as.ctd: Coerce data into CTD object
In oce: Analysis of Oceanographic Data

Description Usage Arguments Value Converting rsk objects Author(s) References See Also Examples

Assemble data into a ctd-class dataset.

as.ctd(salinity, temperature = NULL, pressure = NULL,
  conductivity = NULL, scan = NULL, time = NULL, other = NULL,
  units = NULL, flags = NULL, missingValue = NULL, type = "",
  serialNumber = "", ship = NULL, cruise = NULL, station = NULL,
  startTime = NULL, longitude = NULL, latitude = NULL,
  deploymentType = "unknown", pressureAtmospheric = 0,
  sampleInterval = NA, profile = NULL, debug = getOption("oceDebug"))

`salinity`	There are several distinct choices for `salinity`. (1) It can be a vector indicating the practical salinity through the water column. In that case, `as.ctd` employs the other arguments listed below. (2) it can be something (a data frame, a list or an `oce` object) from which practical salinity, temperature, pressure, and conductivity can be inferred. In this case, the relevant information is extracted and the other arguments to `as.ctd` are ignored, except for `pressureAtmospheric`. If the first argument has salinity, etc., in matrix form (as can happen with some objects of `argo-class`), then only the first column is used, and a warning to that effect is given, unless the `profile` argument is specified and then that specific profile is extracted. (3) It can be an object of `rsk-class`, (see “Converting rsk objects” for details). (4) It can be unspecified, in which case `conductivity` becomes a mandatory argument, because it will be needed for computing actual salinity, using `swSCTp`.
`temperature`	in-situ temperature [^\circ degC], defined on the ITS-90 scale; see “Temperature units” in the documentation for `swRho`.
`pressure`	Vector of pressure values, one for each `salinity` and `temperature` pair, or just a single pressure, which is repeated to match the length of `salinity`.
`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).
`scan`	optional scan number. If not provided, this will be set to `seq_along(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, defaults are set for `pressure`, `temperature`, `salinity`, and `conductivity`. Since these are simply guesses, users are advised strongly to supply `units`. See “Examples”.
`flags`	if supplied, this is a `list` containing data-quality flags. The elements of this list must have names that match the data provided to the object.
`missingValue`	optional missing value, indicating data that should be taken as `NA`. Set to `NULL` to turn off this feature.
`type`	optional type of CTD, e.g. "SBE"
`serialNumber`	optional serial number of instrument
`ship`	optional string containing the ship from which the observations were made.
`cruise`	optional string containing a cruise identifier.
`station`	optional string containing a station identifier.
`startTime`	optional indication of the start time for the profile, which is used in some several plotting functions. This is best given as a `POSIXt` time, but it may also be a character string that can be converted to a time with `as.POSIXct`, using `UTC` as the timezone.
`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, then they are stored in the `data` slot.
`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, perhaps also including an upcast; `"moored"` if the device is installed on a fixed mooring, `"thermosalinograph"` (or `"tsg"`) if the device is mounted on a moving vessel, to record near-surface properties, or `"towyo"` if the device is repeatedly lowered and raised.
`pressureAtmospheric`	A numerical value (a constant or a vector), that is subtracted from pressure before storing it in the return value. (This altered pressure is also used in calculating `salinity`, if that is to be computed from `conductivity`, etc., using `swSCTp` (see `salinity` above).
`sampleInterval`	optional numerical value indicating the time between samples in the profile.
`profile`	optional positive integer specifying the number of the profile to extract from an object that has data in matrices, such as for some `argo` objects. Currently the `profile` argument is only utilized for `argo-class` objects.
`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.

An object of ctd-class.

If the salinity argument is an object of rsk-class, then as.ctd passes it, pressureAtmospheric, longitude, latitude ship, cruise, station and deploymentType to rsk2ctd, which builds the ctd object that is returned by as.ctd. The other arguments to as.ctd are ignored in this instance, because rsk objects already contain their information. If required, any data or metadata element can be added to the value returned by as.ctd using oceSetData or oceSetMetadata, respectively.

The returned rsk-class object contains pressure in a form that 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 difficulties, 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.

Dan Kelley

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.

library(oce)
## 1. fake data, with default units
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)
# Add a new column
fluo <- 5 * exp(-pressure / 20)
ctd <- oceSetData(ctd, name="fluorescence", value=fluo,
                  unit=list(unit=expression(mg/m^3), scale=""))
summary(ctd)

## 2. fake data, with supplied units (which are the defaults, actually)
ctd <- as.ctd(salinity, temperature, pressure,
    units=list(salinity=list(unit=expression(), scale="PSS-78"),
    temperature=list(unit=expression(degree*C), scale="ITS-90"),
    pressure=list(unit=expression(dbar), scale="")))