Extract Something From an argo Object

Generally, the [[ method lets users extract information from oce objects, without having to know the details of the internal storage. For many oce sub-classes, [[ can also return quantities that are computed from the object's contents.

Usage

# S4 method for class 'argo'
x[[i, j, ...]]

Arguments

x: an argo object.
i: character value indicating the name of an item to extract.
j: optional additional information on the i item.
...: ignored.

Details

A two-step process is used to try to find the requested information. First, a class-specific function is used (see “Details of the Specialized Method”). If this yields nothing, then a general method is used (see “Details of the General Method”). If both methods fail, then [[ returns NULL.

Some understanding of the subclass is required to know what can be retrieved with [[. When dealing with an unfamiliar subclass, it can be useful to first use x[["?"]] to get a listing of the retrievable items. See “Details of the Specialized Method” for more information.

Details of the Specialized Method

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.

The results from argo[[i]] or argo[[i,j]] depend on the nature of i and (if provided) j. The details are as follows.

If i is "?", then the return value is a list containing four items, each of which is a character vector holding the names of things that can be accessed with [[. The data and metadata items hold the names of entries in the object's data and metadata slots, respectively. The dataDerived and metadataDerived items hold the names of things that can be inferred from the object's contents, e.g. "SA" is named in dataDerived, indicating that argo[["SA"]] is permitted (to compute Absolute Salinity).
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.

Details of the General Method

Note: the text of this section is identical for all oce subclasses, and so some of what you read here may not be relevant to the class being described in this help page.

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 (or NULL if there is no such unit). 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).
If the object holds hydrographic information (pressure, salinity, temperature, longitude and latitude) then another set of possibilities arises. 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.

Author

Dan Kelley

Examples

data(argo)
# 1. show that dataset has 223 profiles, each with 56 levels
dim(argo[["temperature"]])
#> [1]  56 223

# 2. show importance of focussing on data flagged 'good'
fivenum(argo[["salinity"]], na.rm = TRUE)
#> [1]  0.000 34.890 34.926 35.042 47.899
fivenum(argo[["salinity"]][argo[["salinityFlag"]] == 1], na.rm = TRUE)
#> [1] 32.850 34.890 34.926 35.042 35.842