cnvName2oceName: Infer Variable Name, Units and Scale From a Seabird Header
In dankelley/oce: Analysis of Oceanographic Data
cnvName2oceName R Documentation
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:
'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.
Author(s)
Dan Kelley
References
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()
dankelley/oce documentation built on May 8, 2024, 10:46 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
| cnvName2oceName | R Documentation |
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
|
debug |
an integer specifying whether debugging information is
to be printed during the processing. This is a general parameter that
is used by many |
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:
'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
.cnvfile 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.
Author(s)
Dan Kelley
References
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 namedSBEDataProcessing_7.26.4.pdfand had release date 12/08/2017, and this was the reference version used in codingoce.
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()
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.