CTD profiles from a tidal creek in Corte Madera Marsh, Northern San Francisco Bay, California, 2022-2023

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?
   McGill, Samantha C., 20240806, CTD profiles from a tidal creek in Corte Madera Marsh, 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:

   • https://doi.org/10.5066/P1XZFGCX

   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, CA.

   Online Links:

   • https://doi.org/10.5066/P1XZFGCX

   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: -122.5058680
   East_Bounding_Coordinate: -122.5050730
   North_Bounding_Coordinate: 37.9307330
   South_Bounding_Coordinate: 37.9302660
   

3. What does it look like?

   NBM_CTD_kayak.jpg (JPEG)

   Image of kayaker moving the kayak into position where the CTD profile will be collected. The CTD is shown on the kayak, behind the kayaker.

4. Does the data set describe conditions during a particular time period?

   Beginning_Date: 09-Aug-2022

   Ending_Date: 20-Feb-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:

      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 1/298.257223563.
      
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)
   • Samantha C. McGill
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: 20-Jan-2023 (process 1 of 3)

   Conductivity, salinity, optical backscatter and pressure (CTD) data were collected in a tidal creek in Corte Madera Marsh, with an RBR maestro multi-channel logger. Profiles were collected on 4 days: August 8 and 9 of 2022 and January 19 and 20 of 2023. Data from water samples collected during this activity are available as a separate download.

   Date: 16-Jul-2024 (process 2 of 3)

   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 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). 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. Data not part of this study were removed during post-processing. Minor cleaning of the data was performed, as there were some instances when the CTD hit the creek bed and had mud obscuring sensors during the upcast. Users are still advised to assess data quality carefully.

   Date: 16-Jul-2024 (process 3 of 3)

   Files are named with a convention that uses a multi-element alphanumeric code delimited by underscores. The first element for this dataset represents the projects name and the year it started (e.g. 'NBM22' for North Bay Marshes 2022); the second element indicates the type of data (e.g., CTD), 'a' or 'b' indicating the season, (e.g. a respresents Summer, b represents Winter); the next element 'prof' indicates the data were collected in a profiling manner; the final element ('-cal') indicates the data has been calibrated and corrected for observed atmospheric pressure variations.

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.
2. How accurate are the geographic locations?
   Horizontal accuracy derived from GPS instrumentation is less than 1 m, however position information was recorded at the water surface prior to each profile. Displacement down current while lowering the CTD was severe during periods of high flow. 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.
3. How accurate are the heights or depths?
   No formal assessment of vertical accuracy was performed. Manufacturer 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.

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 two (2) different files, each containing multiple profiling days. The first three letters refer to the project name 'NBM' (North Bay Marshes); '22' refers to the year the project started (2022); An 'a' or 'b' indicates the season where 'a' is Summer and 'b' is Winter; 'prof' indicates the data are profiles; and '-cal' indicates all calibrations including atmospheric pressure correction have been applied to the 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:	Files contains CTD profile data in NetCDF CF-1.8 format in format NetCDF (version Python 3.11.7) Size: 0.3028
     Network links:	https://doi.org/10.5066/P1XZFGCX

     Data format:	File contains CTD profile data in NetCDF format in format NetCDF (version Python 3.11.7) Size: 0.3212
     Network links:	https://doi.org/10.5066/P1XZFGCX

   • Cost to order the data: None

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

USA

831-427-4747 (voice)

pcmsc_data@usgs.gov

Metadata standard:

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