cnvName2oceName {oce}R Documentation

Infer variable name, units and scale from a Seabird (.cnv) header line

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 correspondances, 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 to be decoded are as follows.

# 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 [1]. The .cnv convention for multiple sensors is to include optional extra digits in the name, and these are indicated with ~ 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 [1], plus names not listed there but present in data files supplied by prominent archiving agencies. If an SBE name is not recogized, 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 renameData 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
alt altimeter m
altM altimeter m
accM acceleration m/s^2
bat~ beamAttenuation 1/m
C2-C1S/m conductivityDifference S/m
C2-C1mS/cm conductivityDifference mS/cm
C2-C1uS/cm conductivityDifference uS/cm
c~mS/cm conductivity mS/cm
c~S/m conductivity S/m
c~uS/cm conductivity uS/cm
CStarAt~ beamAttenuation 1/m
CStarTr~ beamTransmission percent
density~~ density kg/m^3
depS depth m
depSM depth m
depF depth m
depFM depth m
dz/dtM descentRate m/s
f~ frequency Hz
f~~ frequency Hz
flC~ fluorescence ug/l; Chelsea Aqua 3
flCM fluorescence ug/l; Chelsea Mini Chl Con
flCUVA~ fluorescence ug/l; Chelsea UV Aquatracka
flEC-AFL~ fluorescence mg/m^3; WET Labs ECO-AFL/FLtab
flS fluorescence -; Seatech
flSP fluorescence -; Seapoint
flSPR fluorescence -; Seapoint, Rhodamine
flSPuv fluorescence -; Seapoint, UV
flT fluorescence -; Turneri 10-005 flT
gpa geopotentialAnomaly -; J/kg
latitude latitude degN
longitude longitude degE
n2satML/L nitrogenSaturation ml/l
n2satMg/L nitrogenSaturation mg/l
n2satumol/kg nitrogenSaturation umol/kg
nbin nbin
opoxMg/L oxygen mg/l; Optode, Anderaa
opoxML/L oxygen ml/l; Optode, Anderaa
opoxMm/L oxygen umol/l; Optode, Anderaa
opoxPS oxygen percent; Optode, Anderaa
oxsatML/L oxygen ml/l; Weiss
oxsatMg/L oxygen mg/l; Weiss
oxsatMm/Kg oxygen umol/kg; Weiss
oxsolML/L oxygen ml/l; Garcia-Gordon
oxsolMg/L oxygen mg/l; Garcia-Gordon
oxsolMm/Kg oxygen umol/kg; Garcia-Gordon
par~ PAR -; Biospherical/Licor
par/log PAR log; Satlantic
ph pH -
potemp~68C thetaM degC; IPTS-68
potemp~90C thetaM degC; ITS-90
pr pressure dbar 1
prM pressure dbar
pr50M pressure dbar; SBE50
prSM pressure dbar
prDM pressure dbar; digiquartz
prdE pressure psi; strain gauge 2
prDE pressure psi; digiquartz 2
prdM pressure dbar; strain gauge
prSM pressure dbar; strain gauge
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
scan scan -
seaTurbMtr~ turbidity FTU; SeaPoint
secS-priS salinityDifference -, PSS-78
sigma-t sigmaT kg/m^3
sigma-theta sigmaTheta kg/m^3 5
sigma-é sigmaTheta kg/m^3 5
spar spar -
specc conductivity uS/cm
sva specificVolumeAnomaly 1e-8 m^3/kg;
svCM~ soundSpeed m/s; Chen-Millero
T2~68C temperatureDifference degC; IPTS-68
T2~90C temperatureDifference degC; ITS-90
t~68 temperature degC; IPTS-68
t~90 temperature degC; ITS-90
t~68C temperature degC; IPTS-68
t~90C temperature degC; ITS-90
t090Cm temperature degC; ITS-90
t4990C temperature degC; ITS-90
tnc90C temperature degC; ITS-90
tsa thermostericAnomaly 1e-8 m^3/kg
tv290C temperature degC; ITS-90
t4968C temperature degC; IPTS-68
tnc68C temperature degC; IPTS-68
tv268C temperature degC; IPTS-68
t190C temperature degC; ITS-90
tnc290C temperature degC; ITS-90
tnc268C temperature degC; IPTS-68
t3890C~ temperature degC; ITS-90
t38~90C temperature degC; ITS-90
t3868C~ temperature degC; IPTS-68
t38~38C temperature degC; IPTS-68
timeH time hour; elapsed
timeJ time day; elapsed
timeK time s; since Jan 1, 2000
timeM time minute; elapsed
timeN time s; NMEA since Jan 1, 1970
timeQ time s; NMEA since Jan 1, 2000
timeS time s; elapsed
turbflTC~ turbidity NTU; Turner Cyclops
turbflTCdiff turbidityDifference NTU; Turner Cyclops
turbWETbb~ turbidity 1/(m*sr); WET Labs ECO
turbWETbbdiff turbidityDifference 1/(m*sr); WET Labs ECO
turbWETntu~ turbidity NTU; WET Labs ECO
turbWETntudiff turbidityDifference NTU; WET Labs ECO
upoly~ upoly -
user~ user -
v~~ voltage V
wetBAttn beamAttenuation 1/m; WET Labs AC3
wetBTrans beamTransmission percent; WET Labs AC3
wetCDOM~ fluorescence mg/m^3; WET Labs CDOM
wetCDOMdiff fluorescenceDifference mg/m^3; WET Labs CDOM
wetChAbs fluorescence 1/m; WET Labs AC3 absorption
wetStar~ fluorescence mg/m^3; WET Labs WETstar
wetStardiff fluorescenceDifference mg/m^3; WET Labs WETstar
xmiss beamTransmission percent; Chelsea/Seatech
xmiss~ beamTransmission percent; Chelsea/Seatech

Notes:

Value

a list containing name (the oce name), nameOriginal (the SBE name) and unit.

Author(s)

Dan Kelley

References

1. A SBE data processing manual is at http://www.seabird.com/document/sbe-data-processing-manual.

See Also

Other things related to ctd data: [[,ctd-method, [[<-,ctd-method, as.ctd, ctd-class, ctdDecimate, ctdFindProfiles, ctdRaw, ctdTrim, ctd, handleFlags,ctd-method, oceNames2whpNames, oceUnits2whpUnits, plot,ctd-method, plotProfile, plotScan, plotTS, read.ctd.itp, read.ctd.odf, read.ctd.sbe, read.ctd.woce.other, read.ctd.woce, read.ctd, subset,ctd-method, summary,ctd-method, woceNames2oceNames, woceUnit2oceUnit, write.ctd

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


[Package oce version 0.9-22 Index]