argoNames2oceNames: Convert Argo Data Name to Oce Name

Description

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).

Usage

argoNames2oceNames(names, ignore.case = TRUE)

Value

A character vector of the same length as names, but with replacements having been made for all known quantities.

Arguments

names: vector of character strings containing names in the Argo convention.
ignore.case: 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.

Author

Dan Kelley, with help from Anna Victor

Details

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`

References

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