ODFNames2oceNames: Translate from ODF Names to Oce Names

Description Usage Arguments Details Value A note on unit conventions Consistency warning Author(s) References See Also

View source: R/odf.R

Description

Translate data names in the ODF convention to similar names in the Oce convention.

Usage

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ODFNames2oceNames(
  ODFnames,
  ODFunits = NULL,
  columns = NULL,
  PARAMETER_HEADER = NULL,
  debug = getOption("oceDebug")
)

Arguments

ODFnames

Vector of strings holding ODF names.

ODFunits

Vector of strings holding ODF units.

columns

Optional list containing name correspondances, as described for read.ctd.odf().

PARAMETER_HEADER

Optional list containing information on the data variables.

debug

an integer specifying whether debugging information is to be printed during the processing. This is a general parameter that is used by many oce functions. Generally, setting debug=0 turns off the printing, while higher values suggest that more information be printed. If one function calls another, it usually reduces the value of debug first, so that a user can often obtain deeper debugging by specifying higher debug values.

Details

The following table gives the regular expressions that define recognized ODF names, along with the translated names as used in oce objects. If an item is repeated, then the second one has a 2 appended at the end, etc. Note that quality-control columns (with names starting with "QQQQ") are not handled with regular expressions. Instead, if such a flag is found in the i-th column, then a name is constructed by taking the name of the (i-1)-th column and appending "Flag".

Regexp Result Notes
ALTB_*.* altimeter
ATTU_*.* attenuation
BATH_*.* barometricDepth Barometric depth (of sensor? of water column?)
BEAM_*.* a Used in adp objects
CNTR_*.* scan Used in ctd objects
CRAT_*.* conductivity Conductivity ratio
COND_*.* conductivity Conductivity in mS/cm or S/m (unit detected)
CNDC_*.* conductivity Conductivity in mS/cm or S/m (unit detected)
DCHG_*.* discharge
DEPH_*.* pressure Sensor depth below sea level
DOXY_*.* oxygen Used mainly in ctd objects
ERRV_*.* error Used in adp objects
EWCT_*.* u Used in adp and cm objects
FFFF_*.* flagArchaic Old flag name, replaced by QCFF
FLOR_*.* fluorometer Used mainly in ctd objects
FWETLABS fwetlabs Used in ??
GEOP geopotential
HCDM directionMagnetic
HCDT directionTrue
HCSP speedHorizontal
LATD_*.* latitude
LOND_*.* longitude
NSCT_*.* v Used in adp objects
NONE_*.* noWMOcode
OCUR_*.* oxygenCurrent Used mainly in ctd objects
OSAT_*.* oxygenSaturation Used mainly in ctd objects
OTMP_*.* oxygenTemperature Used mainly in ctd objects
OXYV_*.* oxygenVoltage Used mainly in ctd objects
PHPH_*.* pH
POTM_*.* theta Used mainly in ctd objects
PRES_*.* pressure Used mainly in ctd objects
PSAL_*.* salinity Used mainly in ctd objects
PSAR_*.* par Used mainly in ctd objects
QCFF_*.* flag Overall flag
REFR_*.* reference
SIGP_*.* sigmaTheta Used mainly in ctd objects
SIGT_*.* sigmat Used mainly in ctd objects
SNCN_*.* scanCounter Used mainly in ctd objects
SPAR_*.* SPAR
SPVA_*.* specificVolumeAnomaly
SYTM_*.* time Used in many objects
TE90_*.* temperature Used mainly in ctd objects
TEMP_*.* temperature Used mainly in ctd objects
TOTP_*.* pressureAbsolute Used mainly in ctd objects
UNKN_*.* - The result is context-dependent
VAIS_*.* BVFrequency
VCSP_*.* w Used in adp objects

Any code not shown in the list is transferred to the oce object without renaming, apart from the adjustment of suffix numbers. The following code have been seen in data files from the Bedford Institute of Oceanography: ALTB, PHPH and QCFF.

Value

A vector of strings.

A note on unit conventions

Some older ODF files contain non-standard units for conductivity, including mho/m, mmho/cm, and mmHo. As the units for conductivity are important for derived quantities (e.g. salinity), such units are converted to standard units (e.g. S/m and mS/cm). (This was once done with a warning, but on 2020-02-07 the warning was removed, since it did not indicate a problem with the file or the data scanning; rather, it was a simple matter of nudging towards uniformity in a way that ought to confuse no users, akin to converting m**3 to m^3, which is also done here without warning.)

Consistency warning

There are disagreements on variable names. For example, the “DFO Common Data Dictionary” (reference 1) has unit millimole/m^3 for NODC and MEDS, but it has unit mL/L for BIO and IML.

Author(s)

Dan Kelley

References

For sources that describe the ODF format, see the documentation for the odf.

See Also

Other functions that interpret variable names and units from headers: cnvName2oceName(), oceNames2whpNames(), oceUnits2whpUnits(), unitFromStringRsk(), unitFromString(), woceNames2oceNames(), woceUnit2oceUnit()

Other things related to odf data: CTD_BCD2014666_008_1_DN.ODF.gz, ODF2oce(), ODFListFromHeader(), [[,odf-method, [[<-,odf-method, odf-class, plot,odf-method, read.ctd.odf(), read.odf(), subset,odf-method, summary,odf-method


oce documentation built on March 28, 2021, 9:09 a.m.