R: Convert Argo Data Name to Oce Name

argoNames2oceNames {oce} | R Documentation

## 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.

### Details

The inference of names was done by inspection of some data files, based on reference 1. It should be noted, however, that the data files examined contain some names that are not undocumented 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.

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`

### Value

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

### References

1. Argo User's Manual Version 3.3, Nov 89th, 2019, available at https://archimer.ifremer.fr/doc/00187/29825/

2. 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

### See Also

Other things related to argo data: `[[,argo-method`, `[[<-,argo-method`, `argo-class`, `argoGrid()`, `argo`, `as.argo()`, `handleFlags,argo-method`, `plot,argo-method`, `read.argo()`, `subset,argo-method`, `summary,argo-method`

[Package oce version 1.2-0 Index]