Extract Something From an amsr 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 'amsr'
x[[i, j, ...]]

Arguments

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

Value

[[ returns numeric matrix data.

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

The [[ method handles both old-format and new-format amsr objects. Old-format objects are read by read.amsr() from from gzipped files holding data in raw format, from which [[ computes numeric results with linear relationships provided at at http://www.remss.com/missions/amsre. By contrast, new-format objects are read from NetCDF files that hold the data as 4-byte numeric values that are read directly, without applying a scaling transformation. The other difference is that old-format objects contain day and night values, e.g. SSTDay and SSTNight, whereas new-format objects contain single values that combine these, e.g. SST.

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 are things that [[ can compute and then return.

Data within the data slot may be found directly (for both new-format and old-format objects) or indirectly (only for old-style objects). For example, SST works by direct lookup for new-format objects, but it is computed using SSTNight and SSTDay for old-format objects. Use e.g. a[["?"]] for any given object, to see what can be retrieved.

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

# Histogram of SST values (for an old-format dataset)
library(oce)
data(amsr)
hist(amsr[["SST"]])