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oce (version 1.8-3)

ODFNames2oceNames: 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")
)

Value

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

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.

Author

Dan Kelley

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 CodeOce NameNotes
ABSHhumidityAbsolute
ACO2CO2Atmosphere
ALKWalkalinity
ALKYalkalinityTotal
ALP0apha0
ALTBaltimeter
ALTSaltitude
AMONammonium
ATMPpressureAtmosphere
ATMSpressureAtmosphereSealevel
ATRKalongTrackDisplacement
ATTUattenuation
AUTHauthority
BATHbarometricDepth
BATTbatteryVoltage
BEAMa
BNO7bestNODC7NumberThat is an "oh" letter, not a zero
CALKcarbonateAlkalinity
CHLRchlorinity
CHLSchlorosity
CNDCconductivity
CNTRscan
CONDconductivity
CORGcarbonOrganic
CPHLchlorophyll
CRATconductivityConductivity ratio (may have spurious unit)
CMNTcomment
CNDCconductivity
CONDconductivity
CTOTcarbonTotal
DCHGdischarge
DENSdensity
DEPHpressure
DEWTtemperatureDewpoint
DOC_carbonOrganicDissolved
DON_nitrogenOrganicDissolved
DOXYoxygen
DPDTdpdt
DRDPdrogueDepth
DPWTdryWeight
DRYTtemperatureDryBulb
DYNHdynamicHeight
ERRVerrorVelocity
EWCMuMagnetic
EWCTu
FFFFoverall(FFFF)Archaic overall flag, replaced by QCFF
FLORfluorometer
GDIRwindDirectionGust
GEOPgeopotential
GSPDwindSpeedGust
HCDMdirectionMagnetic
HCDTdirectionTrue
HCSPspeedHorizontal
HEADheading
HSULhydrogenSulphide
IDENsampleNumber
LABTtemperatureLaboratory
LATDlatitude
LHISlifeHistory
LONDlongitude
LPHTpHLaboratory
MNSVretentionFilterSize
MNSZorganismSizeMinimum
MODFadditionalTaxonomicInformation
MXSZorganismSizeMaximum
NETRnetSolarRadiation
NONEnoWMOcode
NORGnitrogenOrganic
NSCMvMagnetic
NSCTv
NTOTnitrogenTotal
NTRAnitrate
NTRInitrite
NTRZnitrite+nitrate
NUM_scansPerAverage
OBKSturbidity
OCURoxygenCurrent
OPPRoxygenPartialPressure
OSAToxygenSaturation
OTMPoxygenTemperature
OXYGoxygenDissolved
OXYMoxygenDissolved
OXYVoxygenVoltage
OXV_oxygenVoltageRaw
PCO2CO2
PHA_phaeopigment
PHOSphosphate
PHPHpH
PHT_pHTotal
PIM_particulateInorganicMatter
PHY_phytoplanktonCount
POC_particulateOrganicCarbon
POM_particulateOrganicMatter
PON_particulateOrganicNitrogen
POTMtheta
PRESpressure
PSALsalinity
PSARPSAR
PTCHpitch
QCFFoverall(QCFF)Overall flag (see also archaic FFFF)
RANGrange
REFRreference
RELHhumidityRelative
RELPrelativeTotalPressure
ROLLroll
SDEVstandardDeviation
SECCSecchiDepth
SEX_sex
SIG0sigma0
SIGPsigmaTheta
SIGTsigmat
SLCAsilicate
SNCNscanCounter
SPARSPAR
SPEHhumiditySpecific
SPFRsampleFraction
SPVOspecificVolume
SPVAspecificVolumeAnomaly
STRAstressAmplitude
STRDstressDirection
STRUstressU
STRVstressV
SSALsalinity
SVELsoundVelocity
SYTMtime
TAXNtaxonomicName
TE90temperature
TEMPtemperature
TEXZTtext
TICWtotalInorganicCarbon
TILTtilt
TOTPpressureAbsolute
TPHSphosphorousTotal
TRANlightTransmission
TRB_turbidity
TRBHtrophicDescriptor
TSM_suspendedMatterTotal
TSN_taxonomicSerialNumber
TURBturbidity
UNKN-
UREAurea
VAISBVFrequency
VCSPw
VMXLwaveHeightMaximum
VRMSwaveHeightMean
VTCAwavePeriod
WDIRwindDirection
WETTtemperatureWetBulb
WSPDwindSpeed
WTWTwetWeight
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.

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

Run this code
ODFNames2oceNames("TEMP_01")$names # "temperature"

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