Time-series of biogeochemical and flow data from a tidal salt-marsh creek, Sage Lot Pond, Waquoit Bay, Massachusetts, 2012-2016 (ver. 2.0, July 2023)

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• 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?
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  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?
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  4. Where are the gaps in the data? What is missing?
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• Who wrote the metadata?

What does this data set describe?

1. How might this data set be cited?
   Mann, Adrian G., O'Keefe Suttles, Jennifer A., Gonneea, Meagan E., Brosnahan, Sandra M., Brooks, Thomas W., Wang, Zhaohui A., Ganju, Neil K., and Kroeger, Kevin D., 2019, Time-series of biogeochemical and flow data from a tidal salt-marsh creek, Sage Lot Pond, Waquoit Bay, Massachusetts, 2012-2016 (ver. 2.0, July 2023): data release DOI:10.5066/P9STIROQ, U.S. Geological Survey, Reston, VA.

   Online Links:

   • https://doi.org/10.5066/P9STIROQ
   • https://www.sciencebase.gov/catalog/item/5cd475e6e4b062989a9e94e8

   Other_Citation_Details:

   Suggested citation: Mann, A.G., O'Keefe Suttles, J.A., Gonneea, M.E., Brosnahan, S.M., Brooks, T.W., Wang, Z.A., Ganju, N.K., and Kroeger, K.D., 2019, Time-series of biogeochemical and flow data from a tidal salt-marsh creek, Sage Lot Pond, Waquoit Bay, Massachusetts, 2012-2016 (ver. 2.0, July 2023): U.S. Geological Survey data release, https://doi.org/10.5066/P9STIROQ.

2. What geographic area does the data set cover?

   West_Bounding_Coordinate: -70.516300
   East_Bounding_Coordinate: -70.506910
   North_Bounding_Coordinate: 41.556570
   South_Bounding_Coordinate: 41.551500
   

3. What does it look like?

   https://www.sciencebase.gov/catalog/file/get/5cd475e6e4b062989a9e94e8?name=SLPCreek_browse_graphic.jpg (JPEG)

   Aerial photo of the study site, taken by Jim Rassman. The red box indicates the location of the instrument deployments.

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

   Beginning_Date: 06-Nov-2012

   Ending_Date: 31-Dec-2016

   Currentness_Reference:

   ground condition

5. What is the general form of this data set?

   Geospatial_Data_Presentation_Form: tabular 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?
      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 North American Datum of 1983.
      The ellipsoid used is Geodetic Reference System 80.
      The semi-major axis of the ellipsoid used is 6378137.0.
      The flattening of the ellipsoid used is 1/298.257222101.
      

      Vertical_Coordinate_System_Definition:

      Altitude_System_Definition:

      Altitude_Datum_Name: North American Vertical Datum of 1988
      Altitude_Resolution: 1.0
      Altitude_Distance_Units: centimeters
      Altitude_Encoding_Method:

      Explicit elevation coordinate included with horizontal coordinates

7. How does the data set describe geographic features?

   SLPCreekSensorData

   Continuous water-quality, water elevation and flow data measured in a marsh creek draining into Sage Lot Pond, Waquoit Bay, MA between 2012-2016 (Source: Adrian Mann)

   Collection_Date

   A numeric identifier of the date the measurement was collected in the format of mm/dd/yyyy. (Source: Producer defined)

   Range of values
   Minimum:	11/01/2012
   Maximum:	12/31/2016
   Units:	MM/DD/YYYY

   Collection_Time_UTC

   Time of collection in UTC (HH:MM) (Source: Producer defined)

   Range of values
   Minimum:	0:00
   Maximum:	24:00
   Units:	HH:MM

   WaterTemp_C

   Surface water temperature in degrees Celsius, measured by a Conductivity/Temperature sensor (measurement range -5 to 50 degrees Celsius) on a YSI EXO2 multiparameter sonde. Blank values indicate that no data were collected. (Source: Producer defined)

   Range of values
   Minimum:	-3.040
   Maximum:	33.417
   Units:	Degrees Celsius

   Salinity_psu

   Surface water salinity in psu, measured by a Conductivity/Temperature sensor on a YSI EXO2 multiparameter sonde and calculated from Conductivity and Temperature using algorithms found in Standard Methods for the Examination of Water and Wastewater (17th ed), American Public Health Association, Washington, D.C, 1989. The use of the Practical Salinity Scale results in values that are unitless, since the measurements are carried out in reference to the conductivity of standard seawater at 15 deg C. Missing values indicate that either no measurement was made, or the data were omitted because it was determined that error due to sensor drift and fouling exceeded the correction threshold as described in the attribute accuracy report. (Source: Producer defined)

