This function is used internally by read.argo()
to convert Argo-convention
data names to oce-convention names. Users should not call this directly, since
its return value may be changed at any moment (e.g. to include units as well
as names).
argoNames2oceNames(names, ignore.case = TRUE)
A character vector of the same length as names
, but with
replacements having been made for all known quantities.
vector of character strings containing names in the Argo convention.
a logical value passed to gsub()
, indicating whether to
ignore the case of input strings. The default is set to TRUE
because some data
files use lower-case names, despite the fact that the Argo documentation specifies
upper-case.
Dan Kelley, with help from Anna Victor
Initially, Feb 2016, the inference of names was initially done
by an inspection of some data files, based on reference 1. Later, in June
2023, broader inspection of more files and documents yielded about ten
additions, and a single correction: VRSpH
was renamed
phSensorVoltageDifference
, to match related names that had been added.
It should be noted that the data files examined contain some names that are not documented in reference 1, and others that are listed only in its changelog, with no actual definitions being given. For example, the files had six distinct variable names that seem to relate to phase in the oxygen sensor, but these are not translated by the present function because these variable names are not defined in reference 1, or not defined uniquely in reference 2.
The names are converted with
gsub()
, using the ignore.case
argument of the present
function.
The procedure
is to first handle the items listed in the following table, with string
searches anchored to the start of the string. After that,
the qualifiers
_ADJUSTED
, _ERROR
and _QC
,
are translated to Adjusted
, Error
, and QC
, respectively.
An incomplete list of name translations is as follows, where ~
represents digit sequences in some instances and letters
in others. Note that until June 2023, pHSensorVoltageDifference
was called VRSpH
.
Argo name | oce name |
BBP | bbp |
BETA_BACKSCATTERING | betaBackscattering |
BPHASE_OXY | bphaseOxygen |
C~PHASE_DOXY | C~phaseOxygen |
CDOM | CDOM |
CNDC | conductivity |
CHLA | chlorophyllA |
CP | beamAttenuation |
CYCLE_NUMBER | cycleNumber (both this and cycle are handled by the [[ operator) |
DATA_CENTRE | dataCentre |
DATA_MODE | dataMode |
DATA_STATE_INDICATOR | dataStateIndicator |
DC_REFERENCE | DCReference |
DIRECTION | direction |
DOWN_IRRADIANCE | downwellingIrradiance |
DOWNWELLING_PAR | downwellingPAR |
FIRMWARE_VERSION | firmwareVersion |
FIT_ERROR_NITRATE | fitErrorNitrate |
FLUORESCENCE_CDOM | fluorescenceCDOM |
FLUORESCENCE_CHLA | fluorescenceChlorophyllA |
IB_PH | pHBaseCurrent |
IK_PH | pHCounterCurrent |
INST_REFERENCE | instReference |
JULD | juld (and used to compute time ) |
JULD_QC_LOCATION | juldQCLocation |
LATITUDE | latitude |
LONGITUDE | longitude |
MOLAR_DOXY | oxygenUncompensated |
MTIME | mtime |
NB_SAMPLE_CTD | nbSampleCtd |
PH_IN_SITU_FREE | pHFree |
PH_IN_SITU_TOTAL | pH |
PI_NAME | PIName |
PLATFORM_NUMBER | id |
POSITION_ACCURACY | positionAccuracy |
POSITIONING_SYSTEM | positioningSystem |
PROFILE | profile |
PROJECT_NAME | projectName |
RAW_DOWNWELLING_IRRADIANCE | rawDownwellingIrradiance |
RAW_DOWNWELLING_PAR | rawDownwellingPAR |
RAW_UPWELLING_RADIANCE | rawUpwellingRadiance |
STATION_PARAMETERS | stationParameters |
TEMP | temperature |
TEMP_CPU_CHLA | temperatureCPUChlorophyllA |
TEMP_DOXY | temperatureOxygen |
TEMP_NITRATE | temperatureNitrate |
TEMP_PH | temperaturePH |
TEMP_SPECTROPHOTOMETER_NITRATE | temperatureSpectrophotometerNitrate |
TILT | tilt |
TPHASE_DOXY | tphaseOxygen |
TURBIDITY | turbidity |
UP_RADIANCE | upwellingRadiance |
UV_INTENSITY | UVIntensity |
UV_INTENSITY_DARK_NITRATE | UVIntensityDarkNitrate |
UV_INTENSITY_NITRATE | UVIntensityNitrate |
VRS_PH | pHSensorVoltageDifference |
WMO_INST_TYPE | WMOInstType |
Argo User's Manual Version 3.3, Nov 89th, 2019, available at
https://archimer.ifremer.fr/doc/00187/29825/
online.
Argo list of parameters in an excel spreadsheet, available at
http://www.argodatamgt.org/content/download/27444/187206/file/argo-parameters-list-core-and-b.xlsx
Other things related to argo data:
[[,argo-method
,
[[<-,argo-method
,
argo
,
argo-class
,
argoGrid()
,
as.argo()
,
handleFlags,argo-method
,
plot,argo-method
,
read.argo()
,
read.argo.copernicus()
,
subset,argo-method
,
summary,argo-method