The [[ method works for all oce objects, i.e.
objects inheriting from '>oce. The purpose
is to insulate users from the internal details of oce
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 argo
[[(x, i, j, ...)Character string indicating the name of an item to extract.
Optional additional information on the i item.
Optional additional information (ignored).
There are several possibilities, depending on the nature of i.
Note that '>argo data may contain both unadjusted data and adjusted
data. By default, this extraction function refers to the former, but a
preference for the latter may be set with preferAdjusted(), the
documentation of which explains (fairly complex) details.
If i is "profile" and j is an integer vector,
then an argo object is returned, as specified by j. For example,
argo[["profile", 2:5]] is equivalent to
subset(argo, profile \%in\% 2:5).
If i is "CT", then
Conservative Temperature is returned, as computed with
gsw::gsw_CT_from_t(SA,t,p), where
first SA is computed as explained
in the next item, t is in-situ temperature,
and p is pressure.
If i is "N2", then the square of buoyancy is returned,
as computed with swN2().
If i is "SA", then
Absolute Salinity is returned, as computed with
gsw::gsw_SA_from_SP().
If i is "sigmaTheta", then
potential density anomaly (referenced to zero
pressure) is computed, with swSigmaTheta(), where the
equation of state is taken to be
getOption("oceEOS",default="gsw").
If i is "sigma0", "sigma1", "sigma2", "sigma3" or "sigma4",
then the associated function in the gsw package.
For example, "sigma0" uses gsw::gsw_sigma0(), which returns
potential density anomaly referenced to 0 dbar,
according to the gsw equation of state.
If i is "theta", then
potential temperature (referenced to zero
pressure) is computed, with swTheta(), where the
equation of state is taken to be
getOption("oceEOS",default="gsw").
If i is "depth", then
a matrix of depths is returned.
If i is "id" or "ID", then the id element within
the metadata slot is returned.
If i is in the data slot of x,
then it is returned, otherwise if it is in the metadata slot,
then that is returned, otherwise NULL is returned.
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
in sequence.
A check is made as to whether i names one of the standard
oce slots. If so, [[ returns the slot contents of that slot.
Thus, x[["metadata"]] will retrieve the metadata slot,
while x[["data"]] and x[["processingLog"]] return
those slots.
If 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
named unit, which is an expression(), and
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.
If i is a string ending in "Flag", then the corresponding
data-quality flag is returned (or NULL if there is no such flag).
For example, x[["salinityFlag"]] returns a vector of salinity
flags if x is a ctd object.
If i is "sigmaTheta", then the value of
swSigmaTheta() is called with x as the sole
argument, and the results are returned. Similarly,
swSigma0() is used if i="sigma0", and
swSpice() is used if i="spice". Of course, these
actions only make sense for objects that contain
the relevant items within their data slot.
After these possibilities are eliminated,
the action depends on whether j has been provided.
If j is not provided, or is the string "",
then i is sought
in the metadata slot, and then in the data slot,
returning whichever is found first. In other words, if j
is not provided, the metadata slot takes preference over
the data slot. However, if j is provided, then
it must be either the string "metadata" or "data",
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.)
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).
Other functions that extract parts of oce objects:
[[,adp-method,
[[,adv-method,
[[,amsr-method,
[[,bremen-method,
[[,cm-method,
[[,coastline-method,
[[,ctd-method,
[[,echosounder-method,
[[,g1sst-method,
[[,gps-method,
[[,ladp-method,
[[,landsat-method,
[[,lisst-method,
[[,lobo-method,
[[,met-method,
[[,oce-method,
[[,odf-method,
[[,rsk-method,
[[,sealevel-method,
[[,section-method,
[[,tidem-method,
[[,topo-method,
[[,windrose-method,
[[,xbt-method,
[[<-,adv-method
Other things related to argo data:
[[<-,argo-method,
argo-class,
argoGrid(),
argoNames2oceNames(),
argo,
as.argo(),
handleFlags,argo-method,
plot,argo-method,
read.argo(),
subset,argo-method,
summary,argo-method
# NOT RUN {
data(argo)
# 1. show that dataset has 223 profiles, each with 56 levels
dim(argo[['temperature']])
# 2. show importance of focussing on data flagged 'good'
fivenum(argo[["salinity"]],na.rm=TRUE)
fivenum(argo[["salinity"]][argo[["salinityFlag"]]==1],na.rm=TRUE)
# }
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