   Range of values
   Minimum:	0.130
   Maximum:	32.888
   Units:	psu

   pH

   Measurement of surface-water pH using a pH/ORP sensor (pH measurement range of 0-14 pH units) on a YSI EXO2 multiparameter sonde. pH measures the acidity or alkalinity of water, with a pH of 7 being neutral. A pH of 0 is most acidic and 14 most basic. Missing values indicate that either no measurement was made, or the data were omitted because it was determined that error due to sensor drift and fouling exceeded the correction threshold as described in the attribute accuracy report. (Source: Producer defined)

   Range of values
   Minimum:	6.233
   Maximum:	8.785
   Units:	pH units

   ORP_mV

   Measurement of surface-water oxidation-reducing potential in millivolts using a pH/ORP sensor (ORP measurement range of -999 to 999 mV) on a YSI EXO2 multiparameter sonde. Missing values indicate that either no measurement was made, or the data were omitted because it was determined that error due to sensor drift and fouling exceeded the correction threshold as described in the attribute accuracy report. (Source: producer defined)

   Range of values
   Minimum:	-237.473
   Maximum:	374.217
   Units:	millivolts

   DOsat_perc

   Surface water measurement of dissolved oxygen in percent saturation using an optical dissolved oxygen sensor (measurement range of 0-500% air saturation) on a YSI EXO2 multiparameter sonde. Missing values indicate that either no measurement was made, or the data were omitted because it was determined that error due to sensor drift and fouling exceeded the correction threshold as described in the attribute accuracy report. (Source: Producer defined)

   Range of values
   Minimum:	0.101
   Maximum:	295.400
   Units:	percent air saturation

   DO_mgL

   Surface water measurement of dissolved oxygen in milligrams per liter using an optical dissolved oxygen sensor (measurement range of 0-50 mg/L) on a YSI EXO2 multiparameter sonde. Missing values indicate that either no measurement was made, or the data were omitted because it was determined that error due to sensor drift and fouling exceeded the correction threshold as described in the attribute accuracy report. (Source: Producer defined)

   Range of values
   Minimum:	0.030
   Maximum:	20.898
   Units:	milligrams per liter (mg/L)

   Turbidity_NTU

   Surface water measurement of turbidity in NTU using an optical turbidity sensor (measurement range of 0-999 FNU) on a YSI EXO2 multiparameter sonde. Turbidity is measured in accordance with ASTM D7315-07a “Test Method for Determination of Turbidity Above 1 Turbidity Unit (TU) in Static Mode.” This method calls for this sensor type to report values in formazin nephelometric units (FNU), which is the default calibration unit for the EXO sensor. Turbidity units were converted in the software to nephelometric turbidity units (NTU), which is more commonly used in this application. Blank values indicate that either no measurement was made, or the data were omitted because it was determined that error due to sensor drift and fouling exceeded the correction threshold as described in the attribute accuracy report. (Source: Producer defined)

   Range of values
   Minimum:	0.001
   Maximum:	438.660
   Units:	nephelometric turbidity units (NTU)

   FDOM_QSU

   Surface water measurement of fluorescent dissolved organic matter (fDOM) in parts per billion (ppb) of Quinine Sulfate Equivalent (QSU), corrected for temperature, turbidity and inner filter effects, using an optical fDOM sensor (measurement range of 0-300 ppb QSU) on a YSI EXO2 multiparameter sonde. Missing values indicate that either no measurement was made, or the data were omitted because it was determined that error due to sensor drift and fouling exceeded the correction threshold as described in the attribute accuracy report. (Source: Producer defined)

   Range of values
   Minimum:	0.011
   Maximum:	110.075
   Units:	parts per billion of Quinine Sulfate Units (QSU)

   Chl_ugL

   Surface water measurement of chlorophyll in micrograms per liter (ug/L) using an optical Total Algae-phycoerythrin sensor (measurement range 0-400 ug/L) on a YSI EXO2 multiparameter sonde. The Total Algae sensor uses a blue-emitting LED that excites the chlorophyll a (chl) molecule and generates results in Relative fluorescence units (RFU) or ug/L of pigment. Missing values indicate that either no measurement was made, or the data were omitted because it was determined that error due to sensor drift and fouling exceeded the correction threshold as described in the attribute accuracy report. (Source: Producer defined)

   Range of values
   Minimum:	0.010
   Maximum:	190.184
   Units:	micrograms per liter (ug/L)

   BGA_ugL

   Surface water measurement of Blue-Green Algae (BGA) in micrograms per liter using an optical Total Algae-phycoerythrin (TAL-PE) sensor (measurement range of BGA-PE 0-280 ug/L) on a YSI EXO2 multiparameter sonde. The TAL-PE sensor uses a slightly blue excitation beam that excites the phycoerythrin (PE) accessory pigment. Missing values indicate that either no measurement was made, or the data were omitted because it was determined that error due to sensor drift and fouling exceeded the correction threshold as described in the attribute accuracy report. (Source: Producer defined)

   Range of values
   Minimum:	0.064
   Maximum:	268.148
   Units:	micrograms per liter (ug/L)

