Hydrodynamic time-series data from two marshes and adjacent shallows in Northern San Francisco Bay, California, 2022-2023

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Frequently anticipated questions:

What does this data set describe?

Title:
Hydrodynamic time-series data from two marshes and adjacent shallows in Northern San Francisco Bay, California, 2022-2023
Abstract:
Hydrodynamic and sediment transport time-series data, including water depth, velocity, turbidity, conductivity, and temperature, were collected by the U.S. Geological Survey (USGS) Pacific Coastal and Marine Science Center at shallow subtidal and intertidal sites in Corte Madera Bay and San Pablo Bay National Wildlife Refuge (SPNWF) in San Francisco Bay, CA, as well as on the marsh plain of SPNWF marsh and in a tidal creek and on the marsh plain of Corte Madera Marsh, in 2022 and 2023. Data files are grouped by station, San Pablo subtidal, San Pablo intertidal, San Pablo marsh, Corte Madera subtidal, Corte Madera intertidal, Corte Madera marsh, or Corte Madera tidal creek, then by instrument type. At most stations there were periods of low water when sensors were no longer submerged, resulting in spurious data. In addition, most instruments experienced some degree of biofouling, particularly at the subtidal and intertidal stations. The subtidal stations also occasionally show signs of platform rocking or movement due to strong water flow, and/or from accidental fisher/boater interference. Users are advised to assess data quality carefully, and to check the metadata for instrument information, as platform deployment times and data-processing methods varied.
Supplemental_Information:
Additional information about the field activities from which these data were derived is available online at: https://cmgds.marine.usgs.gov/fan_info.php?fan=2022-619-FA https://cmgds.marine.usgs.gov/fan_info.php?fan=2023-603-FA Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government. Image maps showing locations of sampling sites are located with the Supplemental files accompanying this dataset. Tables of filenames and contents as well as calibration data for optical instruments are also included.
  1. How might this data set be cited?
    McGill, Samantha C., Ferreira, Joanne C.T., Nowacki, Daniel J., and Lacy, Jessica R., 20240806, Hydrodynamic time-series data from two marshes and adjacent shallows in Northern San Francisco Bay, California, 2022-2023: data release DOI:10.5066/P1XZFGCX, U.S. Geological Survey, Pacific Coastal and Marine Science Center Santa Cruz, California.

    Online Links:

    This is part of the following larger work.

    McGill, Samantha C., Lacy, Jessica R., Ferreira, Joanne C.T., Nowacki, Daniel J., Stevens, Andrew W., and Tan, Angela C., 2024, Hydrodynamic and sediment transport data from two marshes and adjacent shallows in Northern San Francisco Bay, California 2022-2023: data release DOI:10.5066/P1XZFGCX, U.S. Geological Survey, Pacific Coastal and Marine Science Center, Santa Cruz, California.

    Online Links:

    Other_Citation_Details:
    Suggested Citation: McGill, S.C., Lacy, J.R., Ferreira, J.C.T., Nowacki, D.J., Stevens, A.W., and Tan, A.C., 2024, Hydrodynamic and sediment transport data from two marshes and adjacent shallows in Northern San Francisco Bay, California 2022-2023: U.S. Geological Survey data release, https://doi.org/10.5066/P1XZFGCX.
  2. What geographic area does the data set cover?
    West_Bounding_Coordinate: -122.5055250
    East_Bounding_Coordinate: -122.4749500
    North_Bounding_Coordinate: 38.1144300
    South_Bounding_Coordinate: 37.9301300
  3. What does it look like?
    NBM_timeseries_stations_map_v1.png (PNG)
    Map showing the locations of each station where time-series data were collected.
  4. Does the data set describe conditions during a particular time period?
    Beginning_Date: 14-Apr-2022
    Ending_Date: 28-Aug-2023
    Currentness_Reference:
    Ground condition at time data were collected.
  5. What is the general form of this data set?
    Geospatial_Data_Presentation_Form: NetCDF files
  6. How does the data set represent geographic features?
    1. How are geographic features stored in the data set?
      Indirect_Spatial_Reference:
      Data were collected continuously at survey locations. Refer to self-contained netCDF files for more location information.
    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 1.0E-5. Longitudes are given to the nearest 1.0E-5. 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?
    Entity_and_Attribute_Overview:
    NetCDF files are self-contained and attribute information may be found in the header of the file itself.
    Entity_and_Attribute_Detail_Citation:
    The entity and attribute information were generated by the individual and/or agency identified as the originator of the data set. Please review the rest of the metadata record for additional details and information.

