Translate ODF CODE Strings to oce Variable Names

Translate ODF CODE strings to oce variable names. This is done differently for data names and quality-control (QC) names.

Usage

ODFNames2oceNames(
  ODFnames,
  columns = NULL,
  PARAMETER_HEADER = NULL,
  debug = getOption("oceDebug")
)

Arguments

ODFnames: vector of character values that hold ODF names.
columns: Optional list containing name correspondances, as described for read.ctd.odf().
PARAMETER_HEADER: Optional list containing information on the data variables.
debug: an integer specifying whether debugging information is to be printed during the processing. This is a general parameter that is used by many oce functions. Generally, setting debug=0 turns off the printing, while higher values suggest that more information be printed. If one function calls another, it usually reduces the value of debug first, so that a user can often obtain deeper debugging by specifying higher debug values.

Value

A list relating ODF names to oce names (see “Examples”).

Details

The following table gives the recognized ODF code names for variables, along with the translated names as used in oce objects. Note that the code names are appended with strings such as "_01", "_02", etc, for repeats. The converted name for an "_01" item is as shown below, and for e.g. "_02" a suffix 2 is added to the oce name, etc.

QC items (which get stored as flags in object's metadata slots) are assigned names that match those of the parameters to which they refer. In parsing ODF files, it is assumed that QC items refer to the data items that precede them. This pattern does not seem to be documented, but it has held in all the files examined by the author, and a similar assumption is made in other software systems. QC items have CODE values that are either start with "QQQQ" or equal "Q<CODE>", where <CODE> matches the corresponding data item.

