Extract Something From a section 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 'section'
x[[i, j, ...]]

Arguments

x: a section 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

There are several possibilities, depending on the nature of i.

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 [[. This list is compiled by examining all the stations in the object, and reporting an entry if it is found in any one of them. 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 data-like and metadata-like things that can be derived from these.
If i is "station", then [[ will return a list() of ctd objects holding the station data. If j is also given, it specifies a station (or set of stations) to be returned. if 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.)
If i is "station ID", then the IDs of the stations in the section are returned.
If i is "dynamic height", then an estimate of dynamic height is returned, as calculated with swDynamicHeight(x).
If i is "distance", then the distance along the section is returned, using geodDist().
If i is "depth", then a vector containing the depths of the stations is returned.
If i is "z", then a vector containing the z coordinates is returned.
If i is "theta" or "potential temperature", then the potential temperatures of all the stations are returned in one vector. Similarly, "spice" returns the property known as spice, using swSpice().
If 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.

If j is "byStation", then a list is returned, with one (unnamed) item per station.

If j is "grid:distance-pressure" or "grid:time-pressure", then a gridded representation of i is returned, as a list with elements: distance (in km) or time (in POSIXct); pressure (in dbar) and field (in whatever unit is used for i). See the examples in the documentation for plot,section-method().

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(section)
length(section[["latitude"]])
#> [1] 2841
length(section[["latitude", "byStation"]])
#> [1] 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[[1]]
#> [1] 36.1384 36.1103 35.9953 35.9372 35.8191