   Water_Elevation_m

   Elevation of the creek surface in meters, adjusted to NAVD88 elevations. Water depth was measured by a Sontek IQ-Plus acoustic doppler current profiler mounted to the bottom of the creek. Water level is determined primarily by using a vertical beam, though an integrated pressure sensor acts as a secondary measurement. The elevation at the top of the instrument surface was measured using real-time kinetic (RTK) GPS. These data are included in Table 2. Water elevation was calculated using the water depth relative to the elevation of the surface of the instrument. The elevation of the ADCP instrument was not directly measured using RTK until January 2015. Prior to that, water level was calculated using the measured elevation of the EXO2 instrument and the mean difference in overlapping depth data from both instruments. Missing values indicate that either no measurement was made, or the data were omitted because it was determined that error exceeded the thresholds outlined in the attribute accuracy report. (Source: Producer defined)

   Range of values
   Minimum:	-0.532
   Maximum:	0.783
   Units:	meters

   Flow_m3s

   Creek surface water discharge in cubic meters per second (m3/s) measured with a Sontek IQ-Plus acoustic doppler current profiler mounted to the bottom of the creek. (Source: Producer defined)

   Range of values
   Minimum:	-0.836
   Maximum:	0.778
   Units:	cubic meters per second

   EXO_QAQC_Table1

   Correction criteria and maximum allowable limits for data corrections (Source: Wagner and others, 2006)

   Parameter

   The name of the chemical parameter being measured (Source: Producer defined)

   Value	Definition
   Temperature	Water temperature in degrees C
   Conductivity	Water conductivity in microsiemens per centimeter
   pH	Measurement of surface-water pH using a pH/ORP sensor
   Dissolved Oxygen	Dissolved oxygen level in water in milligrams per liter or percent air saturation measured with an optical dissolved oxygen sensor
   Turbidity	Turbidity in surface water in nephelometric turbidity units NTU measured with an optical turbidity sensor.
   fDOM	Surface water measurement of fluorescent dissolved organic matter (fDOM) in parts per billion of Quinine Sulfate Equivalent (QSU) using an optical fDOM sensor
   Chlorophyll	Surface water measurement of chlorophyll in micrograms per liter using an optical Total Algae-phycoerythrin sensor

   Data Correction Criteria

   A numeric range of error (in units of measurement or percentage) in sensor readings due to fouling and/or drift beyond which a correction was applied (Source: Producer defined) The acceptable range of error for each sensor, according to Wagner and others, 2006. If the absolute value of drift plus fouling of each sensor parameter exceeded this range, a correction factor was applied to the data.

   Maximum allowable limit

   The maximum numerical limit of correction (in units of measurement or percentage of measured value) due to fouling and drift. (Source: Producer defined) The maximum numerical limit of correction (in units of measurement or percentage of measured value) due to fouling and drift allowable for applying a correction factor, according to Wagner and others, 2006. If error due to fouling and/or drift exceeded this limit, data were removed from the dataset.

   CollectionDates_Table2

   Data collection date ranges, instrument type and instrument horizontal and vertical positional information (Source: producer-defined)

   Instrument Type

   The type of instrument used to collect data (Source: producer-defined)

   Value	Definition
   1	SonTek IQ-Plus Acoustic Doppler Current Profiler
   2	Wetlabs ECO Triplet-w optical sensor
   3	YSI 600 XLM multi-parameter sonde
   4	YSI EXO2 multiparameter sonde; Serial number ending in 2016
   5	YSI EXO2 multiparameter sonde; Serial number ending in 1654
   6	Pro-Oceanus Mini CO2 sensor

   Data Collection Start Date

   The date in mm/dd/yyyy of the start of data collection (Source: producer-defined)

   Range of values
   Minimum:	11/06/2012
   Maximum:	12/31/2016
   Units:	mm/dd/yyyy

   Data Collection End Date

   The date in mm/dd/yyyy of the end of data collection (Source: producer-defined)

   Range of values
   Minimum:	11/9/2012
   Maximum:	12/31/2016
   Units:	mm/dd/yyyy

   Parameter measured

   The type of data collected (Source: producer-defined) Refer to the Attributes section of the Entity "SLPCreekSenorData" for descriptions of measured parameters

   Latitude_Decimal Degrees

   The latitudinal of the sensor position in decimal degrees (Source: producer-defined)

   Range of values
   Minimum:	41.55460
   Maximum:	41.55465
   Units:	decimal degrees

   Longitude_Decimal Degrees

   The longitudinal position of the sensor position in decimal degrees with negative values indicating the western hemisphere (Source: producer-defined)

   Range of values
   Minimum:	-70.50710
   Maximum:	-70.50713
   Units:	producer-defined

   Elevation_meters

   Elevation in meters relative to a vertical control point referenced to the North American Vertical Datum of 1988 (NAVD88). A value of NA indicates data not available. (Source: producer-defined)