ODF Code	Oce Name	Notes
`ABSH`	`humidityAbsolute`
`ACO2`	`CO2Atmosphere`
`ALKW`	`alkalinity`
`ALKY`	`alkalinityTotal`
`ALP0`	`apha0`
`ALTB`	`altimeter`
`ALTS`	`altitude`
`AMON`	`ammonium`
`ATMP`	`pressureAtmosphere`
`ATMS`	`pressureAtmosphereSealevel`
`ATRK`	`alongTrackDisplacement`
`ATTU`	`attenuation`
`AUTH`	`authority`
`BATH`	`barometricDepth`
`BATT`	`batteryVoltage`
`BEAM`	`a`
`BNO7`	`bestNODC7Number`	That is an "oh" letter, not a zero
`CALK`	`carbonateAlkalinity`
`CHLR`	`chlorinity`
`CHLS`	`chlorosity`
`CNDC`	`conductivity`
`CNTR`	`scan`
`COND`	`conductivity`
`CORG`	`carbonOrganic`
`CPHL`	`chlorophyll`
`CRAT`	`conductivity`	Conductivity ratio (may have spurious unit)
`CMNT`	`comment`
`CNDC`	`conductivity`
`COND`	`conductivity`
`CTOT`	`carbonTotal`
`DCHG`	`discharge`
`DENS`	`density`
`DEPH`	`pressure`
`DEWT`	`temperatureDewpoint`
`DOC_`	`carbonOrganicDissolved`
`DON_`	`nitrogenOrganicDissolved`
`DOXY`	`oxygen`
`DPDT`	`dpdt`
`DRDP`	`drogueDepth`
`DPWT`	`dryWeight`
`DRYT`	`temperatureDryBulb`
`DYNH`	`dynamicHeight`
`ERRV`	`errorVelocity`
`EWCM`	`uMagnetic`
`EWCT`	`u`
`FFFF`	`overall(FFFF)`	Archaic overall flag, replaced by `QCFF`
`FLOR`	`fluorometer`
`GDIR`	`windDirectionGust`
`GEOP`	`geopotential`
`GSPD`	`windSpeedGust`
`HCDM`	`directionMagnetic`
`HCDT`	`directionTrue`
`HCSP`	`speedHorizontal`
`HEAD`	`heading`
`HSUL`	`hydrogenSulphide`
`IDEN`	`sampleNumber`
`LABT`	`temperatureLaboratory`
`LATD`	`latitude`
`LHIS`	`lifeHistory`
`LOND`	`longitude`
`LPHT`	`pHLaboratory`
`MNSV`	`retentionFilterSize`
`MNSZ`	`organismSizeMinimum`
`MODF`	`additionalTaxonomicInformation`
`MXSZ`	`organismSizeMaximum`
`NETR`	`netSolarRadiation`
`NONE`	`noWMOcode`
`NORG`	`nitrogenOrganic`
`NSCM`	`vMagnetic`
`NSCT`	`v`
`NTOT`	`nitrogenTotal`
`NTRA`	`nitrate`
`NTRI`	`nitrite`
`NTRZ`	`nitrite+nitrate`
`NUM_`	`scansPerAverage`
`OBKS`	`turbidity`
`OCUR`	`oxygenCurrent`
`OPPR`	`oxygenPartialPressure`
`OSAT`	`oxygenSaturation`
`OTMP`	`oxygenTemperature`
`OXYG`	`oxygenDissolved`
`OXYM`	`oxygenDissolved`
`OXYV`	`oxygenVoltage`
`OXV_`	`oxygenVoltageRaw`
`PCO2`	`CO2`
`PHA_`	`phaeopigment`
`PHOS`	`phosphate`
`PHPH`	`pH`
`PHT_`	`pHTotal`
`PIM_`	`particulateInorganicMatter`
`PHY_`	`phytoplanktonCount`
`POC_`	`particulateOrganicCarbon`
`POM_`	`particulateOrganicMatter`
`PON_`	`particulateOrganicNitrogen`
`POTM`	`theta`
`PRES`	`pressure`
`PSAL`	`salinity`
`PSAR`	`PSAR`
`PTCH`	`pitch`
`QCFF`	`overall(QCFF)`	Overall flag (see also archaic FFFF)
`RANG`	`range`
`REFR`	`reference`
`RELH`	`humidityRelative`
`RELP`	`relativeTotalPressure`
`ROLL`	`roll`
`SDEV`	`standardDeviation`
`SECC`	`SecchiDepth`
`SEX_`	`sex`
`SIG0`	`sigma0`
`SIGP`	`sigmaTheta`
`SIGT`	`sigmat`
`SLCA`	`silicate`
`SNCN`	`scanCounter`
`SPAR`	`SPAR`
`SPEH`	`humiditySpecific`
`SPFR`	`sampleFraction`
`SPVO`	`specificVolume`
`SPVA`	`specificVolumeAnomaly`
`STRA`	`stressAmplitude`
`STRD`	`stressDirection`
`STRU`	`stressU`
`STRV`	`stressV`
`SSAL`	`salinity`
`SVEL`	`soundVelocity`
`SYTM`	`time`
`TAXN`	`taxonomicName`
`TE90`	`temperature`
`TEMP`	`temperature`
`TEXZT`	`text`
`TICW`	`totalInorganicCarbon`
`TILT`	`tilt`
`TOTP`	`pressureAbsolute`
`TPHS`	`phosphorousTotal`
`TRAN`	`lightTransmission`
`TRB_`	`turbidity`
`TRBH`	`trophicDescriptor`
`TSM_`	`suspendedMatterTotal`
`TSN_`	`taxonomicSerialNumber`
`TURB`	`turbidity`
`UNKN`	`-`
`UREA`	`urea`
`VAIS`	`BVFrequency`
`VCSP`	`w`
`VMXL`	`waveHeightMaximum`
`VRMS`	`waveHeightMean`
`VTCA`	`wavePeriod`
`WDIR`	`windDirection`
`WETT`	`temperatureWetBulb`
`WSPD`	`windSpeed`
`WTWT`	`wetWeight`
`ZOO_`	`zooplanktonCount`

Any code not shown in the list is transferred to the oce object without renaming, apart from the adjustment of suffix numbers. The following code have been seen in data files from the Bedford Institute of Oceanography: ALTB, PHPH and QCFF.

References

For sources that describe the ODF format, see the documentation for the odf.

Author

Dan Kelley

Examples

ODFNames2oceNames("TEMP_01")$names # "temperature"
#> [1] "temperature"