Who produced the data set?

  1. Who are the originators of the data set? (may include formal authors, digital compilers, and editors)
    • Samantha C. McGill
    • Joanne C.T. Ferreira
    • Daniel J. Nowacki
    • Jessica R. Lacy
  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
    US

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

Why was the data set created?

The data were collected to determine the relationship between SSC in the shallows and sediment deposition at two different marshes, during a range of tidal, wave, and hydrologic conditions. The goals of the project are to produce information useful for prioritizing marsh restoration sites, assessing restoration actions, and understanding mechanisms of sediment delivery to marshes. These data are intended for researchers, students, policy makers, and the general public.

How was the data set created?

  1. From what previous works were the data drawn?
  2. How were the data generated, processed, and modified?
    Date: 17-Jul-2023 (process 1 of 11)
    Two quadpod platforms were deployed in Northern San Francisco Bay, one in the subtidal shallows of Corte Madera Bay, and a second in the subtidal shallows of San Pablo Bay National Wildlife Refuge. Platforms were turned roughly every 60 days, equating to eight total deployments, named A through H. Each of the two subtidal stations (named PS and CS) included a Nortek single point acoustic doppler velocimeter each with a Seapoint turbidity meter, and an RBR CTD. Both turbidity meters were equipped with a Zebra-Tech hydro-wiper to prevent biofouling.
    Date: 28-Aug-2023 (process 2 of 11)
    Two weightstand (flat weight with center pole) platforms were deployed in Northern San Francisco Bay, one in the intertidal shallows of Corte Madera Bay, and a second in the intertidal shallows of San Pablo Bay National Wildlife Refuge. Platforms were turned roughly every 60 days, equating to nine total deployments, named A through I. Each of the two intertidal stations (named PI and CI) included an RBR bursting pressure sensor and a Seapoint turbidity meter logged by an RBR Virtuoso single-channel data logger. Both turbidity meters were equipped with a Zebra-Tech hydro-wiper to prevent biofouling.
    Date: 18-Jul-2023 (process 3 of 11)
    Two marsh-top platforms, CM and PM, were deployed at Corte Madera Marsh and San Pablo National Wildlife Refuge Marsh, both were positioned directly in line with the intertidal and subtidal sites, at approximately 25 m back from the bay edge. The bay edge was defined as the end of marsh vegetation and start of mudflat. Both platforms included a Seapoint turbidity meter logged by an RBR Virtuoso single-channel data logger, as well as an RBR logger measuring pressure attached to rebar above the marsh surface. Both Seapoint turbidity meters were equipped with Zebra-Tech hydro-wipers to prevent biofouling. Platforms were turned roughly every 60 to 90 days, equating to eight total deployments for CM, named A through H, and five total deployments for PM, named A, C, D, F, and H.
    Date: 18-Jul-2023 (process 4 of 11)
    One platform, CC, consisting of a Nortek Aquadopp acoustic doppler profiler with a Seapoint turbidity meter and a RBR pressure logger were attached to a grate that was deployed directly onto the bottom surface of the channel of a tidal creek located in Corte Madera Marsh. The turbidity meters were equipped with a Zebra-Tech hydro-wiper to prevent biofouling and had a wire cage placed around it, outside of the sensors sample volume, to keep floating debris from catching or damaging the sensor. The platform was turned roughly every 60 days, equating to eight total deployments, named A through H.
    Date: 06-May-2024 (process 5 of 11)
    All recovered data from the retrieved instruments were post-processed using manufacturers software packages and USGS MATLAB codes or USGS Python codes.
    Date: 06-May-2024 (process 6 of 11)
    Data were accumulated into NetCDF files. During post-processing, data collected before deployment and after recovery were removed. Bad data points identified by 1) the deployment and recovery times, 2) data flagged as erroneous by the manufacturer, 3) amplitude or correlation values outside of predetermined quality thresholds for the velocimeter were removed, as were data where pitch and roll exceeded 25 degrees. The files include data of intermittent poor quality due to various reasons which may include but are not limited to biofouling, movement of platform, and exposure during low tides. Despite removal of bad data, some are still present in the files and therefore judgment should be applied when using them, as with all other data files. Use of all data requires careful assessment of data quality.
