as.ctd {oce} | R Documentation |
Coerces a dataset into a ctd dataset.
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"))
salinity |
There are two choices for |
temperature |
in-situ temperature [degC], defined on
the ITS-90 scale; see “Temperature units” in the documentation for
|
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
|
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
|
pressureType |
a character string indicating the type of pressure; may be
|
missingValue |
optional missing value, indicating data that should be
taken as |
quality |
quality flag, e.g. from the salinity quality flag in WOCE data.
(In WOCE, |
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 |
latitude |
optional numerical value containing the latitude in decimal
degrees, positive in the northern hemisphere. See the note on length, for
the |
deploymentType |
character string indicating the type of deployment. Use
|
pressureAtmospheric |
if |
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 |
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.
An object of class
"ctd"
(for details, see
read.ctd
).
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.
The documentation for ctd-class
explains the structure of
CTD objects, and also outlines the other functions dealing with them.
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)