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)

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.

Value

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

Details

The inference of names was done by inspection of some data files, using [1] as a reference. It should be noted, however, that the data files examined contain some names that are not undocumented in [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 [1], or not defined uniquely in [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.

Argo name	oce name
`BBP`	`bbp`
`BETA_BACKSCATTERING`	`betaBackscattering`
`BPHASE_OXY`	`bphaseOxygen`
`CDOM`	`CDOM`
`CNDC`	`conductivity`
`CHLA`	`chlorophyllA`
`CP`	`beamAttenuation`
`CYCLE_NUMBER`	`cycleNumber`
`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`
`INST_REFERENCE`	`instReference`
`JULD`	`juld` (and used to compute `time`)
`JULD_QC_LOCATION`	`juldQCLocation`
`LATITUDE`	`latitude`
`LONGITUDE`	`longitude`
`MOLAR_DOXY`	`oxygenUncompensated`
`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`
`TURBIDITY`	`turbidity`
`UP_RADIANCE`	`upwellingRadiance`
`UV_INTENSITY`	`UVIntensity`
`UV_INTENSITY_DARK_NITRATE`	`UVIntensityDarkNitrate`
`UV_INTENSITY_NITRATE`	`UVIntensityNitrate`
`VRS_PH`	`VRSpH`
`WMO_INST_TYPE`	`WMOInstType`

References

1. Argo User's Manual Version 3.2, Dec 29th, 2015, available at https://archimer.ifremer.fr/doc/00187/29825/40575.pdf (but note that this is a draft; newer versions may have replaced this by now).

2. Argo list of parameters in an excel spreadsheet, available at https://www.argodatamgt.org/content/download/27444/187206/file/argo-parameters-list-core-and-b.xlsx (but note that the certificate at this website was noticed to be invalid on December 17, 2016, so exercise caution in downloading the file).