Hydrodynamic time-series data from Whale's Tail South marsh in Eden Landing Ecological Reserve in Alameda County, CA in 2021 and 2022

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Frequently anticipated questions:

What does this data set describe?

Title:
Hydrodynamic time-series data from Whale's Tail South marsh in Eden Landing Ecological Reserve in Alameda County, CA in 2021 and 2022
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 in South San Francisco Bay and in the Whale's Tail South marsh in Eden Landing Ecological Reserve in Alameda County, CA in 2021 and 2022. Data files are grouped by data type and season (summer and winter). At Bay sites, instruments were deployed on small quadpods. In the tidal creek, instruments were attached to grates mounted directly on the sediment bed. Marsh sites consisted of one transect of six stations perpendicular to the bay-marsh interface, and a second transect perpendicular to a tidal creek. Note that marsh stations were positioned fairly high in the tidal frame (close to the mean higher-high water elevation), so they were inundated less than 10 percent of the time. Instruments at the Bay stations were inundated most of the time but were subaerial at low tide. Data are only valid when the instruments were submerged. Users are advised to assess data quality carefully, and to check 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=2021-627-FA https://cmgds.marine.usgs.gov/fan_info.php?fan=2021-660-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?
    Ferreira, Joanne C.T., McGill, Samantha C., WinklerPrins, Lukas T., Nowacki, Daniel J., and Lacy, Jessica R., 20230412, Hydrodynamic time-series data from Whale's Tail South marsh in Eden Landing Ecological Reserve in Alameda County, CA in 2021 and 2022: data release doi:10.5066/P972R6AW, U.S. Geological Survey, Pacific Coastal and Marine Science Center Santa Cruz, California.

    Online Links:

    This is part of the following larger work.

    Ferreira, Joanne C.T., Lacy, Jessica R., McGill, Samantha C., WinklerPrins, Lukas T., Nowacki, Daniel J., Stevens, Andrew W., and Tan, Angela C., 2023, Hydrodynamic and sediment transport data from Whale's Tail South marsh and adjacent waters in South San Francisco Bay, California 2021-2022: data release doi:10.5066/P9P7I65U, U.S. Geological Survey, Pacific Coastal and Marine Science Center, Santa Cruz, California.

    Online Links:

  2. What geographic area does the data set cover?
    West_Bounding_Coordinate: -122.1676
    East_Bounding_Coordinate: -122.1384
    North_Bounding_Coordinate: 37.5896
    South_Bounding_Coordinate: 37.5829
  3. What does it look like?
  4. Does the data set describe conditions during a particular time period?
    Beginning_Date: 16-Jun-2021
    Ending_Date: 31-Jan-2022
    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 was 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)
    • Joanne C.T. Ferreira
    • Samantha C. McGill
    • Lukas T. WinklerPrins
    • 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?

