Metadata: Identification_Information: Citation: Citation_Information: Originator: Joanne C.T. Ferreira Originator: Samantha C. McGill Originator: Lukas T. WinklerPrins Originator: Daniel J. Nowacki Originator: Jessica R. Lacy Publication_Date: 20230412 Title: Hydrodynamic time-series data from Whale's Tail South marsh in Eden Landing Ecological Reserve in Alameda County, CA in 2021 and 2022 Geospatial_Data_Presentation_Form: NetCDF files Series_Information: Series_Name: data release Issue_Identification: doi:10.5066/P972R6AW Publication_Information: Publication_Place: Pacific Coastal and Marine Science Center Santa Cruz, California Publisher: U.S. Geological Survey Online_Linkage: https://doi.org/10.5066/P972R6AW Larger_Work_Citation: Citation_Information: Originator: Joanne C.T. Ferreira Originator: Jessica R. Lacy Originator: Samantha C. McGill Originator: Lukas T. WinklerPrins Originator: Daniel J. Nowacki Originator: Andrew W. Stevens Originator: Angela C. Tan Publication_Date: 2023 Title: Hydrodynamic and sediment transport data from Whale's Tail South marsh and adjacent waters in South San Francisco Bay, California 2021-2022 Series_Information: Series_Name: data release Issue_Identification: doi:10.5066/P9P7I65U Publication_Information: Publication_Place: Pacific Coastal and Marine Science Center, Santa Cruz, California Publisher: U.S. Geological Survey Online_Linkage: https://doi.org/10.5066/P972R6AW Description: 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. Purpose: 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. 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. Time_Period_of_Content: Time_Period_Information: Range_of_Dates/Times: Beginning_Date: 20210616 Ending_Date: 20220131 Currentness_Reference: Ground condition at time data were collected. Status: Progress: Complete Maintenance_and_Update_Frequency: None planned Spatial_Domain: Bounding_Coordinates: West_Bounding_Coordinate: -122.1676 East_Bounding_Coordinate: -122.1384 North_Bounding_Coordinate: 37.5896 South_Bounding_Coordinate: 37.5829 Keywords: Theme: Theme_Keyword_Thesaurus: USGS Metadata Identifier Theme_Keyword: USGS:1512d958-20c4-46a4-9306-503b11c8e792 Theme: Theme_Keyword_Thesaurus: Global Change Master Directory (GCMD) Theme_Keyword: Water depth Theme_Keyword: Water pressure Theme_Keyword: Sediment transport Theme_Keyword: Currents Theme_Keyword: Water temperature Theme_Keyword: Conductivity Theme_Keyword: Salinity Theme_Keyword: Turbidity Theme_Keyword: Tidal height Theme_Keyword: Pressure sensors Theme_Keyword: Wave height gauges Theme_Keyword: CTD Theme_Keyword: Aquatic ecosystems Theme: Theme_Keyword_Thesaurus: Data Categories for Marine Planning Theme_Keyword: Water-Quality Parameters Theme: Theme_Keyword_Thesaurus: ISO 19115 Topic Category Theme_Keyword: oceans Theme: Theme_Keyword_Thesaurus: USGS Thesaurus Theme_Keyword: time series datasets Theme_Keyword: CTD measurement Theme_Keyword: marine water quality Theme_Keyword: suspended material (water) Theme: Theme_Keyword_Thesaurus: Marine Realms Information Bank (MRIB) keywords Theme_Keyword: seabed Theme_Keyword: field observation Theme_Keyword: wave observations Theme_Keyword: water level measurements Theme_Keyword: physical oceanography Theme: Theme_Keyword_Thesaurus: none Theme_Keyword: U.S. Geological Survey Theme_Keyword: USGS Theme_Keyword: Coastal and Marine Hazards and Resources Program Theme_Keyword: CMHRP Theme_Keyword: Pacific Coastal and Marine Science Center Theme_Keyword: PCMSC Theme_Keyword: Suspended-sediment concentration Theme_Keyword: Shallow-water habitat Theme_Keyword: Tidal shallows Place: Place_Keyword_Thesaurus: Geographic Names Information System Place_Keyword: State of California Place_Keyword: Alameda County Place_Keyword: San Francisco Bay Place: Place_Keyword_Thesaurus: none Place_Keyword: Whale's Tail marsh Place_Keyword: Whale’s Tail South marsh Place_Keyword: Cargill marsh Place_Keyword: Eden Landing Ecological Reserve 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. Point_of_Contact: Contact_Information: Contact_Organization_Primary: Contact_Organization: U.S. Geological Survey, Pacific Coastal and Marine Science Center Contact_Person: PCMSC Science Data Coordinator Contact_Address: Address_Type: mailing and physical Address: 2885 Mission Street City: Santa Cruz State_or_Province: CA Postal_Code: 95060-5792 Country: US Contact_Voice_Telephone: 831-427-4747 Contact_Electronic_Mail_Address: pcmsc_data@usgs.gov Cross_Reference: Citation_Information: Originator: Wiberg, P.L. Originator: Sherwood, C.R. Publication_Date: 2008 Title: Calculating wave-generated bottom orbital velocities from surface-wave parameters. 