    Date: 06-May-2024 (process 7 of 11)
    For each turbidity sensor, a linear least-squares regression with intercept of zero was made between the turbidity values (in NTU or volts) and sample suspended sediment concentration (SSC) values (in milligrams per liter) from in situ measurements coincident to water sample collection. These constants are available as a support file in this data release NBM_Turbidity_to_SSC_calibration_constants.csv. Users should also note the gain setting used when applying a calibration coefficient to the turbidity data, all turbidity to SSC calibration constants were based on 5x gain setting.
    Date: 06-May-2024 (process 8 of 11)
    All pressure data were given a new variable P_1ac, that contains atmospherically corrected pressure data. For this correction, the residual difference between the in-air reading of the pressure sensor and the NOAA station was removed, and is noted in the netCDF file as atmospheric_pressure_correction_offset_applied.
    Date: 06-May-2024 (process 9 of 11)
    Wave statistics were calculated from the bursts of velocity and pressure measured by the ADV and from the bursts of pressure measured by the RBR bursting pressure logger. Calculations were completed using routines available on https://code.usgs.gov/cmgp/stglib. Additional information on frequency cutoffs used for the calculations can be found in the metadata of the nc data file.
    Date: 06-May-2024 (process 10 of 11)
    Files were named with a convention that uses a 12- to 15-digit alpha-numeric code. The first three characters for this dataset are all 'NBM' indicating the experiment name; the fourth and fifth positions represent the calendar year in which the project commenced (22, 2022); the sixth character is a letter representing the embayment (S, San Pablo; C, Corte Madera); the seventh character is a letter representing the station's location (M, marsh; C, tidal creek; I, intertidal; S, subtidal); the eight character is a letter corresponding to the deployment (A through I, where A is the first deployment); the ninth and tenth characters represent the instrument position on the platform, where 01 is the top-most. The eleventh, twelfth, and sometimes thirteenth characters are abbreviations for the instrument type (vec, Norteks Acoustic Doppler Velocimeter; aq, Nortek aquadopp acoustic doppler current profile; pt, RBRs bursting pressure sensor with temperature; pr, RBRs pressure sensor; ctd, RBRs conductivity, temperature, and depth logger; tu, RBRs Virtuoso turbidity logger). There are an additional 1 to 4 characters with a hyphen used to convey information about the data contained in the file. Filenames containing (-a) were used for instruments with singular/averaged observations, the (-a) also appears in the vector filenames to indicate that the file includes the burst data, while filenames with (-s) indicate the statistics/burst averaged observations of the data for bursting instruments. Similarly, (s-a) indicates the file contains wave statistics. For the bursting pressure sensors only (b-cal) indicates the file contains the burst data, and that those pressure data were corrected for atmospheric pressure. Information on the files available for each station and the data each file contains is listed in the NBM_time_series_file_table.csv.
    Date: 31-May-2024 (process 11 of 11)
    The netCDF files were compressed and combined in zipped files. Files were grouped by station (San Pablo Subtidal, Intertidal, Marsh, Corte Madera Subtidal, Intertidal, Marsh or Tidalcreek) and then by instrument type. Instrument type suffixes follow the nomenclature defined above for filenames including a two- or three-character code for the instrument type (vec, Norteks Acoustic Doppler Velocimeter; aqd, Nortek aquadopp acoustic doppler current profile; pt, RBRs pressure sensor with temperature; pr, RBRs pressure sensor; ctd, RBRs conductivity, temperature, and depth logger; tu, RBRs Virtuoso turbidity logger).
  3. What similar or related data should the user be aware of?

