Time Series of Autonomous Carbonate System Parameter Measurements from Crocker Reef, Florida, USA

Metadata also available as - [Outline] - [Parseable text] - [XML]

Frequently anticipated questions:

What does this data set describe?

Title:
Time Series of Autonomous Carbonate System Parameter Measurements from Crocker Reef, Florida, USA
Abstract:
This dataset contains carbonate system data collected by scientists from the U.S. Geological Survey (USGS) St. Petersburg Coastal and Marine Science Center to investigate the effects of carbon cycling, coastal and ocean acidification at Crocker Reef located along the Florida Keys Reef Tract, in Southeast Florida, USA. These data were collected using an autonomous instrument called the Ocean Carbon System version 1 (OCSv1) deployed on the seafloor at Crocker Reef. The OCSv1 consists of five sensors integrated into a Sea-Bird Scientific STOR-X submersible data logger including a Seabird SeapHOx sensor for measurement of pH; a Sea-Bird 16 Plus CTD Recorder for measurement of conductivity (for calculation of salinity), temperature, and depth an Aanderaa oxygen optode for measurement of dissolved oxygen; a Pro-Oceanus CO2-Pro for measurement of CO2; and a Wetlabs Eco-PAR sensor for measurement of photosynthetically active radiation. The dataset is a time series of carbonate system parameters including: water temperature (degrees Celsius, °C), pressure (decibar, dbar), salinity, pHT (pH on the total scale), carbon dioxide (parts per million, ppm), pressure from the CO2-Pro Infrared Gas Analyzer (IRGA) (millibars, mbar), dissolved oxygen (milligrams per liter, mg/L) and photosynthetically active radiation (microEinsteins). Each parameter was measured every hour for 24-hour time periods throughout the duration of deployment. Data were collected under Florida Keys National Marine Sanctuary Permit FKNMS-2013-097. For further information regarding data collection and/or processing methods refer to USGS Open-File Report 2019–1003 (https://doi.org/10.3133/ofr20191003).
  1. How might this data set be cited?
    Yates, Kimberly K., Moore, Christopher S., and Smiley, Nathan A., 20191219, Time Series of Autonomous Carbonate System Parameter Measurements from Crocker Reef, Florida, USA: U.S. Geological Survey Data Release doi:10.5066/P90NCI8T, U.S. Geological Survey, St. Petersburg, FL.

    Online Links:

  2. What geographic area does the data set cover?
    West_Bounding_Coordinate: -80.52644
    East_Bounding_Coordinate: -80.52643
    North_Bounding_Coordinate: 24.90913
    South_Bounding_Coordinate: 24.90912
  3. What does it look like?
  4. Does the data set describe conditions during a particular time period?
    Beginning_Date: 19-Jul-2013
    Ending_Date: 27-Oct-2014
    Currentness_Reference:
    ground condition
  5. What is the general form of this data set?
    Geospatial_Data_Presentation_Form: Tabular Digital Data
  6. How does the data set represent geographic features?
    1. How are geographic features stored in the data set?
      This is a Point data set.
    2. What coordinate system is used to represent geographic features?
  7. How does the data set describe geographic features?
    Crocker-Reef-OCSv1-07192013-to-10272014.csv
    Time series data collected from Crocker Reef, FL, beginning in July 2013 and continuing through October 2014. Data are provided as a comma separated values (CSV) file that contains: coordinates, date, time, water temperature, pressure at depth, salinity, pH, CO2, measurement chamber pressure for CO2, dissolved oxygen, photosynthetically active radiation and data quality flags for each parameter. (Source: USGS)
    Site Description
    Description of the physical location where the measurements were collected. (Source: USGS) The name of the geographic location at the sampling location.
    Latitude
    Latitude coordinates measured in the World Geodetic System of 1984 (Source: USGS)
    Range of values
    Minimum:24.90913
    Maximum:24.90913
    Units:Decimal degrees
    Longitude
    Longitude coordinates measured in the World Geodetic System of 1984 (Source: USGS)
    Range of values
    Minimum:-80.52644
    Maximum:-80.52644
    Units:Decimal degrees
    DATETAG
    A numeric identifier for the calendar date used by the USGS on the day of sample collection. (Source: USGS)
    Range of values
    Minimum:07/19/13
    Maximum:10/27/14
    Units:Units correspond to calendar month, day and year in MM/DD/YY format.
    TIMETAG
    Timestamp showing the time of day each sample was collected. (Source: USGS)
    Range of values
    Minimum:0:30:04
    Maximum:23:30:06
    Units:Hours, minutes, seconds in the format HH:MM:SS or H:MM:SS
    T(W) (C)
    Water temperature measured in degrees Celsius (Source: USGS)
    Range of values
    Minimum:21.47
    Maximum:32.09
    Units:Celsius (C)
    QF_T(W)
    A numeric value that indicates the quality of reported temperature data. (Source: NOAA National Centers for Environmental Information (NCEI) https://www.nodc.noaa.gov/GTSPP/document/codetbls/gtsppcodes/gtspp_qual.html)
    ValueDefinition
    1Flag 1 = QC has been performed and element appears to be correct, Flag 2 = QC has been performed and element appears to be probably good with other elements, Flag 3 = QC has been performed and element appears to be probably bad, Flag 4 = QC has been performed and element appears to be bad, Flag 5 = the value has been modified as a result of QC, Flag 9 = The value of the element is missing.
    PRESS (dbar)
    Pressure measured in decibars (dbar) (Source: USGS)
    Range of values
    Minimum:3.093
    Maximum:4.638
    Units:Decibar
    QF_PRESS
    A numeric value that indicates the quality of the reported pressure data. (Source: NOAA NCEI)
    ValueDefinition
    1Flag 1 = QC has been performed and element appears to be correct, Flag 2 = QC has been performed and element appears to be probably good with other elements, Flag 3 = QC has been performed and element appears to be probably bad, Flag 4 = QC has been performed and element appears to be bad, Flag 5 = the value has been modified as a result of QC, Flag 9 = The value of the element is missing.
    SALINITY
    A numeric value for salinity (Source: USGS)
    Range of values
    Minimum:32.06
    Maximum:36.97
    QF_SALINITY
    A numeric value that indicates the quality of the reported salinity data. (Source: NOAA NCEI)
    ValueDefinition
    1, 2Flag 1 = QC has been performed and element appears to be correct, Flag 2 = QC has been performed and element appears to be probably good with other elements, Flag 3 = QC has been performed and element appears to be probably bad, Flag 4 = QC has been performed and element appears to be bad, Flag 5 = the value has been modified as a result of QC, Flag 9 = The value of the element is missing.
    pHT
    A numeric value for pH using the total scale. (Source: USGS)
    Range of values
    Minimum:7.950
    Maximum:8.142
    QF_pHT
    A numeric value that indicates the quality of the reported total scale pH data. (Source: NOAA NCEI)
    ValueDefinition
    1Flag 1 = QC has been performed and element appears to be correct, Flag 2 = QC has been performed and element appears to be probably good with other elements, Flag 3 = QC has been performed and element appears to be probably bad, Flag 4 = QC has been performed and element appears to be bad, Flag 5 = the value has been modified as a result of QC, Flag 9 = The value of the element is missing.
    CO2 (ppm)
    A numeric value for the concentration of CO2 in parts per million by volume. (Source: USGS)
    Range of values
    Minimum:271.7
    Maximum:533.1
    Units:parts per million (ppm)
    QF_CO2
    A numeric value that indicates the quality of the reported CO2 concentration data. (Source: NOAA NCEI)
    ValueDefinition
    1, 9Flag 1 = QC has been performed and element appears to be correct, Flag 2 = QC has been performed and element appears to be probably good with other elements, Flag 3 = QC has been performed and element appears to be probably bad, Flag 4 = QC has been performed and element appears to be bad, Flag 5 = the value has been modified as a result of QC, Flag 9 = The value of the element is missing.
    PRES(IRGA) (mbar)
    A numeric value for pressure in the sampling chamber of the infrared gas analyzer of the CO2 sensor. (Source: USGS)
    Range of values
    Minimum:1001
    Maximum:1110
    Units:mbar
    QF_PRES(IRGA)
    A numeric value that indicates the quality of the reported IRGA pressure data. (Source: NOAA NCEI)
    ValueDefinition
    1, 9Flag 1 = QC has been performed and element appears to be correct, Flag 2 = QC has been performed and element appears to be probably good with other elements, Flag 3 = QC has been performed and element appears to be probably bad, Flag 4 = QC has been performed and element appears to be bad, Flag 5 = the value has been modified as a result of QC, Flag 9 = The value of the element is missing.
    OXYGEN (mg/L)
    A numeric identifier for the concentration of oxygen in milligrams per liter of seawater. (Source: USGS)
    Range of values
    Minimum:0.00
    Maximum:15.49
    Units:milligrams/L
    QF_OXYGEN
    A numeric value that indicates the quality of the reported oxygen concentration data. (Source: NOAA NCEI)
    ValueDefinition
    1, 2, 3, 4Flag 1 = QC has been performed and element appears to be correct, Flag 2 = QC has been performed and element appears to be probably good with other elements, Flag 3 = QC has been performed and element appears to be probably bad, Flag 4 = QC has been performed and element appears to be bad, Flag 5 = the value has been modified as a result of QC, Flag 9 = The value of the element is missing.
    PAR (microEinsteins)
    A numeric value for the concentration of photosynthetically available radiation. (Source: USGS)
    Range of values
    Minimum:0.0
    Maximum:1599.0
    Units:microEinsteins
    QF_PAR
    A numeric value that indicates the quality of the reported PAR data. (Source: NOAA NCEI)
    ValueDefinition
    1, 9Flag 1 = QC has been performed and element appears to be correct, Flag 2 = QC has been performed and element appears to be probably good with other elements, Flag 3 = QC has been performed and element appears to be probably bad, Flag 4 = QC has been performed and element appears to be bad, Flag 5 = the value has been modified as a result of QC, Flag 9 = The value of the element is missing.

