cnvName2oceName: Infer Variable Name, Units and Scale From a Seabird Header

In oce: Analysis of Oceanographic Data

Infer Variable Name, Units and Scale From a Seabird Header

Description

This function is used by read.ctd.sbe() to infer data names and units from the coding used by Teledyne/Seabird (SBE) .cnv files. Lacking access to documentation on the SBE format, the present function is based on inspection of a suite of CNV files available to the oce developers.

Usage

cnvName2oceName(h, columns = NULL, debug = getOption("oceDebug"))

Arguments

h	The header line.
columns	Optional list containing name correspondences, as described for read.ctd.sbe().
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

A few sample header lines that have been encountered are:

# name 4 = t068: temperature, IPTS-68 [deg C]
# name 3 = t090C: Temperature [ITS-90, deg C]
# name 4 = t190C: Temperature, 2 [ITS-90, deg C]

Examination of several CNV files suggests that it is best to try to infer the name from the characters between the "=" and ":" characters, because the material after the colon seems to vary more between sample files.

The table given below indicates the translation patterns used. These are taken from reference 1. The .cnv convention for multiple sensors is to include optional extra digits in the name, and these are indicated with ~ or ⁠~~⁠ in the table; their decoding is done with grep().

It is important to note that this table is by no means complete, since there are a great many SBE names listed in their document (reference 1), plus names not listed there but present in data files supplied by prominent archiving agencies. If an SBE name is not recognized, then the oce name is set to that SBE name. This can cause problems in some other processing steps (e.g. if swRho() or a similar function is called with an oce object as first argument), and so users are well-advised to rename the items as appropriate. The first step in doing this is to pass the object to summary(), to discover the SBE names in question. Then consult the SBE documentation to find an appropriate name for the data, and either manipulate the names in the object data slot directly or use oceRenameData() to rename the elements. Finally, please publish an 'issue' on the oce Github site ⁠https://github.com/dankelley/oce/issues⁠ so that the developers can add the data type in question. (To save development time, there is no plan to add all possible data types without a reasonable and specific expression user interest. Oxygen alone has over forty variants.)

