ODFNames2oceNames: Translate ODF CODE Strings to oce Variable Names

In dankelley/oce: Analysis of Oceanographic Data

Translate ODF CODE Strings to oce Variable Names

Description

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.

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.

Value

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

Author(s)

Dan Kelley

References

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

See Also

Other functions that interpret variable names and units from headers: cnvName2oceName(), oceNames2whpNames(), oceUnits2whpUnits(), unitFromString(), unitFromStringRsk(), woceNames2oceNames(), woceUnit2oceUnit()

Other things related to odf data: CTD_BCD2014666_008_1_DN.ODF.gz, ODF2oce(), ODFListFromHeader(), [[,odf-method, [[<-,odf-method, odf-class, plot,odf-method, read.ctd.odf(), read.odf(), subset,odf-method, summary,odf-method

Examples

ODFNames2oceNames("TEMP_01")$names # "temperature"

dankelley/oce documentation built on May 8, 2024, 10:46 p.m.