Hydrographic data obtained with instrumented elephant seals are provided in a netCDF format following recommandations of the ``Marine-mammals NetCDF formats and conventions'' Version 1.2 [PDF] which is derived from the Argo netCDF User's manual. The Argo netCDF format is a standard used to store Argo float data on Argo data servers, and thus it is well adapted to record hydrographic profile data. Because marine mammals behave very much like Argo floats from the point of view of data sampling, this format is particularly well adapted to the storage of marine mammal hydrographic data.
File naming convention
A single file is available for each single CTD-SRDL dataset (i.e. one tag deployment on one animal). The file name uses the SMRU naming convention (giving a deployment code, a tag identifier, and the year), with the suffix “_prof.nc”.
The same format is used to distribute a version with vertically interpolated profiles (on a regular grid with 1 dbar depth interval). For this version of the data, the suffix “_interp_prof.nc” is used. Note that this version is a mirror copy of the xxx_prof.nc file, except for the hydrographic profile data that are given on a regular vertical grid.
Global attributes
Global attributes of the netCDF files provide important metadata:
- pi_name = name of the principal investigator
- species = string of character for the species
- platform_code = Unique identifier number for the tag dataset
- wmo_platform_code = WMO number when available
- smru_platform_code = SMRU name (used in the file name)
- deployment_code = SMRU deployment code
- distribution_statement = "Follow MEOP data policy standards, cf. http://www.meop.net/the-dataset/data-access.html. Data available free of charge. User assumes all risk for use of data. User must display citation in any publication or product using data. User must contact PI prior to any commercial use of data"
- citation = "The marine mammal data were collected and made freely available by the International MEOP Consortium and the national programs that contribute to it (http://www.meop.net)" ;
- positioning_system = {“argos”,“gps”}
- number_of_ts_profiles = ...
- number_of_t_profiles = ...
Variables
The data file contains the raw and adjusted pressure, temperature, and salinity data with their associated quality flags. Adjustment equations are also stored with the corresponding coefficients. Here is a (non-exhaustive) list of the most relevant variables:
- PI_NAME: Name of the principal investigator
- STATION_PARAMETERS: List of available parameters
- PLATFORM_NUMBER: Generic unique identifier (same as platform_code)
- CYCLE_NUMBER: profile index, integer ranging from 1 (first dive) to N (last dive).
- JULD_LOCATION: Julian day of the location relative to the 01/01/1950.
- LATITUDE: Latitude of the station, best estimate
- LONGITUDE: Longitude of the station, best estimate
- PRES: Sea pressure in dbar
- PRES_ADJUSTED: Adjusted sea pressure (in practice, pressure was not adjusted, so PRES=PRES_ADJUSTED)
- PRES_ADJUSTED_QC: Quality flag (1 = good data).
- TEMP: In-situ temperature (in degC)
- TEMP_ADJUSTED: Adjusted in-situ temperature (in degC)
- TEMP_INTERP: In-situ temperature interpolated on a regular vertical grid (in degC)
- TEMP_ADJUSTED_QC: Quality flag (1 = good data).
- TEMP_ADJUSTED_ERROR: Rough estimate of accuracy (single value per deployment).
- PSAL: Practical salinity (in psu)
- PSAL_ADJUSTED: Adjusted practical salinity (in psu)
- PSAL_INTERP: Practical salinity interpolated on a regular vertical grid
- PSAL_ADJUSTED_QC: Quality flag (1 = good data).
- PSAL_ADJUSTED_ERROR: Rough estimate of uncertainty (single value per deployment)
- SCIENTIFIC_CALIB_EQUATION: Calibration equations used to adjust data
- SCIENTIFIC_CALIB_COEFFICIENT: Calibration coefficients
How to read data
Matlab and Python tools are available publicly to read and manipulate files with the netCDF format. They are given as an example. Note also that this format can be easily read by the software Ocean Data View (using the Import/Argo formats/Float Profiles menu). More tools can be obtained on GitHub.