Key	Result	Unit;scale	Notes
accM	acceleration	m/s^2
altM	altimeter	m
alt	altimeter	m
⁠bat~⁠	beamAttenuation	1/m
C2-C1mS/cm	conductivityDifference	mS/cm
C2-C1S/m	conductivityDifference	S/m
C2-C1uS/cm	conductivityDifference	uS/cm
cond~mS/cm	conductivity	mS/cm
cond~S/m	conductivity	S/m
cond~uS/cm	conductivity	uS/cm
⁠CStarAt~⁠	beamAttenuation	1/m
⁠CStarTr~⁠	beamTransmission	percent
c~mS/cm	conductivity	mS/cm
c~S/m	conductivity	S/m
c~uS/cm	conductivity	uS/cm
⁠density~~⁠	density	kg/m^3
depFM	depth	m
depF	depth	m
depSM	depth	m
depS	depth	m
dz/dtM	descentRate	m/s
flCM	fluorescence	ug/l; Chelsea Mini Chl Con
⁠flCUVA~⁠	fluorescence	ug/l; Chelsea UV Aquatracka
⁠flC~⁠	fluorescence	ug/l; Chelsea Aqua 3
⁠flEC-AFL~⁠	fluorescence	mg/m^3; WET Labs ECO-AFL/FLtab
⁠flScufa~⁠	fluorescence	-; Turner SCUFA (RFU)
flSPR	fluorescence	-; Seapoint, Rhodamine
flSPuv	fluorescence	-; Seapoint, UV
flSP	fluorescence	-; Seapoint
flS	fluorescence	-; Seatech
flT	fluorescence	-; Turner 10-005 flT
⁠f~⁠	frequency	Hz
⁠f~~⁠	frequency	Hz
gpa	geopotentialAnomaly	-; J/kg
latitude	latitude	degN
longitude	longitude	degE
n2satMg/L	nitrogenSaturation	mg/l
n2satML/L	nitrogenSaturation	ml/l
n2satumol/kg	nitrogenSaturation	umol/kg
nbin	nbin
⁠obsscufa~⁠	backscatter	NTU; Turner SCUFA
opoxMg/L	oxygen	mg/l; Optode, Aanderaa
opoxML/L	oxygen	ml/l; Optode, Aanderaa
opoxMm/L	oxygen	umol/l; Optode, Aanderaa
opoxPS	oxygen	percent; Optode, Aanderaa
oxsatMg/L	oxygen	mg/l; Weiss
oxsatML/L	oxygen	ml/l; Weiss
oxsatMm/Kg	oxygen	umol/kg; Weiss
oxsolMg/L	oxygen	mg/l; Garcia-Gordon
oxsolML/L	oxygen	ml/l; Garcia-Gordon
oxsolMm/Kg	oxygen	umol/kg; Garcia-Gordon
par/log	PAR	log; Satlantic
⁠par~⁠	PAR	-; Biospherical/Licor
ph	pH	-
⁠potemp~68C⁠	thetaM	degC; IPTS-68
⁠potemp~90C⁠	thetaM	degC; ITS-90
pr50M	pressure	dbar; SBE50
prDE	pressure	psi; digiquartz	2
prdE	pressure	psi; strain gauge	2
prDM	pressure	dbar; digiquartz
prdM	pressure	dbar; strain gauge
prM	pressure	dbar
prSM	pressure	dbar
prSM	pressure	dbar; strain gauge
pr	pressure	dbar	1
ptempC	pressureTemperature	degC; ITS-90	3
pumps	pumpStatus
⁠rhodflTC~⁠	Rhodamine	ppb; Turner Cyclops
⁠sal~~⁠	salinity	-, PSS-78	4
sbeox~ML/L	oxygen	ml/l; SBE43
sbeox~Mm/Kg	oxygen	umol/kg; SBE43
sbeox~Mm/L	oxygen	umol/l; SBE43
sbeox~PS	oxygen	percent; SBE43
sbeox~V	oxygenRaw	V; SBE43
sbox~dV/dT	oxygen	dov/dt; SBE43
sbox~ML/L	oxygen	ml/l; SBE43
sbox~Mm/Kg	oxygen	umol/kg; SBE43
sbox~Mm/L	oxygen	umol/l; SBE43
sbox~PS	oxygen	percent; SBE43
sbox~V	oxygenRaw	V; SBE43
scan	scan	-
⁠seaTurbMtr~⁠	turbidity	FTU; Seapoint
secS-priS	salinityDifference	-, PSS-78
sigma-é	sigmaTheta	kg/m^3	5
sigma-t	sigmaT	kg/m^3
sigma-theta	sigmaTheta	kg/m^3	5
spar	spar	-
specc	specificConductance	uS/cm
sva	specificVolumeAnomaly	1e-8 m^3/kg;
⁠svCM~⁠	soundSpeed	m/s; Chen-Millero
t090Cm	temperature	degC; ITS-90
t190C	temperature	degC; ITS-90
⁠T2~68C⁠	temperatureDifference	degC; IPTS-68
⁠T2~90C⁠	temperatureDifference	degC; ITS-90
⁠t3868C~⁠	temperature	degC; IPTS-68
⁠t3890C~⁠	temperature	degC; ITS-90
⁠t38~38C⁠	temperature	degC; IPTS-68
⁠t38~90C⁠	temperature	degC; ITS-90
t4968C	temperature	degC; IPTS-68
t4990C	temperature	degC; ITS-90
timeH	timeH	hour; elapsed
timeJV2	timeJV2	julian day
timeJ	timeJ	julian day
timeK	timeK	s; since Jan 1, 2000
timeM	timeM	minute; elapsed
timeN	timeN	s; NMEA since Jan 1, 1970
timeQ	timeQ	s; NMEA since Jan 1, 2000
timeS	timeS	s; elapsed
tnc268C	temperature	degC; IPTS-68
tnc290C	temperature	degC; ITS-90
tnc68C	temperature	degC; IPTS-68
tnc90C	temperature	degC; ITS-90
tsa	thermostericAnomaly	1e-8 m^3/kg
turbflTCdiff	turbidityDifference	NTU; Turner Cyclops
⁠turbflTC~⁠	turbidity	NTU; Turner Cyclops
turbWETbbdiff	turbidityDifference	1/(m\*sr); WET Labs ECO
⁠turbWETbb~⁠	turbidity	1/(m\*sr); WET Labs ECO
turbWETntudiff	turbidityDifference	NTU; WET Labs ECO
⁠turbWETntu~⁠	turbidity	NTU; WET Labs ECO
tv268C	temperature	degC; IPTS-68
tv290C	temperature	degC; ITS-90
⁠t~68C⁠	temperature	degC; IPTS-68
t~68	temperature	degC; IPTS-68
⁠t~90C⁠	temperature	degC; ITS-90
t~90	temperature	degC; ITS-90
⁠upoly~⁠	upoly	-
⁠user~⁠	user	-
⁠v~~⁠	voltage	V
wetBAttn	beamAttenuation	1/m; WET Labs AC3
wetBTrans	beamTransmission	percent; WET Labs AC3
wetCDOMdiff	fluorescenceDifference	mg/m^3; WET Labs CDOM
⁠wetCDOM~⁠	fluorescence	mg/m^3; WET Labs CDOM
wetChAbs	fluorescence	1/m; WET Labs AC3 absorption
wetStardiff	fluorescenceDifference	mg/m^3; WET Labs WETstar
⁠wetStar~⁠	fluorescence	mg/m^3; WET Labs WETstar
xmiss	beamTransmission	percent; Chelsea/Seatech
⁠xmiss~⁠	beamTransmission	percent; Chelsea/Seatech

