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

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

Value

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

Author(s)

Dan Kelley, with help from Anna Victor

References

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

  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.copernicus(), read.argo(), subset,argo-method, summary,argo-method


[Package oce version 1.8-2 Index]