[[ method works for all
oce objects, i.e.
objects inheriting from oce. The purpose
is to insulate users from the internal details of
objects, by looking for items within the various storage
slots of the object. Items that are not actually stored in
the object can also be extracted, including derived data such
as potential temperature, the units of measurement for
the data, data-quality flags, etc.
# S4 method for section [[(x, i, j, ...)
a section object.
Character string indicating the name of an item to extract.
Optional additional information on the
Optional additional information (ignored).
A two-step process is used to try to find the requested information. First, a class-specific function tries to find it, but if that fails, then a general function is used (see next section).
There are several possibilities, depending on the nature of
i is the string
"station", then the method
will return a
ctd objects holding the station data.
j is also given, it specifies a station (or set of stations) to be returned.
j contains just a single value, then that station is returned, but otherwise
a list is returned. If
j is an integer, then the stations are specified by index,
but if it is character, then stations are specified by the names stored within
their metadata. (Missing stations yield
NULL in the return value.)
"station ID", then the IDs of the stations in the
section are returned.
"dynamic height", then an estimate of dynamic
height is returned, as calculated with
"distance", then the distance along the section is
"depth", then a vector containing the depths
of the stations is returned.
"z", then a vector containing the z
coordinates is returned.
"potential temperature", then
the potential temperatures of all the stations are returned in one
"spice" returns the property known
as spice, using
i is a string ending with
"Flag", then the characters
prior to that ending are taken to be the name of a variable contained
within the stations in the section. If this flag is available in
the first station of the section, then the flag values are looked
up for every station.
"byStation", then a list is returned, with
one (unnamed) item per station.
If the specialized method produces no matches, the following generalized
method is applied. As with the specialized method, the procedure hinges
first on the values of
i and, optionally,
j. The work
proceeds in steps, by testing a sequence of possible conditions
A check is made as to whether
i names one of the standard
oce slots. If so,
[[ returns the slot contents of that slot.
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"]] (note the space),
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.
"sigmaTheta", then the value of
swSigmaTheta() is called with
x as the sole
argument, and the results are returned. Similarly,
swSigma0() is used if
swSpice() is used if
i="spice". Of course, these
actions only make sense for objects that contain
the relevant items within their
After these possibilities are eliminated,
the action depends on whether
j has been provided.
j is not provided, or is the string
i is sought
metadata slot, and then in the
returning whichever is found first. In other words, if
is not provided, the
metadata slot takes preference over
data slot. However, if
j is provided, then
it must be either the string
and it directs where to look.
If none of the above-listed conditions holds, then
NULL is returned,
without the issuance of a warning or error message. (This silent operation
is employed so that
[[ will behave like the normal R version.)
Other functions that extract parts of oce objects:
Other things related to section data:
#>  2841length(section[["latitude", "byStation"]])#>  124# Vector of all salinities, for all stations Sv <- section[["salinity"]] # List of salinities, grouped by station Sl <- section[["salinity", "byStation"]] # First station salinities Sl[]#>  36.1384 36.1103 35.9953 35.9372 35.8191