   Range of values
   Minimum:	-0.7838
   Maximum:	-0.5640
   Units:	meters

   SLPCreek_CO2.csv

   Continuous dissolved CO2, water temperature and pressure measured in a marsh creek draining into Sage Lot Pond, Waquoit Bay, MA between 2014-2016. Contains 9604819 data records. Also available in MATLAB format (SLPCreek_CO2.mat) (Source: Producer Defined)

   dn

   A MATLAB serial date number representing the whole and fractional number of days from a fixed, preset date (January 0, 0000) in the proleptic ISO calendar (Source: Producer Defined)

   Range of values
   Minimum:	735798.46181713
   Maximum:	736677.602928241
   Units:	MATLAB serial date number

   date_time

   Date and Time of collection in UTC (mm/dd/yyyy HH:MM:SS) (Source: Producer Defined)

   Range of values
   Minimum:	7/18/2014 11:05:01
   Maximum:	12/13/2016 14:28:13
   Units:	MATLAB serial date number

   co2_ppm

   Surface water dissolved carbon dioxide (CO2) in parts per million, measured by a Pro-Oceanus Mini-Pro sensor (measurement range 0-10000 ppm). (Source: Producer Defined)

   Value	Definition
   NaN	Excluded CO2 measurements while the sensor was out of the water, at the beginning and end of deployments, or during maintenance.

   Range of values
   Minimum:	117
   Maximum:	9940
   Units:	parts per million
   Resolution:	200

   co2_uatm

   Surface water dissolved carbon dioxide (CO2) in microatmospheres, calculated from sensor readings in ppm using the equation: pCO2 (uatm) = pCO2 (ppm) * pressure(mbar)/1013.25. (Atmospheric pressure in mbar at mean sea level = 1013.25. Reference: CO2-Pro CV User's Manual, Revision 3.0.3, April 5, 2016. (Source: Producer Defined)

   Value	Definition
   NaN	Excluded CO2 measurements while the sensor was out of the water, at the beginning and end of deployments, or during maintenance.

   Range of values
   Minimum:	115.701
   Maximum:	9724.305
   Units:	microatmospheres
   Resolution:	200

   tempC

   Sensor temperature measured by a Pro-Oceanus Mini-Pro sensor (measurement range 0-40 degrees C) (Source: Producer Defined)

   Value	Definition
   NaN	Excluded temperature measurements while the sensor was out of the water, at the beginning and end of deployments, or during maintenance. The temperature sensor is housed within the sensor housing, and therefore values are expected to be higher than the surrounding water temperature.

   Range of values
   Minimum:	3.95
   Maximum:	38.02
   Units:	Degrees Celcius

   pres_mbar

   Measurement of total dissolved gas pressure water by a Pro-Oceanus Mini-Pro sensor (measurement range 0-2000 mbar) (Source: Producer Defined)

   Value	Definition
   NaN	Pressure measurements that were collected while the sensor was put of the water, at the beginning and end of deployments, or during maintenance were excluded.

   Range of values
   Minimum:	801
   Maximum:	1274
   Units:	millibar
   Resolution:	20

   Entity_and_Attribute_Overview:

   The CO2 data are also provided in MATLAB format (SLPCreek_CO2.mat) due to the large size of the dataset. The columns of information are the same in both formats.
   Citations: Standard Methods for the Examination of Water and Wastewater (17th ed). American Public Health Association, Washington, D.C, 1989.
   ASTM D7315-07a Standard Test Method for Determination of Turbidity Above 1 Turbidity Unit (TU) in Static Mode, ASTM International, West Conshohocken, PA, 2007, www.astm.org.
   Wagner, R.J., Boulger, R.W., Jr., Oblinger, C.J., and Smith, B.A., 2006, Guidelines and standard procedures for continuous water-quality monitors—Station operation, record computation, and data reporting: U.S. Geological Survey Techniques and Methods 1-D3, 51 p.
   Weiss, R.F., 1974. Carbon dioxide in water and seawater: the solubility of a non-ideal gas. Mar. Chem., 2: 203-215.

   Entity_and_Attribute_Detail_Citation: Adrian Mann
   

Who produced the data set?

1. Who are the originators of the data set? (may include formal authors, digital compilers, and editors)
   • Mann, Adrian G.
   • O'Keefe Suttles, Jennifer A.
   • Gonneea, Meagan E.
   • Brosnahan, Sandra M.
   • Brooks, Thomas W.
   • Wang, Zhaohui A.
   • Ganju, Neil K.
   • Kroeger, Kevin D.
2. Who also contributed to the data set?
3. To whom should users address questions about the data?
   Adrian G Mann

   Woods Hole Coastal and Marine Science Center

   Physical Scientist

   384 Woods Hole Road

   Woods Hole, MA
   

   U.S.

