argoNames2oceNames: Convert Argo Data Name to Oce Name

Description Usage Arguments Details Value References See Also

View source: R/argo.R

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

1
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 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.

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/ 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(), subset,argo-method, summary,argo-method


dankelley/oce documentation built on April 8, 2021, 3:47 a.m.