primary productivity

Year 2018, 15 minute interval, water quality measurements of water column temperature, salinity, oxygen, and depth in the upper Parker River Estuary near Middle Road Bridge, Newbury, MA.


Year 2018, water quality sonde data.15 minute readings of water column temperature, salinity, oxygen and depth in the upper Parker River Estuary near Middle Rd Bridge, Newbury, MA

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Measurements are made using a YSI 6600 water quality datalogging sonde. YSI Sonde sensors consist of 6150 optical dissolved oxygen probe, 6560 conductivity/temperature probe (thermistor) and non-vented cable with level depth sensor (stainless steel strain gauge).   Sensors are calibrated according to the instrument manual:



Missing data or blank values typically result from periods when the sonde is out of the water for maintenance or during very low tides, noted in the Comments field, or when logged values do not pass post-deployment quality control evaluations.


Raw data are screened in R for outliers using a spike detection equation following Papale et al., 2006 (, which flags differences between sequential datapoints that exceed the median difference found in the data series.  Values flagged by this screen are noted in the Comments field.



Conductivity and Specific Conductivity

The conductivity cell may short due to blockage by detrital material or fouling organisms, resulting in lower than expected conductivity.  Poor/inaccurate conductivity values cause erroneous dissolved oxygen values.



YSI recognizes two conventions regarding calibration of the oxygen sensor: “DOsat%” and “DOsat%Local” (see Appendix J in Manual).  We calibrate to ambient pressure, as per the manual, but in addition to the YSI 6600 default parameter DOsat%, we also report output for DOsat%Local.


DOsat% represents values of % saturation of oxygen standardized to a calibration of 100% in water-saturated air at 1 ATM or 760 mmHg.

DOsat%Local represents values from ODO sensor calibration in water-saturated air where 100% saturation was set relative to ambient air presure at time of calibration.  When using the Local convention, the software of the instrument “remembers” the barometric pressure input at the time of calibration for use in later calculation of the DO concentration in mg/L.


Depth is depth of water above the non-vented strain gauge transducer on the sonde, with the sonde placed as near bottom as practicable: sonde depth ≠ absolute depth.   Depth is calibrated in air to ambient surface pressure before deployment.  The non-vented transducer does not account for changes in ambient atmospheric pressure during deployment.  Corrections that account for these changes may be made using 15-minute barometric pressure data from the Marshview Farm (MFM) weather station to compute correction factors at the same time intervals as the sonde time intervals:

Ambient pressure changes correspond to the following water level changes, 1 mb = 0.0102 meters of water.


Sonde is calibrated in air at ambient pressure to the corresponding depth at pressures relative to 1 ATM

  1 ATM = 760 torr = 760mmHg = 1013.25 mBar (I Torr  = 1.333224 mB).

   1mB = 0.0102 meters of water

If ambient air is 1014.58 mB pressure then sonde should be calibrated to 0.0134 m:

Ambient pressure in mB - standard pressure in mB)  * 0.0101m/mB ,   or

(1014.58 - 1013.25) * .0102 = .0134m

An offset to the depth data (post collection) is then applied based on concurrent measures of barometric pressure

Offset Example table is below.

Ambient ATM (Torr)  Ambient ATM (mB)  Offset  meters

755  1006.58  -.0.0680

756  1007.92  -0.0544

757  1009.25  -0.0408

758  1010.58  -0.0272

759  1011.92  -0.0136

760  1013.25  0.000

761  1014.58  0.0136


Version 01: March 3, 2022 original upload of 2018 data and metadata. Used MarcrosExportEML_HTML (working)pie_excel2007.xlsm 28/12 8:18 PM for QA/QC to EML 2.1.0


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