Dataset: AE2207 Processed CTD with Thermodynamic Calculations

Data Processing:
Data were converted from .hex files to .cnv files using SeaSave on default parameters. Then, each file was read using the seabird python library (https://github.com/castelao/seabird), and cast latitude, longitude, and deployment time were retrieved. For further calculations, pressure, temperature (primary sensor), conductivity (primary sensor), oxygen (primary sensor), beam attenuation, ECO chlorophyll fluorescence, PAR, corrected PAR, and instrument time were retained. Due to a choppy sea state, data from the upper 5 db were trimmed as the measurements were noisy. Then, all scans from the first 4.5 minutes of the cast were removed as these data were associated with the initializing soak at 15m before profiling. Finally, the upcast was removed to retain the downcast.

Using the python implementation of the Gibbs SeaWater oceanographic toolbox from TEOS-10 (https://www.teos-10.org/pubs/gsw/html/gsw_front_page.html), the following thermodynamic calculations were conducted. A corrected depth (height relative to sea surface, meaning a negative number) was calculated from the pressure and latitude. Then, potential salinity was calculated using conductivity, temperature, and pressure. Absolute salinity was calculated from potential salinity, and conservative temperature was calculated from absolute salinity, temperature, and pressure. Density in terms of sigma-theta was calculated using absolute salinity and conservative temperature. Then, oxygen solubility was calculated using the GSW oxygen solubility function with absolute salinity, conservative temperature, pressure, latitude, and longitude. Oxygen saturation was estimated for each scan using the primary oxygen sensor and the derived oxygen solubility. The outputs for the transformed data for each retained scan are contained in the file [first file]. Then, to remove additional instrument noise and standardize profiles across casts, data were smoothed and interpolated to every 0.5 dbar of pressure with a Nadaraya-Watson kernel estimator using a bandwidth of 5 meters. Using the smoothed and binned outputs, the mixed layer depth was calculated using the criterion of an increase in sigma-theta above 0.125 from 10dbar. Then, the DCM depth was calculated by identifying the depth corresponding to the highest chlorophyll fluorescence below the mixed layer depth. The derived mixed layer and dcm depths, as well as the smoothed and 0.5 dbar binned values for the above mentioned variables are included in the file [file 2].

BCO-DMO Processing:
- replaced "NA" with "nd" to indicate "no data";
- converted date/time field to ISO8601 format;
- removed the "id" field (identical to "cast").