These data were collected to measure the physical forces that resuspend sediment, specifically waves and tidal currents, as well as suspended-sediment concentration in the water column. They were collected as part of a study to quantify sediment fluxes and changes in marsh morphology at Whale's Tail marsh in southern San Francisco Bay. 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: 07-Jun-2021 (process 1 of 19)
    Four quadpod platforms were deployed in South San Francisco Bay adjacent to the Whale's Tail marsh. Three sites, BMV, MEN, and MES included a Nortek single point acoustic doppler velocimeter each with a Seapoint turbidity meter, and one BML contained Sequoia Scientific Laser In-situ scattering and transmissometry (LISST) particle size analyzer and an RBR Virtuoso single-channel data logger with Seapoint turbidity meter. All turbidity meters were equipped with a Zebra-Tech hydrowiper to prevent biofouling. Two sites, BMV and MEN, included an RBR CTD.
    Date: 15-Jun-2021 (process 2 of 19)
    Three platforms TCE, TCM, and TCW, each consisting of a Nortek Aquadopp acoustic doppler profiler with a Seapoint turbidity meter attached to a grate placed directly on the bottom surface, were deployed in tidal creeks of the Whale's Tail marsh. All turbidity meters were equipped with a Zebra-Tech hydrowiper to prevent biofouling.
    Date: 16-Jun-2021 (process 3 of 19)
    Two transects of instrumentation BT1-BT5 and CT1-CT4 were deployed on the marsh surface: the five BT instrument platforms were located on a transect perpendicular to the bay shoreline, and four CT instrument platforms located on a transect perpendicular to the tidal creek. All transect instrument sites 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. RBR temperature loggers were placed directly on the marsh surface in seven of these locations at BT3, BT4, BT5, CT1, CT2, CT3 and CT4. In addition, one platform consisting of a Nortek Aquadopp acoustic doppler profiler with a Seapoint turbidity meter was attached to a grate placed directly on the bottom surface in the bay shallows at MEV. All seapoint turbidity meters were equipped with Zebra-Tech hydrowipers to prevent biofouling.
    Date: 21-Jun-2021 (process 4 of 19)
    Deployed one weightstand (flat weight with center pole)with an RBR bursting pressure sensor, extending the Bay Transect at BT0 offshore.
    Date: 18-Jul-2021 (process 5 of 19)
    One platform BML including the Sequoia Scientific Laser In-situ scattering and transmissometry (LISST) particle size analyzer was retrieved from San Francisco Bay. The data from the retrieved instruments were post-processed using manufacturers software packages and USGS MATLAB codes.
    Date: 11-Aug-2021 (process 6 of 19)
    All remaining instruments were retrieved from both San Francisco Bay and Whale's Tail marsh and tidal creeks. The data from the retrieved instruments were post-processed using manufacturers software packages and USGS MATLAB codes.
    Date: 16-Nov-2021 (process 7 of 19)
    Three platforms each consisting of a Nortek Aquadopp acoustic doppler profiler with a Seapoint turbidity meter attached to a grate placed directly on the bottom surface were deployed in tidal creeks of the Whale's Tail marsh TCE, TCM, and TCW. All turbidity meters were equipped with a Zebra-Tech hydrowiper to prevent biofouling.
    Date: 23-Nov-2021 (process 8 of 19)
    Four quadpod platforms were deployed in South San Francisco Bay adjacent to the Whale's Tail marsh. Three sites BMV, MEN, and MES included a Nortek single point acoustic doppler velocimeter each with a Seapoint turbidity meter, and one BML contained Sequoia Scientific Laser In-situ scattering and transmissometry (LISST) particle size analyzer and an RBR Virtuoso single-channel data logger with Seapoint turbidity meter. All turbidity meters were equipped with a Zebra-Tech hydrowiper to prevent biofouling. Two of the sites BMV and MEN included an RBR CTD. A weightstand (flat weight with center pole) with an RBR pressure sensor was deployed in the bay shallows offshore along the Bay transect at BT0.
    Date: 01-Dec-2021 (process 9 of 19)
    Two transects of instrumentation BT1-BT5 and CT1-CT4 were deployed on the marsh surface: the five BT instrument platforms were located on a transect perpendicular to the bay shoreline, and the four CT instrument platforms located on a transect perpendicular to the tidal creek. All transect instrument sites 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. RBR temperature loggers were placed directly on the marsh surface in seven of these locations at BT3, BT4, BT5, CT1, CT2, and CT4. In addition, one platform consisting of a Nortek Aquadopp acoustic doppler profiler with a Seapoint turbidity meter was attached to a grate placed directly on the bottom surface in the bay shallowsat MEV. All seapoint turbidity meters were equipped with Zebra-Tech hydrowipers to prevent biofouling.
    Date: 04-Jan-2022 (process 10 of 19)
    Deployed one RBRduet pressure and temperature logger on the marsh surface in Cargill Marsh at CAR.
    Date: 25-Jan-2022 (process 11 of 19)
    Instruments were retrieved from both marsh-top transects BT1-BT5, CT1-CT4 and the marsh edge station at MEV. The data from the retrieved instruments were post-processed using manufacturers software packages and USGS MATLAB codes.
    Date: 28-Jan-2022 (process 12 of 19)
    Tidal creek stations were recovered at TCE, TCM, and TCW. The data from the retrieved instruments were post-processed using manufacturers software packages and USGS MATLAB codes.
    Date: 31-Jan-2022 (process 13 of 19)
    Bay platforms were recovered from BT0, BML, BMV, MEN, and MES. The data from the retrieved instruments were post-processed using manufacturers software packages and USGS MATLAB codes.
    Date: 04-Feb-2022 (process 14 of 19)
    Station CAR in Cargill marsh was recovered. The data from the retrieved instrument was post-processed using manufacturers software packages and USGS MATLAB codes.
    Date: 04-Nov-2022 (process 15 of 19)