Notes:

1. 'pr' is in a Dalhousie-generated data file but seems not to be in reference 1.

2. This is an odd unit, and so if ⁠sw*⁠ functions are called on an object containing this, a conversion will be made before performing the computation. Be on the lookout for errors, since this is a rare situation.

3. Assume ITS-90 temperature scale, since sample .cnv file headers do not specify it.

4. Some files have PSU for this. Should we handle that? And are there other S scales to consider?

5. The 'theta' symbol (here shown accented e) may appear in different ways with different encoding configurations, set up within R or in the operating system.

Author(s)

Dan Kelley

References

1. A SBE data processing manual was once at ⁠http://www.seabird.com/document/sbe-data-processing-manual⁠, but as of summer 2018, this no longer seems to be provided by SeaBird. A web search will turn up copies of the manual that have been put online by various research groups and data-archiving agencies. As of 2018-07-05, the latest version was named SBEDataProcessing_7.26.4.pdf and had release date 12/08/2017, and this was the reference version used in coding oce.

See Also

Other things related to ctd data: CTD_BCD2014666_008_1_DN.ODF.gz, [[,ctd-method, [[<-,ctd-method, as.ctd(), ctd, ctd-class, ctd.cnv.gz, ctdDecimate(), ctdFindProfiles(), ctdFindProfilesRBR(), ctdRaw, ctdRepair(), ctdTrim(), ctd_aml.csv.gz, d200321-001.ctd.gz, d201211_0011.cnv.gz, handleFlags,ctd-method, initialize,ctd-method, initializeFlagScheme,ctd-method, oceNames2whpNames(), oceUnits2whpUnits(), plot,ctd-method, plotProfile(), plotScan(), plotTS(), read.ctd(), read.ctd.aml(), read.ctd.itp(), read.ctd.odf(), read.ctd.odv(), read.ctd.saiv(), read.ctd.sbe(), read.ctd.ssda(), read.ctd.woce(), read.ctd.woce.other(), setFlags,ctd-method, subset,ctd-method, summary,ctd-method, woceNames2oceNames(), woceUnit2oceUnit(), write.ctd()

Other functions that interpret variable names and units from headers: ODFNames2oceNames(), oceNames2whpNames(), oceUnits2whpUnits(), unitFromString(), unitFromStringRsk(), woceNames2oceNames(), woceUnit2oceUnit()

oce documentation built on Sept. 11, 2024, 7:09 p.m.