oce (version 0.9-18)

as.ctd: Coerce data into ctd dataset

Description

Coerces a dataset into a ctd dataset.

Usage

as.ctd(salinity, temperature=NULL, pressure=NULL, conductivity=NULL,
       SA=NULL, CT=NULL, oxygen=NULL,
       nitrate=NULL, nitrite=NULL, phosphate=NULL, silicate=NULL,
       scan=NULL, time=NULL, other=NULL,
       units=NULL, pressureType="sea",
       missingValue=NA, quality=NULL, 
       filename="", type="", model="", serialNumber="",
       ship="", scientist="", institute="", address="", cruise="", station="", 
       date="", startTime="", recovery="",
       longitude=NA, latitude=NA,
       deploymentType="unknown",
       pressureAtmospheric=0, waterDepth=NA,
       sampleInterval=NA, src="",
       debug=getOption("oceDebug"))

Arguments

salinity

There are two choices for salinity. First, it can be a vector indicating the practical salinity through the water column. In that case, as.ctd employs the other arguments listed below. The second choice is that

temperature

in-situ temperature [$^\circ$C], defined on the ITS-90 scale; see Temperature units in the documentation for swRho.

pressure

pressure through the water column. If only one value is given, then it is repeated to match the length of the temperature vector.

conductivity

electrical conductivity ratio through the water column (optional). To convert from raw conductivity in milliSeimens per centimeter divide by 42.914 to get conductivity ratio (see Culkin and Smith, 1980).

SA

absolute salinity (as in TEOS-10). If given, the supplied absolute salinity is converted internally to UNESCO-defined practical salinity.

CT

conservative temperature (as in TEOS-10). If given, the supplied conservative temperature is converted internally to UNESCO-defined in-situ temperature.

oxygen

optional oxygen concentration

nitrate

optional nitrate concentration [micromole/kg]

nitrite

optional nitrite concentration [micromole/kg]

phosphate

optional phosphate concentration [micromole/kg]

silicate

optional silicate concentration [micromole/kg]

scan

optional scan number. If not provided, this will be set to 1:length(salinity).

time

optional vector of times of observation

other

optional list of other data columns that are not in the standard list

units

an optional list containing units. If not supplied, a default of list(temperature=list(unit=expression(degree*C), scale="ITS-90"), salinity=list(unit=expression(ratio), scale="", pressure=list(unit=expression(dbar), scale="")

pressureType

a character string indicating the type of pressure; may be "absolute", for total pressure, i.e. the sum of atmospheric pressure and sea pressure, or "sea".

missingValue

optional missing value, indicating data that should be taken as NA.

quality

quality flag, e.g. from the salinity quality flag in WOCE data. (In WOCE, quality=2 indicates good data, quality=3 means questionable data, and quality=4 means bad data.

filename

filename to be stored in the object

type

type of CTD, e.g. "SBE"

model

model of instrument

serialNumber

serial number of instrument

ship

optional string containing the ship from which the observations were made.

scientist

optional string containing the chief scientist on the cruise.

institute

optional string containing the institute behind the work.

address

optional string containing the address of the institute.

cruise

optional string containing a cruise identifier.

station

optional string containing a station identifier.

date

optional string containing the date at which the profile was started.

startTime

optional string containing the start time.

recovery

optional string indicating the recovery time.

longitude

optional numerical value containing longitude in decimal degrees, positive in the eastern hemisphere. If this is a single number, then it is stored in the metadata slot of the returned value; if it is a vector of numbers, they are

latitude

optional numerical value containing the latitude in decimal degrees, positive in the northern hemisphere. See the note on length, for the longitude argument.

deploymentType

character string indicating the type of deployment. Use "unknown" if this is not known, "profile" for a profile (in which the data were acquired during a downcast, while the device was lowered into the water column, p

pressureAtmospheric

if NA (the default), then pressure is copied from the pressure argument or from the contents of the first argument (as described above for salinity). Otherwise, if pressureAtmospheric is a nu

waterDepth

optional numerical value indicating the water depth in metres. This is different from the maximum recorded pressure, although the latter is used by some oce functions as a guess on water depth, the most important example being

sampleInterval

optional numerical value indicating the time between samples in the profile.

src

optional string indicating data source

debug

a flag that can be set to TRUE to turn on debugging.

Value

• An object of class "ctd" (for details, see read.ctd).

Details

If the first argument is an rsk-class object, the pressure it contains may need to be adjusted, because rsk objects may contain either absolute pressure or sea pressure. This adjustment is handled automatically by as.ctd, by examination of the metadata item named pressureType (described in the documentation for read.rsk). Once the sea pressure is determined, adjustments may be made with the pressureAtmospheric argument, although in that case it is better considered a pressure adjustment than the atmospheric pressure.

rsk-class objects may store sea pressure or absolute pressure (the sum of sea pressure and atmospheric pressure), depending on how the object was created with as.rsk or read.rsk. However, ctd-class objects store sea pressure, which is needed for plotting, calculating density, etc. This poses no difficulities, however, because as.ctd automatically converts absolute pressure to sea pressure, if the metadata in the rsk-class object indicates that this is appropriate. Further alteration of the pressure can be accomplished with the pressureAtmospheric argument, as noted above.

References

Culkin, F., and Norman D. Smith, 1980. Determination of the concentration of potassium chloride solution having the same electrical conductivity, at 15 C and infinite frequency, as standard seawater of salinity 35.0000 ppt (Chlorinity 19.37394 ppt). IEEE Journal of Oceanic Engineering, 5, pp 22-23.

See Also

The documentation for ctd-class explains the structure of CTD objects, and also outlines the other functions dealing with them.

Examples

library(oce)
pressure <- 1:50
temperature <- 10 - tanh((pressure - 20) / 5) + 0.02*rnorm(50)
salinity <- 34 + 0.5*tanh((pressure - 20) / 5) + 0.01*rnorm(50)
ctd <- as.ctd(salinity, temperature, pressure)
summary(ctd)
plot(ctd)