ODFNames2oceNames: Translate from ODF Names to Oce Names

Description

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

Usage

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.

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), with a warning.

Consistency warning

There are disagreements on variable names. For example, the ``DFO Common Data Dictionary'' [1] has unit millmole/m^3 for NODC and MEDS, but it has unit mL/L for BIO and IML.

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.

References

1. The Department of Fisheries and Oceans Common Data Dictionary may be available at http://www.isdm.gc.ca/isdm-gdsi/diction/code_search-eng.asp?code=DOXY) although that link seems to be unreliable. As of September 2017, the link https://slgo.ca/app-sgdo/en/docs_reference/format_odf.html seems to be a good place to start.