Conductivity-Temperature-Depth (CTD) profile data from transects of Whales Tail Marsh tidal creeks, South San Francisco Bay, California during 2021 and 2022

Frequently anticipated questions:

• What does this data set describe?
  1. How might this data set be cited?
  2. What geographic area does the data set cover?
  3. What does it look like?
  4. Does the data set describe conditions during a particular time period?
  5. What is the general form of this data set?
  6. How does the data set represent geographic features?
  7. How does the data set describe geographic features?
• Who produced the data set?
  1. Who are the originators of the data set?
  2. Who also contributed to the data set?
  3. To whom should users address questions about the data?
• Why was the data set created?
• How was the data set created?
  1. From what previous works were the data drawn?
  2. How were the data generated, processed, and modified?
  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?
  2. How accurate are the geographic locations?
  3. How accurate are the heights or depths?
  4. Where are the gaps in the data? What is missing?
  5. How consistent are the relationships among the data, including topology?
• How can someone get a copy of the data set?
  1. Are there legal restrictions on access or use of the data?
  2. Who distributes the data?
  3. What's the catalog number I need to order this data set?
  4. What legal disclaimers am I supposed to read?
  5. How can I download or order the data?
• Who wrote the metadata?

What does this data set describe?

1. How might this data set be cited?
   Joanne C. T. Ferreira, and Nowacki, Daniel J., 20240807, Conductivity-Temperature-Depth (CTD) profile data from transects of Whales Tail Marsh tidal creeks, South San Francisco Bay, California during 2021 and 2022: data release DOI:10.5066/P17ZUBYC, U.S. Geological Survey, Pacific Coastal and Marine Science Center, Santa Cruz, California.

   Online Links:

   • https://doi.org/10.5066/P17ZUBYC

   This is part of the following larger work.
   Joanne C. T. Ferreira, Nowacki, Daniel J., and Stevens, Andrew W., 2024, Oceanographic, water-quality, bathymetric, and discharge data from Whales Tail Marsh tidal creeks, South San Francisco Bay, California, 2021-2023: data release DOI:10.5066/P17ZUBYC, U.S. Geological Survey, Pacific Coastal and Marine Science Center, Santa Cruz, California.

   Online Links:

   • https://doi.org/10.5066/P17ZUBYC

   Other_Citation_Details:

   Suggested Citation: Ferreira, J.C.T., Nowacki, D.J., and Stevens, A.S., 2024, Oceanographic, water-quality, bathymetric, and discharge data from Whales Tail Marsh tidal creeks, South San Francisco Bay, California, 2021-2023: U.S. Geological Survey data release, https://doi.org/10.5066/P17ZUBYC.

2. What geographic area does the data set cover?

   West_Bounding_Coordinate: -122.1419
   East_Bounding_Coordinate: -122.1412
   North_Bounding_Coordinate: 37.5865
   South_Bounding_Coordinate: 37.5836
   

3. What does it look like?
4. Does the data set describe conditions during a particular time period?

   Beginning_Date: 15-Jun-2021

   Ending_Date: 04-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
   

6. How does the data set represent geographic features?
   1. How are geographic features stored in the data set?
      

      Indirect_Spatial_Reference:

      GPS location was taken with a handheld GPS immediately before each CTD profile.

   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 0.0001. Longitudes are given to the nearest 0.0001. Latitude and longitude values are specified in Decimal degrees. The horizontal datum used is D_WGS_1984.
      The ellipsoid used is WGS_1984.
      The semi-major axis of the ellipsoid used is 6378137.0.
      The flattening of the ellipsoid used is 1/298.2572236.
      

      Vertical_Coordinate_System_Definition:

      Depth_System_Definition:

      Depth_Datum_Name: Local surface
      Depth_Resolution: 0.01
      Depth_Distance_Units: meters
      Depth_Encoding_Method: Explicit depth coordinate included with horizontal coordinates
      

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
   • Daniel J. Nowacki
2. Who also contributed to the data set?
3. To whom should users address questions about the data?
   PCMSC Science Data Coordinator

   U.S. Geological Survey, Pacific Coastal and Marine Science Center

   2885 Mission Street

   Santa Cruz, CA
   

   USA

   831-427-4747 (voice)

   pcmsc_data@usgs.gov

Why was the data set created?

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: 28-Jul-2021 (process 1 of 5)

   Conductivity, salinity, optical backscatter and pressure (CTD) data were collected with an RBRmaestro multi-channel logger at site TCE (Tidal Creek East) intermittently over the period from June 17,2021 to July 28, 2021. The instrument was hand lowered from a kayak at various locations across the tidal creek after ADCP transect data collection was completed. Data from water samples collected during this activity have been previously published. See cross reference.

   Date: 07-Dec-2021 (process 2 of 5)

   Conductivity, salinity, optical backscatter and pressure (CTD) data were collected with an RBRmaestro multi-channel logger on tidal creek site TCM (Tidal Creek Main channel) on December 3-4,2021 and on tidal creek site TCE on December 6-7, 2021. The instrument was hand lowered from a kayak at various locations across the tidal creek after ADCP transect data collection was completed. Data from water samples collected during this activity have been previously published. See cross reference.

   Date: 04-Jan-2022 (process 3 of 5)

   Conductivity, salinity, optical backscatter, and pressure (CTD) data were collected with an RBRmaestro multi-channel logger at site TCM intermittently over the period from January 3-4,2022. The instrument was hand lowered from a kayak at various locations across the tidal creek after ADCP transect data collection was completed. Data from water samples collected during this activity have been previously published. See cross reference.

