as.ctd | R Documentation |
Assemble data into a ctd object. This function is complicated (spanning approximately 500 lines of code) because it tries to handle many special cases, and tries to make sensible defaults for unspecified parameters. If odd results are found, users might find it helpful to call this function with the first argument being a simple vector of Practical Salinity values, in which case the processing of the other arguments is relatively straightforward.
as.ctd( salinity, temperature = NULL, pressure = NULL, conductivity = NULL, scan = NULL, time = NULL, units = NULL, flags = NULL, missingValue = NULL, type = "", serialNumber = NULL, ship = NULL, cruise = NULL, station = NULL, startTime = NULL, longitude = NULL, latitude = NULL, deploymentType = "unknown", pressureAtmospheric = 0, sampleInterval = NULL, profile = NULL, debug = getOption("oceDebug") )
salinity |
may be (1) a numeric vector holding Practical Salinity,
(2) a list or data frame holding |
temperature |
a numeric vector containing in-situ temperature in
degC on the ITS-90 scale; see “Temperature units” in the
documentation for |
pressure |
a numeric vector containing sea pressure values, in decibars.
Typically, this vector has the same length as |
conductivity |
an optional numeric vector containing electrical conductivity ratio through the water column. To convert from raw conductivity in milliSeimens per centimeter divide by 42.914 to get conductivity ratio (see Culkin and Smith, 1980). |
scan |
optional numeric vector holding scan number. If not provided,
this is set to seq_along |
time |
optional vector of times of observation. |
units |
an optional list containing units. If not supplied,
defaults are set for |
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 |
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 |
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 |
A ctd object.
If the salinity
argument is an object of rsk,
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 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 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 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 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, volume 5, pages 22-23.
Other things related to ctd data:
CTD_BCD2014666_008_1_DN.ODF.gz
,
[[,ctd-method
,
[[<-,ctd-method
,
cnvName2oceName()
,
ctd-class
,
ctd.cnv
,
ctdDecimate()
,
ctdFindProfiles()
,
ctdRaw
,
ctdRepair()
,
ctdTrim()
,
ctd_aml.csv
,
ctd
,
d200321-001.ctd
,
d201211_0011.cnv
,
handleFlags,ctd-method
,
initialize,ctd-method
,
initializeFlagScheme,ctd-method
,
oceNames2whpNames()
,
oceUnits2whpUnits()
,
plot,ctd-method
,
plotProfile()
,
plotScan()
,
plotTS()
,
read.ctd.aml()
,
read.ctd.itp()
,
read.ctd.odf()
,
read.ctd.odv()
,
read.ctd.sbe()
,
read.ctd.ssda()
,
read.ctd.woce.other()
,
read.ctd.woce()
,
read.ctd()
,
setFlags,ctd-method
,
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="")))
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