
    While every effort was made to be precise in measurements; quality, preservation, and measurements of individual cores, determined recorded sediment intervals in core logs. Estimating the percent sand in cores from handwritten core logs is, fundamentally, subjective. Users are advised to read the companion open-file report accompanying this data release for additional information.
  2. How accurate are the geographic locations?
    Data are as accurate as source data used. Users are advised to read the metadata record for the sources for horizontal accuracy details. No further accuracy tests were conducted.
  3. How accurate are the heights or depths?
    Data are as accurate as source data used. Users are advised to read the metadata record for the sources for horizontal accuracy details. No further accuracy tests were conducted.
  4. Where are the gaps in the data? What is missing?
    There are additional sediment cores that have core logs that were not included in this data release for several possible reasons, the cores was outside of this project study area, they have been released as part of another study, or the original core could not be located/determined.
  5. How consistent are the relationships among the observations, including topology?
    Attributes mean the same thing throughout the data set.

How can someone get a copy of the data set?

Are there legal restrictions on access or use of the data?
Access_Constraints No access constraints
Use_Constraints USGS-authored or produced data and information are in the public domain from the U.S. Government and are freely redistributable with proper metadata and source attribution. Please recognize and acknowledge the U.S. Geological Survey
  1. Who distributes the data set? (Distributor 1 of 1)
    U.S. Geological Survey - CMGDS
    2885 Mission Street
    Santa Cruz, CA

    831-427-4747 (voice)
    pcmsc_data@usgs.gov
  2. What's the catalog number I need to order this data set? These data are available in csv format accompanied by CSDGM FGDC-compliant metadata.
  3. What legal disclaimers am I supposed to read?
    Unless otherwise stated, all data, metadata and related materials are considered to satisfy the quality standards relative to the purpose for which the data were collected. Although these data and associated metadata have been reviewed for accuracy and completeness and approved for release by the U.S. Geological Survey (USGS), no warranty expressed or implied is made regarding the display or utility of the data on any other system or for general or scientific purposes, nor shall the act of distribution constitute any such warranty.
  4. How can I download or order the data?
    • Availability in digital form:
      Data format: cvs table in format comma-delimited text (version Microsoft Excel 2302 Build 16130.20766) Size: 0.299
      Network links: https://doi.org/10.5066/P9Y7W1ZM
    • Cost to order the data: None.

  5. What hardware or software do I need in order to use the data set?
    These data can be viewed with any spreadsheet or word processing software capable of opening CSV files.

Who wrote the metadata?

Dates:
Last modified: 23-Jul-2025
Metadata author:
U.S. Geological Survey, Pacific Coastal and Marine Science Center
Attn: PCMSC Science Data Coordinator
2885 Mission Street
Santa Cruz, CA

831-427-4747 (voice)
pcmsc_data@usgs.gov
Metadata standard:
Content Standard for Digital Geospatial Metadata (FGDC-STD-001-1998)
This page is <https://cmgds.marine.usgs.gov/catalog/pcmsc/DataReleases/CMGDS_DR_tool/DR_P9Y7W1ZM/SanFranciscoCoreSedimentAnalysis_metadata.faq.html>
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