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

  1. How well have the observations been checked?
    No formal attribute accuracy tests were conducted. Data were collected in a complex and changing physical environment. Sites are intermittently inundated and affected by tidal and atmospheric variation. Instruments at the same site are submerged or partially submerged at varying times. Ambient air temperature, as well as water temperature, may affect measurements. Biological fouling may have impacted data quality. Data are raw unless noted in the netCDF file metadata, as the removal of bad data is highly interpretative and may result in a loss of information, preventing further analysis and understanding. Individual instrument accuracy can be found on each manufacturer’s website.
  2. How accurate are the geographic locations?
    Horizontal accuracy derived from GPS instrumentation is less than 1 m.
  3. How accurate are the heights or depths?
    There are two sources of uncertainty associated with vertical positioning of the instruments: 1) the measuring tools used during instrument mounting, 2) the amount of settling that occurs during deployment. No corrections were made to the data to account for these errors. Users may refer to the pre-deployment sensor heights provided in the datafiles in addition to the nominal heights of the sensors which are also found in the data files to verify changes in sensor elevation. The heights provided do not account for any sinking that may have occurred during the deployment.
  4. Where are the gaps in the data? What is missing?
    Dataset is considered complete for the information presented, as described in the abstract. Data outside of the deployment and recovery times have been removed. Users are advised to read the metadata in each netCDF file carefully for additional details affecting individual instruments and sensors.
  5. How consistent are the relationships among the observations, including topology?
    No formal logical accuracy tests were conducted. Data fall within expected ranges, however due to the intermittent and gradual inundation of tidal and marsh sites, some measurements will be in air while others are in water (including at the same site). Data spikes that reflect the changing conditions have been retained as the assessment of data quality and accuracy may be useful in interpretation and analysis.

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 as the originators of the dataset and in products derived from these data. This information is not intended for navigation purposes.
  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? Downloadable data in netCDF format and compressed into zipped archives. Files were grouped by station (San Pablo Subtidal, Intertidal, Marsh, Corte Madera Subtidal, Intertidal, Marsh or Tidalcreek) and then by instrument type. Instrument type suffixes follow the nomenclature defined above for filenames including a two- or three-character code for the instrument type (vec, Norteks Acoustic Doppler Velocimeter; aqd, Nortek aquadopp acoustic doppler current profile; pt, RBRs bursting pressure sensor with temperature; pr, RBRs pressure sensor; ctd, RBRs conductivity, temperature, and depth logger; tu, RBRs Virtuoso turbidity logger). Information on the files available and the data in each file is listed in the NBM_time_series_file_table.csv.
  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: Downloadable zip file of time-series data in netCDF format following CF 1.8 Metadata Conventions. File download sizes range from 2.6 to 3510.418 MB. in format NetCDF (version netCDF-4, CF-1.8) Data are in NetCDF formats. Size: 8240.7
      Network links: https://doi.org/10.5066/P1XZFGCX
    • Cost to order the data: None.

  5. What hardware or software do I need in order to use the data set?
    The downloadable data file has been compressed with the "zip" command and can be unzipped with Winzip or other archive utilities. To utilize these data, the user must have software capable of uncompressing the WinZip file and importing and viewing a NetCDF file.

Who wrote the metadata?

Dates:
Last modified: 06-Aug-2024
Metadata author:
PCMSC Science Data Coordinator
U.S. Geological Survey, Pacific Coastal and Marine Science Center
2885 Mission Street
Santa Cruz, CA
United States

831-427-7520 (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_P1XZFGCX/timeseries_metadata.faq.html>
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