   508-548-8700 x2316 (voice)

   amann@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: 2016 (process 1 of 10)

   A YSI EXO2 multiparameter sonde was deployed on a semi-continuous basis between November 1, 2012 and December 31, 2016 near the mouth of a tidal creek which flows into Sage Lot Pond, located within Waquoit Bay National Estuarine Research Reserve in Mashpee, Massachusetts. Latitude and Longitude were measured with a handheld Garmin 76Cx GPSmap unit in the field at time of collection. The EXO2 sonde was instrumented with sensors to measure and record ambient water temperature, specific conductivity, dissolved oxygen, turbidity, fluorescent Dissolved Organic Matter (fDOM), pH, Oxidation Reduction Potential (ORP), Total Algae (chlorophyll and blue green algae-Phycoerythrin), and pressure at regular intervals during deployment periods. Sample intervals were set for either 2 minutes or 8 minutes in 2012-2014, and 5 minutes thereafter. Proprietary KorEXO software was used to calibrate sensors and download data. Salinity in practical salinity units (psu) was calculated from conductivity and temperature within the software. Turbidity was also converted from formazin nephelometric units (FNU) to nephelometric turbidity units (NTU) within the software.
   An automatic wiper was set to wipe the sensor faces every 20 minutes to prevent fouling. Each sensor was wrapped with anti-fouling copper tape; a copper anti-fouling guard cup was also placed around the sensors. The sonde was mounted vertically in a fixed position on a mounting plate which was attached to a post that had been driven into the bottom of the creek. The sonde was positioned so that the height of the sensor face was approximately 40 cm from the bottom of the creek. Sensor height above the sediment was measured at the start and end of each deployment with a meter stick. After a period of time (typically 2-3 weeks), the deployed sensor was removed from the creek and brought back to the lab for a post-deployment check, data downloading and sensor cleaning.
   Between 2012 and 2014, alternate sensors were occasionally deployed simultaneously alongside the EXO2 as a comparison test or if we suspected a problem with EXO2 sensor performance. These instruments included a YSI 600XLM, and a Wetlabs ECO triplet. These instruments were maintained with the same protocol as the EXO2 sonde. This process step took place from 2012 to 2016. Person who carried out this activity:
   

   Jennifer O'Keefe Suttles

   Woods Hole Coastal and Marine Science Center

   384 Woods Hole Road

   Woods Hole, MA
   

   US

   508-548-8700 x2385 (voice)

   jokeefesuttles@usgs.gov

   Date: 2016 (process 2 of 10)

   A Sontek IQ-Plus acoustic Doppler current profiler (ADCP) was deployed in the channel of a tidal creek which flows into Sage Lot Pond, located within Waquoit Bay National Estuarine Research Reserve in Mashpee, Massachusetts. The ADCP was co-deployed with the water quality sonde. Data included in this report are water elevation in meters (calculated from water level) and flow data in cubic meters per second collected every 15 minutes, almost consecutively, between November 1, 2012 to December 31, 2016.
   The ADCP was mounted on a solid platform secured into the creek bottom; it was positioned in the center of the channel at least 3 m distance from other sensors or structures in the creek. Precise elevation measurements of the instrument itself were measured using Real-Time Kinetic GPS (RTK) once per season, or if the instrument was re-positioned. These elevations are included in Table 2. However, prior to July 11, 2014 the elevation of the ADCP instrument was not directly measured using RTK and water level was calculated using the measured elevation of the EXO2 instrument and the mean difference in overlapping depth data from both instruments. The channel geometry of the creek was measured using a measuring stick and a level line across the channel for reference, and entered into the IQ SensorNet instrument software to calculate discharge area. The channel geometry was re-measured each time the instrument was re-positioned or removed from the creek for servicing. Debris and fouling on the surface of the instrument were periodically cleaned with a mop. Data from the instrument were downloaded in the field onto a laptop during regular field checks, and was further processed in the lab. This process step took place from 2012 to 2016. Person who carried out this activity:
   

   Sandra Brosnahan

   Woods Hole Coastal and Marine Science Center

   384 Woods Hole Road

   Woods Hole, MA
   

   US

   508-548-8700 x2265 (voice)

   sbrosnahan@usgs.gov

   Date: 2016 (process 3 of 10)

   A high-frequency CO2 sensor (Pro-Oceanus Mini CO2) was deployed in the creek adjacent to the YSI EXO2 instrument from 2014 to 2016 to measure dissolved CO2 (pCO2) in the surface water. The pCO2 data were recorded every 2 seconds in 2014 and 2015, and every 30 minutes in 2016. The sensor was calibrated annually by the manufacturer, Pro-Oceanus. During deployment, the sensor was checked monthly to change the battery and clean the instrument. Details of data collection dates and instrument type used are included in CollectionDates_Table2.csv. This process step took place from 2014 to 2016 and the process date indicates the most recent. However, the data were newly added as part of version 2.0 in 2023. Person who carried out this activity:
   