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 Online_Linkage: https://doi.org/10.1016/j.cageo.2008.02.010 Data_Quality_Information: Attribute_Accuracy: Attribute_Accuracy_Report: 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. Logical_Consistency_Report: 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. Completeness_Report: 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. Positional_Accuracy: Horizontal_Positional_Accuracy: Horizontal_Positional_Accuracy_Report: Horizontal accuracy derived from GPS instrumentation is less than 1 m. Vertical_Positional_Accuracy: Vertical_Positional_Accuracy_Report: 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. Lineage: Process_Step: Process_Description: 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. Process_Date: 20210607 Process_Step: Process_Description: 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. Process_Date: 20210615 Process_Step: Process_Description: 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. Process_Date: 20210616 Process_Step: Process_Description: Deployed one weightstand (flat weight with center pole)with an RBR bursting pressure sensor, extending the Bay Transect at BT0 offshore. Process_Date: 20210621 Process_Step: Process_Description: 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. Process_Date: 20210718 Process_Step: Process_Description: 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. Process_Date: 20210811 Process_Step: Process_Description: 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. Process_Date: 20211116 Process_Step: Process_Description: 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. Process_Date: 20211123 Process_Step: Process_Description: 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. Process_Date: 20211201 Process_Step: Process_Description: Deployed one RBRduet pressure and temperature logger on the marsh surface in Cargill Marsh at CAR. Process_Date: 20220104 Process_Step: Process_Description: 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. Process_Date: 20220125 Process_Step: Process_Description: 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. Process_Date: 20220128 Process_Step: Process_Description: 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. Process_Date: 20220131 Process_Step: Process_Description: Station CAR in Cargill marsh was recovered. The data from the retrieved instrument was post-processed using manufacturers software packages and USGS MATLAB codes. Process_Date: 20220204 Process_Step: Process_Description: 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. Process_Date: 20221104 Process_Step: Process_Description: 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. Process_Date: 20230110 Process_Step: Process_Description: 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. Process_Date: 20230113 Process_Step: Process_Description: 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). Process_Date: 20230130 Process_Step: Process_Description: 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) Process_Date: 20230516 Spatial_Data_Organization_Information: Indirect_Spatial_Reference: Data were collected continuously at survey locations. Refer to self-contained NetCDF files for more location information. Spatial_Reference_Information: Horizontal_Coordinate_System_Definition: Geographic: Latitude_Resolution: 1.0E-5 Longitude_Resolution: 1.0E-5 Geographic_Coordinate_Units: Decimal degrees Geodetic_Model: Horizontal_Datum_Name: World Geodetic System 1984 (WGS84) Ellipsoid_Name: WGS84 Semi-major_Axis: 6378137.0 Denominator_of_Flattening_Ratio: 298.257223563 Entity_and_Attribute_Information: Overview_Description: 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. Distribution_Information: Distributor: Contact_Information: Contact_Organization_Primary: Contact_Organization: U.S. Geological Survey - CMGDS Contact_Address: Address_Type: mailing and physical Address: 2885 Mission Street City: Santa Cruz State_or_Province: CA Postal_Code: 95060 Contact_Voice_Telephone: 831-427-4747 Contact_Electronic_Mail_Address: pcmsc_data@usgs.gov Resource_Description: 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. Distribution_Liability: 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. Standard_Order_Process: Digital_Form: Digital_Transfer_Information: Format_Name: NetCDF Format_Version_Number: MATLAB Format_Specification: Data are in NetCDF formats. Format_Information_Content: Downloadable zip file of time-series data in netCDF format following EPIC Metadata Conventions. File download sizes range from 58 kB to 1006 MB. File_Decompression_Technique: WinZip or archive utility Transfer_Size: 1214 Digital_Transfer_Option: Online_Option: Computer_Contact_Information: Network_Address: Network_Resource_Name: https://doi.org/10.5066/P972R6AW Access_Instructions: Data can be downloaded using the Network_Resource_Name link and scrolling down to the Time Series Data section. Fees: None. Technical_Prerequisites: 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. Metadata_Reference_Information: Metadata_Date: 20230517 Metadata_Contact: Contact_Information: Contact_Person_Primary: Contact_Person: PCMSC Science Data Coordinator Contact_Organization: U.S. Geological Survey, Pacific Coastal and Marine Science Center Contact_Address: Address_Type: mailing and physical Address: 2885 Mission Street City: Santa Cruz State_or_Province: CA Postal_Code: 95060 Country: United States Contact_Voice_Telephone: 831-427-7520 Contact_Electronic_Mail_Address: pcmsc_data@usgs.gov Metadata_Standard_Name: Content Standard for Digital Geospatial Metadata Metadata_Standard_Version: FGDC-STD-001-1998