    Data were accumulated into NetCDF files. During post-processing, data collected before deployment and after recovery were removed from the time series for the nortek velocimeter and acoustic doppler profiler data. 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 the pressure was measured at less than 0.01m and corrected for atmospheric pressure. The files include data of intermittent poor quality due to interference by vegetation caught on frames. In a few datasets with persistent vegetative interference the compromised data were removed, as noted in the associated metadata. Turbidity data are raw unless otherwise noted and include high values that may be attributable to vegetation. For each 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 Regression_constants_for_converting_turbidity_to_SSC(mg_per_L).csv. Use of all data requires careful assessment of data quality. LISST volume concentrations are most accurate when the optical percent transmission is above 30, as light passing through the sample volume is unlikely to be scattered by more than one particle. Low quality LISST data at the end of a few files were removed, however some bad data are still present in the files and therefore judgment should be applied when using them, as with all other data files. Pressure and temperature logger data is raw unless noted in the netcdf file metadata as the removal of bad data is highly interperative and may result in a loss of information.
    Date: 10-Jan-2023 (process 16 of 19)
    Wave statistics (Root-mean square (RMS) wave height, representative period, peak period, representative bottom orbital velocity, and representative orbital velocity direction) were calculated from the bursts of velocity and pressure measured by the ADVs, following the spectral method described in Wiberg and Sherwood (2008). For these calculations, the low- frequency cutoff was set to 1/6 s-1 and the burst-specific high-frequency cutoff was set to hf = (9.81/(4*pi*depth))0.5, where depth is meters of water above the sensor.
    Date: 13-Jan-2023 (process 17 of 19)
    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 'WTS' or 'WTW' indicating summer or winter deployment for the experiment name; the fourth and fifth positions represent the calendar year in which the data were collected (21, 2021); the sixth, seventh and eighth characters are an alphanumeric code for the site name (MEN, BT0, etc.); the ninth and tenth characters represent the instrument position on the platform, where 01 is the top-most. The instrument number was omitted for MET, the meteorological station. For the WTS nortek vector data, 'A' or 'B' is appended to indicate the time series was split into parts due to a change in the platform orientation during instrument maintenance. Next is a two- or three-character code 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; t, RBRs temperature sensor; ctd, RBRs conductivity, temperature, and depth logger; tu, RBRs Virtuoso turbidity logger; ls, Sequoia Scientifics LISST). There are an additional 2 to 3 characters for instruments that collect in a bursting pattern to indicate whether the file includes the burst data (-b) or the statistics and/or singular observations of the burst (-s). This indicator is omitted if there is no bursting pattern. Similarly, a (-wv) suffix indicates this is wave property data from the instrument. Information on the files available and the data in each file is listed in the WTS_file_table.csv for the summer data and the WTW_file_table.csv for the winter data.
    Date: 30-Jan-2023 (process 18 of 19)
    The netcdf files were compressed and combined in zipped files. Files were grouped by time period for summer (WTS21) and winter (WTW21) and further divided by primary instrument type to facilitate user access. Suffixes follow the nomenclature defined above for filenames including s a two- or three-character code 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; t, RBRs temperature sensor; ctd, RBRs conductivity, temperature, and depth logger; tu, RBRs Virtuoso turbidity logger; ls, Sequoia Scientifics LISST).
    Date: 16-May-2023 (process 19 of 19)
    Edits were made to correct spelling in author name. No data were changed. The metadata available from a harvester may supersede metadata bundled within a download file. Users are advised to compare the metadata date of this file to any similar file to ensure they are using the most recent version. (scochran@usgs.gov)
  3. What similar or related data should the user be aware of?
    Wiberg, P.L., and Sherwood, C.R., 2008, Calculating wave-generated bottom orbital velocities from surface-wave parameters..

    Online Links:

    Other_Citation_Details:
    Wiberg, P.L., and Sherwood, C.R., 2008, Calculating wave-generated bottom orbital velocities from surface-wave parameters: Computers and Geosciences, v. 23, p. 1243-1262, doi: 10.1016/j.cageo.2008.02.010

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. 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 none
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 time period for summer (WTS21) and winter (WTW21) and further divided by primary instrument type to facilitate user access. Suffixes follow the nomenclature defined above for filenames including s a two- or three-character code 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; t, RBRs temperature sensor; ctd, RBRs conductivity, temperature, and depth logger; tu, RBRs Virtuoso turbidity logger; ls, Sequoia Scientifics LISST). Information on the files available and the data in each file is listed in the WTS_file_table.csv for the summer data and the WTW_file_table.csv for the winter data.
  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 EPIC Metadata Conventions. File download sizes range from 58 kB to 1006 MB. in format NetCDF (version MATLAB) Data are in NetCDF formats. Size: 1214
      Network links: https://doi.org/10.5066/P972R6AW
    • 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 utilites. 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: 16-May-2023
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_P972R6AW/WT_timeseries_metadata.faq.html>
Generated by mp version 2.9.51 on Tue May 16 16:48:22 2023