   Adrian Mann

   Woods Hole Coastal and Marine Science Center

   384 Woods Hole Road

   Woods Hole, MA
   

   US

   508-548-8700 x2316 (voice)

   amann@usgs.gov

   Date: 2016 (process 4 of 10)

   Raw data files from the EXO2 were downloaded in the field or in the lab after each deployment and backed up onto a hard drive as well as to a Woods Hole Coastal and Marine Science Center (WHCMSC) network server. Each deployment file was then exported into MATLAB(version 2014a) for further evaluation and processing. Initially, excess pre- and post- deployment data were removed (i.e. data collected when the sonde was not deployed in the creek). Corrections to data, due to sensor fouling and drift (assessed during calibration checks between deployments), were then applied as appropriate, and any remaining data that were out of sensor range were omitted. Data collected from additional sensors that were periodically deployed concurrently with the EXO2 Sonde were also corrected for drift and fouling, and were merged with the EXO data only if the EXO data was not acceptable. Turbidity, fDOM, Chlorophyll and Blue-Green Algae (BGA) data were further screened using a “despike” MATLAB script which filtered the data when a jump in values exceeded a threshold of 20 units (well beyond the expected range of values between sample points), and removed spikes that were greater than 50% from a 5 point median filter of the signal. This process step took place from 2012 to 2016. Person who carried out this activity:
   

   Jennifer O'Keefe Suttles

   Woods Hole Coastal and Marine Science Center

   384 Woods Hole Road

   Woods Hole, MA
   

   US

   508-548-8700 x2385 (voice)

   jokeefesuttles@usgs.gov

   Date: 2016 (process 5 of 10)

   Raw data files from the SonTek IQ-Plus ADCP were downloaded in the field or every 3-4 weeks. Data were visually evaluated with the IQ software in the field before continuing with data collection. Raw data were brought back to the lab and backed-up onto a hard drive as well as to a WHCMSC network server. Each deployment file was then imported into MATLAB (version 2014a) for further evaluation and processing. Data were evaluated between deployments based on a predetermined acceptable ratio of signal to noise. Data with an SNR ratio that fell outside of this threshold (acceptable SNR threshold ranged from 4 to 70; per recommendation by SonTek technical support) were removed. Depth values less than 0.01 m were also removed. Data that were deemed erroneous from a known disturbance in the creek, large storm or ice cover were omitted as appropriate. This process step took place from 2012 to 2016. Person who carried out this activity:
   

   Sandra Brosnahan

   Woods Hole Coastal and Marine Science Center

   384 Woods Hole Road

   Woods Hole, MA
   

   US

   508-548-8700 x2265 (voice)

   sbrosnahan@usgs.gov

   Date: 10-Jul-2017 (process 6 of 10)

   After corrected for drift and fouling, fDOM data were also corrected for temperature, turbidity and inner filter effect, based on the procedures followed by Downing and others, 2012. Correction equations were based on an in-house laboratory experiment on October 5, 2017 using water collected from the Sage Lot Pond study site. Because turbidity values in the lab experiment did not exceed 220 NTU, a constant correction value, equivalent to turbidity value 220 NTU (0.2144 Quinine Sulfate Equivalent (QSU)), was used for any samples with turbidity values above 220 NTU. Otherwise, the exponential correction factor was applied. Turbidity values exceeding 500 NTU, remaining after data were corrected, were omitted as it was determined that these were unreliable values for this study site.
   Citation: Downing, B.D., Pellerin, B.A., Bergamaschi, B.A., Saraceno, J.F., and Kraus, T.E.C., 2012, Seeing the light: The effects of particles, dissolved materials, and temperature on in situ measurements of DOM fluorescence in rivers and streams: Limnology and Oceanography-Methods, v. 10, p. 767-775, https://aslopubs.onlinelibrary.wiley.com/doi/pdf/10.4319/lom.2012.10.767. Person who carried out this activity:
   

   Jennifer O'Keefe Suttles

   Woods Hole Coastal & Marine Science Center

   384 Woods Hole Road

   Woods Hole, MA
   

   US

   508-548-8700 x2385 (voice)

   jokeefesuttles@usgs.gov

   Date: 2019 (process 7 of 10)

   Finally, all corrected chemical and flow data were adjusted and interpolated onto the same time stamp at a regular 5-minute sample interval using MATLAB (version 2014a). The xlswrite function was used to write the data out as a comma-separated values file. Person who carried out this activity:
   

   Adrian Mann

   Woods Hole Coastal and Marine Science Center

   Physical Scientist

   384 Woods Hole Road

   Woods Hole, MA
   

   US

   508-548-8700 x2236 (voice)

   amann@usgs.gov

   Date: 2019 (process 8 of 10)