   Date: 14-Jun-2024 (process 4 of 5)

   Data were collected in a single file over multiple days for each data collection interval. Data not part of this study were removed during post-processing. The raw data files downloaded from the CTD were processed and converted to netCDF using the stglib python library, a package of code to process data consistent with procedures of the USGS Coastal/Marine Hazards and Resources Program. In stglib, attributes conforming to Climate and Forecast (CF) Conventions version 1.8 were added. All times are in Coordinated Universal Time (UTC). Corrected pressure data (P_1ac) were calculated by finding an offset with local atmospheric pressure readings when the pressure sensor was reading in air just prior to deployment. Pressure data were corrected using the offset and a time-series of local atmospheric pressure from NOAA station 9414523 Redwood City, CA, over the course of the deployment to remove the atmospheric contribution to the deployed pressure data. The resulting corrected pressure variable is the pressure due to seawater (standard_name "sea_water_pressure_due_to_seawater" in netCDF files).

   Date: 14-Jun-2024 (process 5 of 5)

   Data quality assurance and quality control (QAQC) was performed by inspecting all variables and replacing spurious values with NaN. Details of which portions of data were flagged and replaced are available in the metadata in each netCDF file and information about the individual QAQC trimming functions are available in the stglib documentation (https://stglib.readthedocs.io/en/latest/) in the "Instrument configuration file" section. Files are named with a convention that uses a multi-element alphanumeric code delimited by underscores. The first element for this dataset represents location and time of year (e.g. WTS21 or WTW21 for Whales Tail Summer 2021 or Winter 2021); the second element (e.g. CTDaprof) indicates the type of data (CTD), 'a' or 'b' indicating the first or second file of the time of year where more than one datafile was collected, and the type of data acquisition (e.g. prof indicates profiling rather than data collected at a fixed point); the suffix '-cal' indicates the data has been corrected for observed atmospheric pressure variations.

3. What similar or related data should the user be aware of?
   Joanne C. T. Ferreira, 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.

   Online Links:

   • https://doi.org/10.5066/P972R6AW

   Other_Citation_Details:

   Water samples collected during the transecting data collection are published in this data release.

   Joanne C. T. Ferreira, Nowacki, Daniel J., and SeanPaul M. La Selle, 2024, Sediment core data collected from Cargill Marsh, South San Francisco Bay, California during field activities 2022-643-FA and 2023-681-FA: data release DOI:10.5066/P15AORBR, U.S. Geological Survey, Pacific Coastal and Marine Science Center, Santa Cruz, CA.

   Online Links:

   • https://doi.org/10.5066/P15AORBR

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. The RBR Maestro CTD has the following accuracies: a conductivity range of 0 to 85 mS/cm with accuracy 0.003 mS/cm, a temperature range of -5 to 35 degrees Celsius with accuracy of 0.002 degrees Celsius, a pressure range of 0 - 100 dbar with accuracy of 0.05 dbar.
2. How accurate are the geographic locations?
   Horizontal accuracy derived from Garmin GPSmap 78sc instrumentation is 3 m with a resolution of 0.3 m. As position information was recorded at the water surface prior to each profile, some change in position results from non-coincident measurement from a moving platform. In addition, displacement down current while lowering the CTD was severe during periods of high flow and, in extreme cases, it is possible the profile did not reach the target of 0.5 m above bottom. The primary value of these data is to identify edge versus mid-channel locations as tidal creek width varies, as well as confirmation of the particular tidal creek observed. Where GPS location data is not available a value of NaN has been filled in the data. As all measurements within a file are on the same tidal creek transect location, a general value for the location may be inferred.
3. How accurate are the heights or depths?
   RBR Maestro CTD specification of 0.05 meter accuracy with better than 0.001 meter resolution.
4. Where are the gaps in the data? What is missing?
   Dataset is considered complete for the information presented, as described in the abstract. Users are advised to read the metadata for each part of this data release carefully for additional details.
5. How consistent are the relationships among the observations, including topology?
   Data fall within expected ranges. We recommend users plot the downcast (from the beginning of a cast to the maximum value of P_1ac) to view the cleanest data. In some cases, multiple profiles were taken at the edges of the tidal creek as well as mid-channel. Some of these profiles are extremely shallow and may be considered as a data point rather than a profile during those conditions.

How can someone get a copy of the data set?

1. Who distributes the data set? (Distributor 1 of 1)
   
   U.S. Geological Survey - CMGDS

   2885 Mission Street

   Santa Cruz, CA
   

   USA

   1-831-427-4747 (voice)

   pcmsc_data@usgs.gov
2. What's the catalog number I need to order this data set? Downloadable data in netCDF format. There are three (3) different files, each containing multiple profiling days. The first two letters 'WT' refer to the location at the Whales Tail Marsh, the next letter refers to the season, 'S' for summer or 'W' for winter, '21' for the year 2021 at the start of the season, 'prof' indicates the data are profiles, and '-cal' indicates all calibrations including atmospheric pressure correction have been applied to the data. An 'a' or 'b' has been added to the winter filenames where 'a' is in December, 2021 and 'b' is in January, 2022.
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:	Files contains CTD profile data in netCDF following Climate and Forecast (CF) metadata convention 1.8 in format netCDF (version netCDF-4, CF-1.8) Size: 1.280
     Network links:	https://doi.org/10.5066/P17ZUBYC

   • Cost to order the data: None

Who wrote the metadata?

Dates:

Last modified: 07-Aug-2024

Metadata author:

PCMSC Science Data Coordinator

U.S. Geological Survey, Pacific Coastal and Marine Science Center

2885 Mission Street

Santa Cruz, CA

USA

831-427-4747 (voice)

pcmsc_data@usgs.gov

Metadata standard:

Content Standard for Digital Geospatial Metadata (FGDC-STD-001-1998)