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James Clark Ross JCR106B Underway and Surface Meteorology Document

Cruise Information

Metadata Summary

Instrument Description

Data were collected using the integrated underway system on the RRS James Clark Ross. Contacts for specific instrumentation enquires can be found on the British Antarctic Survey (BAS, Antarctic Marine Engineering Department (AME) website ( BAS website ).

The data were logged on a PC-based oceanlogger logging system, built in-house at BAS, with the primary purpose of logging measurements from various of the ship's continuously-run data sources. Accordingly, it draws data from the ship's pumped non-toxic supply, plus assorted meteorological parameters. The instruments with an analogue output are connected to self-contained digitising Nudam modules located close to the relevant instrument. The modules are then interrogated by the controlling PC using the RS485 protocol.

Navigation and bathymetry

At the time of the cruise, the JCR used a combination of an Ashtec ADU5, a Glonass GG24 and a Trimble 4000 system for navigation and determination of ship positional and motion data.

Sea-floor depth measurements are determined with a Simrad EA500 hydrographic echosounder and a hull-mounted tranducer.

Meteorology

The following meteorological instrumentation was used:

Where two sensors are used, they are physically mounted in close proximity to each other. Two are used for redundancy purposes.

Sea surface hydrography

The following oceanographic instrumentation was used:

Originator's Data Processing

Sampling Strategy

The underway oceanlogger system was run continuously throughout the cruise with data processed in the following sequence.

1. Navigation
2. Bathymetry
3. Oceanlogger

Data Processing

The data processing for each stage will now be described individually. A full description of the processing steps is described in the JCR106B cruise report listed in the references.

Navigation

On a daily basis an ASCII file, get_bestnav, containing the RVS 'bestnav' position data at 30-second intervals is produced containing the ship's latitude, longitude, distance traveled and direction. The resulting navigational output is converted into a .mat file, a standard Matlab output file with the application of a Matlab script that combines all daily output produced into a master file, bestnav_all_jr106.mat and checks to see if values are flagged as good.

Bathymetry

Sea-floor depth measurements from the Simrad EA500 hydrographic echosounder and a hull mounted transducer were converted into an ASCII file on a daily basis at 2-6 second intervals. The bathymetry data were then mapped to the same 30 second time interval as the navigational data. The merged_all_jr106s.mat file containing navigation and bathymetry data from the leg was output by this process.

Meteorology and sea surface hydrography (Oceanlogger)

The data from the oceanographic and meteorological instrumentation were read into Unix daily to produce an ocean.*** file for the particular Julian day (where *** is the Julian day), at intervals from 2 seconds upwards. The data are mapped and converted to the same time interval as the navigational data, using the bestnav_all_jr106.mat file. Corresponding latitudes and longitudes from the bathymetry data are also included in the output file. The daily mapped data are saved in the oceanlog_30sec_all_jr106s.mat containing data for the entire cruise leg.

BODC Processing

Data were received as three binary .mat Matlab files named bestnav_all_jr106.mat, merged_all_jr106s and oceanlog_30sec_all_jr106s.mat. Each file contains the navigation, bathymetry and oceanographic/meteorological data respectively. Each file contains both position and time data. The data span 18:24:29 on the 29th August 2004 to 23:59:29 on the 10th September 2004, and so include data from the previous JCR106 leg of the cruise but do not include the complete passage to port at the end of the cruise. Data from the previous leg of the cruise have been trimmed from this series and included in the series for the previous leg.

All underway sea surface hydrography, meteorology and ship's navigation files are merged into a common file using time (GMT) as the primary linking key. Data calibrations are applied as appropriate (see calibrations section).

The transfer mapping of the data is as follows:

* Time is mapped to common AADYAA01 and AAFDZZ01 data channels with a 30 second temporal resolution.

RVS flag indicates the format of the flag channels as received (Research Vessel Services format), these have been converted to BODC flags during processing.

Each data channel is visually inspected on a graphics workstation and any spikes or periods of dubious data are flagged as suspect. The capabilities of the workstation screening software allows all possible comparative screening checks between channels (e.g. to ensure corrected wind data have not been influenced by changes in ship's heading). The system also has the facility of simultaneously displaying the data and the ship's position on a map to enable data screening to take oceanographic climatology into account.

Additional Navigation Processing Steps

Positions were checked for gaps and improbable speeds. 31 gaps of less than 2 minutes were identified, these were filled and interpolated data points flagged as 'T'.