   Excel (version 2013) was used to create separate tables which document additional information associated with these data. Table 1 (EXO_QAQC_Table1.csv) documents the correction criteria and maximum allowable limits for data corrections. Table 2 (Collection Dates_Table2.csv) documents the data collection date ranges, instrument type and instrument horizontal and vertical positional information. These tables were then exported as Comma-separated values files using "save as". These tables are described in the entity and attribute section. Person who carried out this activity:
   

   Adrian Mann

   Woods Hole Coastal and Marine Science Center

   Physical Scientist

   384 Woods Hole Road

   Woods Hole, MA
   

   US

   508-548-8700 x2236 (voice)

   amann@usgs.gov

   Date: 06-Aug-2020 (process 9 of 10)

   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

   Date: 2023 (process 10 of 10)

   Raw data files from the Pro-Oceanus Mini CO2 sensor were downloaded in the field every 3-4 weeks between July 2014 and December 2016. Raw data were backed-up onto a hard drive as well as to a WHCMSC network server. Each deployment file was then imported into MATLAB (version 2014a) for further evaluation and processing. Data that were logged while the sensor was out of the water, during sensor warm-up periods at the beginning of deployments, or during maintenance were excluded. Sensor pressure, temperature and CO2 readings that were unstable or fell outside of physical bounds were also excluded. Deployment files were appended in MATLAB by year, and then appended into a single MATLAB file. The "writetable" function in MATLAB was used to write the data out as a comma-separated values file. Due to the large size of the data file, 9604819 rows of data, the data are also provided in MATLAB format. This process step took place from 2014 to 2016. The final combining of the individual files and cleanup was completed and prepared for release in 2023.

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?
   Drift and fouling of each sensor on the YSI EXO2 sonde were evaluated after each field deployment. Correction factors based on fouling and drift were calculated and applied according to Wagner and others, 2006. Fouling was determined as the difference between a sensor reading in solution prior to cleaning and after cleaning. Calibration drift was determined as the difference between the prepared value of a calibration solution and cleaned sensor reading in calibration solution. If the absolute value of the sum of the fouling and drift are beyond a predetermined acceptable amount of fouling (Table 1, Wagner and others, 2006), then a correction factor (calculated from these fouling and drift assessments) would be applied to the data. If the data required a correction factor beyond an acceptable threshold (Table 1), the data were removed from the dataset. Fouling was determined in three different ways during the 2012-2016 field seasons: field comparison of dirty deployed EXO and clean replacement EXO; laboratory comparison of sensor data in a bucket of field water prior to and after cleaning; laboratory comparison of sensor data in known standards prior to and after cleaning. Bucket tests were not ideal for all parameters; for some parameters the concentration in the bucket was near to the detection limit of the sensor (for example turbidity and total algae). Field comparison was not available for all deployments (due to battery failure of deployed sondes). Comparison in standards was most consistently assessed. Calibration drift was assessed on cleaned sensors post deployment. After the fouling evaluation was complete, sensors were cleaned and placed in clean standards. Readings were noted and sensors were recalibrated, if necessary, prior to next deployment. Data from optical sensors not included in Wagner and others, 2006 (fluorescent dissolved organic matter (fDOM) and chlorophyll) were corrected using the same criteria as turbidity.
   Water flow and water depth data were measured by a SonTek IQ-Plus Acoustic Doppler current profiler (ADCP), using SonTek IQ Firmware version 1.10. The minimum operating depth of the IQ-plus is 0.08 meters, and maximum is 5.0 meters. Water level accuracy was 0.1% of measured depth or +-0.003 meters, whichever was greater. Pressure sensor accuracy was 0.1% of full scale, and sensor range was 10 meters. Velocity accuracy was +-1% of measured velocity, or +-0.5 centimeters per second. Data were evaluated between deployments, based on the signal to noise ratio. Data with a signal to noise ratio below 4 were omitted, as the velocity signal may become compromised. Depth values less than 0.01 meters were also removed because they were determined to be below detection.
   Dissolved CO2 was measured by a Pro-Oceanus Mini CO2 sensor. Dissolved CO2 accuracy was ±2% of the max range, and resolution was 0.1% of the max range. Accuracy of Total Dissolved Gas Pressure was ±1%. The measurement range of CO2 was 0-10,000 ppm. Note: the temperature sensor of the Pro-Oceanus Mini CO2 sensor is housed inside of the sensor housing. Therefore, the temperature readings are higher than the surrounding water temperature. The CO2 in uatm is reliable to 3 decimal places.
   Citation used: Wagner, R.J., Boulger, R.W., Jr., Oblinger, C.J., and Smith, B.A., 2006, Guidelines and standard procedures for continuous water-quality monitors—Station operation, record computation, and data reporting: U.S. Geological Survey Techniques and Methods 1-D3, 51 p.
2. How accurate are the geographic locations?
   Latitude and Longitude were measured with a handheld Garmin 76Cx GPSmap unit in the field at time of collection. The GPS unit indicated accuracy was within 3 meters. No formal positional accuracy tests were conducted.
3. How accurate are the heights or depths?
   Prior to September 2015, elevation of the water level sensor was obtained using rod and optical level survey. Elevation measurements were relative to a vertical control point referenced to the North American Vertical Datum of 1988 (NAVD88) based on long-term GPS base station occupations using a Trimble receiver with accuracy within 3 centimeters. Error associated with readings relative to the vertical control point was less than 1 centimeter. After September 2015, elevation of the water level sensor was measured with a Trimble Real-Time Kinematic (RTK) GPS. Accuracy was 2-3 cm according to instrument corrections. No formal positional accuracy tests were conducted.
4. Where are the gaps in the data? What is missing?
   Missing values indicate that either no measurement was made, or the data were omitted because it was determined that error due to sensor drift and fouling exceeded the correction threshold (in the case of the EXO2 sensors), or the signal to noise ratio fell outside of the acceptable threshold (in the case of the SonTek IQ ADCP) as described in the Attribute Accuracy Report. Data that were logged with the Pro-Oceeanus CO2 sensor while the sensor was out of the water, during sensor warm-up periods at the beginning of deployments, or during maintenance were excluded.
5. How consistent are the relationships among the observations, including topology?
   Water chemical data were primarily measured with a YSI EXO2 sonde (s/n 12J102016) between 2012 and 2016. Between 2012 and 2014, alternate sondes (YSI 600XLM, Wetlabs ECO triplet) were occasionally deployed simultaneously as a comparison test or if we suspected a problem with EXO2 sensor performance. These instruments were maintained with the same protocol as the EXO2 sonde. Data from the YSI 600XLM and Wetlabs were only substituted if EXO data was not acceptable. Throughout the 2015 field season, two EXO2 sondes (s/n 12J102016 and s/n 12J101654) were used interchangeably at this location. Water level data were also collected between 2012 and 2016, while CO2 data were only collected from 2014 to 2016. Details of data collection dates and instrument type used are included in CollectionDates_Table2.csv.

