ODFNames2oceNames: Translate ODF CODE strings to Oce Variable Names

View source: R/odf.R

ODFNames2oceNamesR Documentation

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(), unitFromStringRsk(), unitFromString(), 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"


oce documentation built on July 6, 2022, 1:06 a.m.