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.
cnvName2oceName(h, columns = NULL, debug = getOption("oceDebug"))
The header line.
Optional list containing name correspondences, as described for
read.ctd.sbe()
.
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.
Dan Kelley
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:
'pr' is in a Dalhousie-generated data file but seems not to be in reference 1.
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.
Assume ITS-90 temperature scale, since sample .cnv
file headers do not specify it.
Some files have PSU for this. Should we handle that? And are there other S scales to consider?
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.
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
.
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()