Who produced the data set?

  1. Who are the originators of the data set? (may include formal authors, digital compilers, and editors)
    • Kimberly K. Yates
    • Christopher S. Moore
    • Nathan A. Smiley
  2. Who also contributed to the data set?
    Please acknowledge the USGS St. Petersburg Coastal and Marine Science Center and cite the USGS data release associated with this metadata record as the source for all products developed from these data.
  3. To whom should users address questions about the data?
    Kimberly Yates
    United States Geological Survey
    600 4th Street South
    St. Petersburg, FL
    US

    727-502-8059 (voice)
    kyates@usgs.gov

Why was the data set created?

This dataset was acquired to assist USGS staff with the quantification, analysis and interpretation of geochemical time series data that will ultimately be used in assessments and research of or related to carbon cycling, coastal and ocean acidification.

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: 2018 (process 1 of 2)
    OCSv1 Description: The OCSv1 consists of 5 sensors, 1 pump, 1 submersible data logger, a submersible battery pack, and a seafloor mounting system. The equipment models are: Pro-Oceanus CO2-Pro for measurement of carbon dioxide concentration; Sea-Bird SeaFET sensor for measurement of pH on the total scale; Sea-Bird 16 Plus CTD Recorder for measurement of conductivity, salinity, temperature and depth; Sea-Bird/WET Labs ECO-PAR for measurement of photosynthetically active radiation (PAR); Aanderaa oxygen optode for measurement of dissolved oxygen; Sea-Bird STOR-X data logger; and a Sea-Bird SBE-5P submersible pump. Sensor resolution is as follows: Pro-Oceanus CO2-Pro 0.01 ppm; 1 mbar for PRESS(IRGA); SeaFET 0.004 pH; Sea-Bird 16 Plus Recorder 0.0001 °C for temperature; 0.00005 siemens for conductivity (used by the instrument to calculate salinity) and 0.002% of full scale range for pressure; Aanderra optode 0.003 mg/L for dissolved oxygen (based on resolution of 0.1 micromoles per liter); and ECO-PAR 14-bit digital output resolution.
    The sensors were packaged as a single unit in a custom-designed platform that was mounted on the seafloor. The Sea-Bird SBE-5P submersible pump pulled water through a stainless or copper mesh strainer and pumped the water to the CO2-Pro CV for pCO2 measurement. Water flow from the CO2-Pro was then pumped through the flow through cap of the SeaFET. The sensors not requiring flow were located in close proximity to the pump intake and measured ambient water. The STOR-X and sensors were powered by a 240 amp-hour submersible battery system.
    The STOR-X distributed power to the attached sensors according to a custom schedule. The OCSv1 operated 24 hours per day, with a sampling acquisition period once every hour at the half-hour mark prefaced by a 20-minute warm up period for the CO2-Pro CV. The sampling acquisition period ran for approximately 00:01:10. The CO2 sensor re-zeroed every 8 hours and collected approximately 22 CO2 and PRESS(IRGA) measurements during each sampling period. The ECO-PAR sensor collected approximately 7 PAR measurements per sample period. The SeaFET collected approximately 10 pH measurements per sample period. The 16 Plus CTD collected 1 conductivity, temperature, and pressure measurement per sampling period. The Aanderaa optode collected approximately 7 oxygen measurements per sample period.
    Data Storage and Preprocessing: Data were managed and stored by the STOR-X data logger. Acquired data were saved into sensor-specific .raw files that contained the information for each Julian day. Downloading this data from the site occurred at regular intervals to ensure the sensor's operational status. Downloading these .raw files from the STOR-X required the use of STORXCom software to communicate between the STOR-X and a computer. Once the data were downloaded, SatCon version 1.5 data conversion program converted the .raw files into .dat files and applied any processing required. Individual sensor Julian day .dat files were then combined into one large multi-day dataset per sensor. These files were opened in Microsoft (MS) Excel and saved in .xlsx format. The combined multi-day files contained headers for each individual day file that were strung together; these headers were manually removed in MS Excel leaving only the top header line. Multi-day files were then processed through a custom averaging code written in Pearl, designed by David Zawada (USGS). This code averaged the multiple measurements from each sensor per sampling period to generate a single averaged value for each sensor per sampling period, reported at the start time of the sampling period and day. In addition to averaging parameter values, the code also provided the mean, standard deviation, minimum and maximum for each sampling period. Averaged data for each sensor parameter were then manually merged into a single .xlsx file for further processing. Data files were deleted from the STOR-X after confirmation of successful download and storage of parameter data.
    Advanced Data Processing: Preliminary QA/QC of sensor data was performed after averaged data were compiled into .xlsx files and after advanced data processing was performed. The SeaFET pH data were corrected for salinity and temperature, using Sea-Bird 16 Plus CTD recorder data through a MS Excel macro provided by Satlantic. The Satlantic macro was also used to perform a single point calibration of the SeaFET pH data using discrete pH measurements determined in-situ and concurrently with OCS sample acquisition. Discrete pH measurements were performed using spectrophotometric pH methods. Once corrections were completed, parameter data were plotted to examine sensor performance and identify non-trending outliers. Cross validation of sensor parameters was performed to further analyze outliers and identify questionable or bad data points. Further validation of pH and CO2 sensor data was performed by comparing sensor values to values measured in discrete water samples. CO2 was calculated from discrete measurements of pH and dissolved inorganic carbon (performed using carbon coulometry methods). Measurement of sensor data was periodically validated with discrete data. Person who carried out this activity:
    Kimberly Yates
    USGS
    600 4th Street South
    St. Petersburg, Florida
    USA

