argoNames2oceNames: Convert Argo Data Name to Oce Name

In dankelley/oce: Analysis of Oceanographic Data

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, argo-class, argoGrid(), as.argo(), handleFlags,argo-method, plot,argo-method, read.argo(), read.argo.copernicus(), subset,argo-method, summary,argo-method

dankelley/oce documentation built on April 18, 2024, 9:51 a.m.