as.ctd {oce} | R Documentation |
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 = "", cruise = "", station = "", startTime = NULL, longitude = NA, latitude = NA, deploymentType = "unknown", pressureAtmospheric = 0, sampleInterval = NA, profile = NULL, debug = getOption("oceDebug"))
salinity |
There are three choices for |
temperature |
in-situ temperature [^\circ degC], defined on
the ITS-90 scale; see “Temperature units” in the documentation for
|
pressure |
Vector of pressure values, one for each |
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
|
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 |
flags |
if supplied, this is a |
missingValue |
optional missing value, indicating data that should be
taken as |
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
|
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 |
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 |
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
|
debug |
an integer specifying whether debugging information is
to be printed during the processing. This is a general parameter that
is used by many |
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 ctd-class
.
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.
Other things related to ctd
data: [[,ctd-method
,
[[<-,ctd-method
,
cnvName2oceName
, ctd-class
,
ctdDecimate
, ctdFindProfiles
,
ctdRaw
, ctdTrim
,
ctd
, handleFlags,ctd-method
,
oceNames2whpNames
,
oceUnits2whpUnits
,
plot,ctd-method
, plotProfile
,
plotScan
, plotTS
,
read.ctd.itp
, read.ctd.odf
,
read.ctd.sbe
,
read.ctd.woce.other
,
read.ctd.woce
, read.ctd
,
subset,ctd-method
,
summary,ctd-method
,
woceNames2oceNames
,
woceUnit2oceUnit
, write.ctd
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="")))