    727-502-8059 (voice)
    kyates@usgs.gov
    Date: 13-Oct-2020 (process 2 of 2)
    Added keywords section with USGS persistent identifier as theme keyword. Person who carried out this activity:
    U.S. Geological Survey
    Attn: VeeAnn A. Cross
    Marine Geologist
    384 Woods Hole Road
    Woods Hole, MA

    508-548-8700 x2251 (voice)
    508-457-2310 (FAX)
    vatnipp@usgs.gov
  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?
    All sensor data were subject to preliminary QA/QC. A two-step procedure has been taken to remove outliers. During the first step, data beyond acceptable measurement ranges for the sensors were flagged with a quality flag of 4 to indicate bad data. Next, data parameters were plotted to examine temporal trends and cross-correlation (for example, pCO2 vs. pH), as predictable relationships (linear or exponential) have been observed in previous discrete and autonomous measurements at Crocker Reef. Data points that deviate from temporal and/or correlation trends were flagged with a quality flag of 4 (indicating bad data).
  2. How accurate are the geographic locations?
    Accuracy was checked against global positioning system (GPS) values provided by the manufacturer. Garmin GPSMAP64st and Garmin GPSmap 60CSx FPSMAP60 accuracy, < 10 meters
  3. How accurate are the heights or depths?
    Accuracy was checked against GPS values provided by the manufacture. Garmin GPSMAP64st and Garmin GPSmap 60CSx FPSMAP60 accuracy, < 10 meters
  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 rest of the metadata record carefully for additional details.
  5. How consistent are the relationships among the observations, including topology?
    Data were checked to ensure all values fall within the range of analysis for each sensor, and outliers were marked with a quality flag of 4. Data were checked for missing or duplicate data points. Missing data points were marked with a value of -99. Geospatial data were plotted in either ArcGIS or in Google Earth to verify accuracy of the location.

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:
Public domain data from the U.S. Government are freely redistributable with proper metadata and source attribution. The U.S. Geological Survey requests to be acknowledged as originators of the data in future products or derivative research.
  1. Who distributes the data set? (Distributor 1 of 1)
    Kimberly Yates
    United States Geological Survey
    600th 4th Street South
    St. Petersburg, Florida
    USA

    727-502-8059 (voice)
    kyates@usgs.gov
  2. What's the catalog number I need to order this data set?
  3. What legal disclaimers am I supposed to read?
    Although these data have been processed successfully on a computer system at the 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. The USGS shall not be held liable for improper or incorrect use of the data described and (or) contained herein. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government.
  4. How can I download or order the data?

Who wrote the metadata?

Dates:
Last modified: 13-Oct-2020
Metadata author:
Kimberly K. Yates
United States Geological Survey
Research Oceanographer
600th 4th Street South
St. Petersburg, FL
USA

727-502-8059 (voice)
kyates@usgs.gov
Metadata standard:
Content Standard for Digital Geospatial Metadata (FGDC-STD-001-1998)
This page is <https://cmgds.marine.usgs.gov/catalog/spcmsc/Crocker-Reef-OCSv1-metadata.faq.html>
Generated by mp version 2.9.50 on Tue Sep 21 18:18:46 2021