How can someone get a copy of the data set?

1. Who distributes the data set? (Distributor 1 of 1)
   
   ScienceBase

   U.S. Geological Survey - ScienceBase

   Denver Federal Center, Building 810, Mail Stop 302

   Denver, CO
   

   US

   1-888-275-8747 (voice)

   sciencebase@usgs.gov
2. What's the catalog number I need to order this data set? This dataset contains sensor data in CSV format (SLPCreekSensorData.csv), a CSV table of correction criteria and maximum allowable limits for data corrections (EXO_QAQC_Table1.csv), and a CSV table of data collection date ranges, instrument type and instrument horizontal and vertical positional information (CollectionDates_Table2.csv). Version 2.0 includes the CO2 sensor data in a comma-separated values format (SLPCreek_CO2.csv) and MATLAB format (SLPCreek_CO2.mat). Additionally, CSDGM metadata describing these tables is available in XML format and a browse graphic of the study site (SLPCreek_browse_graphic.jpg).
3. What legal disclaimers am I supposed to read?
   Neither the U.S. Government, the Department of the Interior, nor the USGS, nor any of their employees, contractors, or subcontractors, make any warranty, express or implied, nor assume any legal liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, nor represent that its use would not infringe on privately owned rights. The act of distribution shall not constitute any such warranty, and no responsibility is assumed by the USGS in the use of these data or related materials. Any use of trade, product, or firm 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?
   • Availability in digital form:

     Data format:	The dataset contains the data in comma-separated values format, as well as supplemental information in two additional CSV files. One dataset also has a MATLAB version of the data. CSDGM metadata in XML format describing all the files is also included. in format Comma-separated values Size: 731
     Network links:	https://www.sciencebase.gov/catalog/file/get/5cd475e6e4b062989a9e94e8 https://www.sciencebase.gov/catalog/item/5cd475e6e4b062989a9e94e8 https://doi.org/10.5066/P9STIROQ

     Data format:	The CO2 dataset is available in MATLAB format as well as its comma-separated values formatted data. The other dataset is available as comma-separated values as well as supplemental information in two additional CSV files. CSDGM metadata in XML format describing the files is also included. in format MAT (version MATLAB version 2014a) Size: 731
     Network links:	https://www.sciencebase.gov/catalog/file/get/5cd475e6e4b062989a9e94e8 https://www.sciencebase.gov/catalog/item/5cd475e6e4b062989a9e94e8 https://doi.org/10.5066/P9STIROQ

   • Cost to order the data: none

Who wrote the metadata?

Dates:

Last modified: 27-Jul-2023

Metadata author:

Adrian G Mann

Woods Hole Coastal and Marine Science Center

Physical Scientist

384 Woods Hole Road

Woods Hole, MA

United States

508-548-8700 (voice)

whsc_data_contact@usgs.gov

Contact_Instructions:

The metadata contact email address is a generic address in the event the person is no longer with the USGS.

Metadata standard:

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