[[ method works for all
oce objects, i.e.
objects inheriting from
oce-class. The purpose,
as with the related replacement method,
is to insulate users from the internal details of
objects, by looking for items within the various storage
slots of the object. Items not actually stored can also be
extracted, including derived data, units of measurement,
and data-quality flags.
The method uses a two-step process to try to find the
requested information. First, a class-specific function
is used to try to access the requested information (see
“Details of the specialized ... method”).
Second, if no match is found, a general function is used
(see ‘Details of the general method’). If neither
method can locates the requested item,
NULL is returned.
## S4 method for signature 'ctd' x[[i, j, ...]]
Character string indicating the name of item to extract.
Optional additional information on the
Optional additional information (ignored).
If the specialized method produces no matches, the following generalized
method is applied. As with the specialized method, the procedure hinges
first on the value of
First, a check is made as to whether
i names one of the standard
oce slots, and returns the slot contents if so. Thus,
x[["metadata"]] will retrieve the
i is a string ending in the
"Unit", then the characters preceding that string
are taken to be the name of an item in the data object, and a list
containing the unit is returned. This list consists of an item
unit, which is an
an item named
scale, which is a string describing the
measurement scale. If the string ends in
" unit", e.g.
x[["temperature unit"]], then just the expression is returned,
and if it ends in
" scale", then just the scale is returned.
i is a string ending in
"Flag", then the corresponding
data-quality flag is returned (or
NULL if there is no such flag).
x[["salinityFlag"]] returns a vector of salinity
x is a ctd object.
If none of the preceding conditions are met, a check is done
to see if the
metadata slot contains an item with
the provided name, and that is returned, if so. A direct match
is required for this condition.
data slot is checked to see if it contains
an item with the name indicated by
i. In this case, a partial
match will work; this is accomplished by using
If none of the above-listed conditions holds, then
NULL is returned.
Some uses of
[[,ctd-method involve direct retrieval of
items within the
data slot of the
while other uses involve calculations based on items in that
data slot. For an example, all
should hold an item named
temperature in the
slot, so for example
x[["temperature"]] will retrieve that
item. By contrast,
x[["sigmaTheta"]] is taken to be a
request to compute sigma[theta], and so
it yields a call to
swTheta(x) even if
data slot of
x might happen to contain an item
theta. This can be confusing at first, but it tends
to lead to fewer surprises in everyday work, for otherwise the
user would be forced to check the contents of any
object under analysis, to determine whether that item will be looked
up or computed. Nothing is lost in this scheme, since the data
within the object are always accessible with
It should be noted that the accessor is set up to retrieve quantities
in conventional units. For example,
used on a
.cnv file that stores pressure in psi, it will
be stored in the same unit within the
ctd object, but
x[["pressure"]] will return a value that has been converted
to decibars. (Users who need the pressure in PSI can
Similarly, temperature is
returned in the ITS-90 scale, with a conversion having been performed with
T90fromT68, if the object holds temperature in
IPTS-68. Again, temperature on the IPTS-68
scale is returned with
This preference for computed over stored quantities is accomplished
by first checking for computed quantities, and then falling
back to the general
[[ method if no match is found.
Some quantities are optionally computed. For example, some data files
(e.g. the one upon which the
section dataset is based)
nitrite along with the sum of nitrite and nitrate, the
latter with name
`NO2+NO3`. In this case, e.g.
will detect the setup, and subtract nitrite from the sum to yield
Below is a list of computed quantities, or at least quantites that are
typically not stored in data files. (This is a vague statement because
Seabird software permits calculation of many of these and hence storage
Conservative Temperature: Conservative Temperature,
gsw_CT_from_t in the
density: seawater density, computed with
(Note that it may be better to call that function directly, to gain
control of the choice of equation of state, etc.)
depth: Depth in metres below the surface, computed
N2: Square of Brunt-Vaisala frequency, computed with
potential temperature: Potential temperature in the
UNESCO formulation, computed with
This is a synonym for
Rrho: Density ratio, computed with
Absolute Salinity: Absolute Salinity,
gsw_SA_from_SP in the
The calculation involves location as well as measured water properties.
If the object
x does not containin information on the location,
then 30N and 60W is used for the calculation, and a warning is generated.
sigmaTheta: A form of potential density anomaly, computed with
sigma0 Equal to
sigmaTheta, i.e. potential density anomaly
referenced to a pressure of 0dbar, computed with
sigma1: Potential density anomaly
referenced to a pressure of 1000dbar, computed with
sigma2: Potential density anomaly
referenced to a pressure of 2000dbar, computed with
sigma3: Potential density anomaly
referenced to a pressure of 3000dbar, computed with
sigma4: potential density anomaly
referenced to a pressure of 4000dbar, computed with
SP: Salinity on the Practical Salinity Scale, which is
salinity in the
spice: a variable that is in some sense orthogonal to density,
SR: Reference Salinity computed with
gsw_SR_from_SP in the
Sstar: Preformed Salinity computed with
gsw_SR_from_SP in the
SA for a note on longitude and latitude.
theta: potential temperature in the UNESCO formulation,
swTheta(x). This is a synonym for
z: Vertical coordinate in metres above the surface, computed with
Other functions that extract parts of
Other things related to
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