Additional Bathymetric Processing Steps

The GEBCO bathymetry channel (MBANGBCE) was added the dataset and an intercomparison of the bathymetry and the GEBCO bathymetry conducted.

Additional Meteorological Processing Steps

Duplicate channels were intercompared during screening and merged if applicable. When TIR and PAR channels were merged (to parameters CSLRR1XS and IRRDSSXS) the greatest value at each time was taken.

Calibration

Calibrations of the salinity, temperature and chlorophyll values against the underway salinity samples and CTD profiles were undertaken by BODC. For all parameters the offset (reference minus parameter to calibrate) failed the Anderson-Darling test for normality. All offsets appeared homogeneous so linear regression was used.

Salinity

Attempts to calibrate the salinity against discrete samples taken from the underway supply and against calibrated CTD profiles were undertaken. When the data were viewed initially it was clear that values of salinity were highly variable in the upper water column whilst the ship was within the Kangerdlugssuaq Fjord system. For this reason, only salinities outside the fjord are used in calibration.

Regression of salinity offsets vs time

Regression of discrete salinities vs the difference between discrete sample and TSG salinity

In both regressions the R ² is too small (<95%) and the P value too large (>0.05) for the results to be considered significant.

When plotted a small offset from zero is visible throughout the series. This has a mean of 0.015 and a standard deviation of 0.031 (N=17). The high standard deviation suggests the the offset should not be applied.

Regression of salinity offsets vs time

Regression of salinity offsets vs the surface value

In both regressions the R ² is too small (<95%) and the P value too large (>0.05) for the results to be considered significant.

When a mean offset is calculated for the entire series the values is 0.0547 (N=13) with a standard deviation of 0.797. The standard deviation is greater than a mean so the offset has not been applied

Sea Surface Temperature (SST)

An inter-comparison between the underway SST and the uncalibrated CTD temparature profiles was undertaken, this assumed a seawater intake depth on the ship of 6 m. When the data were viewed initially it was clear that values of temperature were highly variable in the upper water column whilst the ship was within the Kangerdlugssuaq Fjord system. For this reason, only temperatures outside the fjord are used.

Regression of temperature offsets vs time

Regression of temperature offsets vs the surface value

In both regressions the R ² is too small (<95%) and the P value too large (>0.05) for the results to be considered significant.

There is a mean offset in temperature of -0.1101 with a standard deviation of 0.1138. The standard deviation is of a similar magnitude to the offset so the offset will not be applied to the series.

Chlorophyll

On visual inspection the chlorophyll did not exhibit the high variability observed when the ship was in the fjord like in the salinity and temperature series so the entire series of values is used for an inter-comparsion between the underway and CTD values.

Regression of chlorophyll offsets vs time

The P value of 0.025 suggests a time dependence in the offsets which is confirmed by visual inspection of the data.

Regression of chlorophyll offsets vs the surface value

This shows there is not significant variation with chlorophyll though.

The mean offset for the series is -0.0028 with a standard deviation of 0.1058 so not offset is to be applied.

Because both the parameters considered are uncalibrated and no discrete samples were taken is is not known which sensor is responsible for the suggested time dependent offset so no calibration will be applied.

Data Quality Reports

Navigation

During screening 11 spikes in the ships heading were flagged.

Bathymetry

Bathymetry was compared to corresponding GEBCO bathymetric values and 3 spikes were flagged as 'M'.

Oceanography and Meteorology

During the cruise there were periods when the pump was switched off or the lines to the instruments were blocked with ice. These are easily identified as low values (~0) in the INFLTF01 flow rate channel. During these periods corresponding data in CNDCSG01, PSALSU01, TMESSG01 and SVELSG01 are flagged as 'M'. The parameters CPHLUMTF and TMESFL01 lag the pump by up to 5 minutes or have slower response times and have extra values flagged.

Whilst the ship was in port the TEMPHU01 has values flagged as 'M' because the ship is warming the surrounding water.

In low light the PAR and TIR light instruments (parameters IRRDSS01, IRRDSS02, CSLRZZ01 and CSLRZZ02) recorded small negative values. The negative values have been flagged 'M' by BODC. A possible cause is that a recent dark offset had not been applied to the measurements by the originator.

References

Cruise report - JR106b , RRS James Clark Ross, NERC AutoSub under ice thematic Programme, Kangerdlugssuaq Fjord and Shelf, East Greenland.

BODC Quality Control Flags