R: Extract Something From an amsr Object

[[,amsr-method {oce} | R Documentation

## Extract Something From an amsr Object

### Description

Extract something from the `metadata` or `data` slot of an `amsr-class` object.

The `[[` method works for all `oce` objects, i.e. objects inheriting from `oce-class`. The purpose, as with the related replacement method, `[[<-`, is to insulate users from the internal details of `oce` objects, by looking for items within the various storage slots of the object. Items not actually stored can also be extracted, including derived data, units of measurement, and data-quality flags.

The method uses a two-step process to try to find the requested information. First, a class-specific function is used to try to access the requested information (see “Details of the specialized ... method”). Second, if no match is found, a general function is used (see ‘Details of the general method’). If neither method can locates the requested item, `NULL` is returned.

### Usage

    ## S4 method for signature 'amsr'
    x[[i, j, ...]]

### Arguments

`x` | An `amsr` object, i.e. one inheriting from `amsr-class`.
`i` | Character string indicating the name of item to extract.
`j` | Optional additional information on the `i` item.
`...` | Optional additional information (ignored).

### Details

Partial matches for `i` are permitted for `metadata`, and `j` is ignored for `metadata`.

Data within the `data` slot may be found directly, e.g. `j="SSTDay"` will yield sea-surface temperature in the daytime satellite, and `j="SSTNight"` is used to access the nighttime data. In addition, `j="SST"` yields an average of the night and day values (using just one of these, if the other is missing). This scheme works for all the data stored in `amsr` objects, namely: `time`, `SST`, `LFwind`, `MFwind`, `vapor`, `cloud` and `rain`. In each case, the default is to calculate values in scientific units, unless `j="raw"`, in which case the raw data are returned.

The `"raw"` mode can be useful in decoding the various types of missing value that are used by `amsr` data, namely `as.raw(255)` for land, `as.raw(254)` for a missing observation, `as.raw(253)` for a bad observation, `as.raw(252)` for sea ice, or `as.raw(251)` for missing SST due to rain or missing water vapour due to heavy rain. Note that something special has to be done for e.g. `d[["SST", "raw"]]` because the idea is that this syntax (as opposed to specifying `"SSTDay"`) is a request to try to find good data by looking at both the Day and Night measurements. The scheme employed is quite detailed. Denote by "A" the raw value of the desired field in the daytime pass, and by "B" the corresponding value in the nighttime pass. If either A or B is 255, the code for land, then the result will be 255. If A is 254 (i.e. there is no observation), then B is returned, and the reverse holds also. Similarly, if either A or B equals 253 (bad observation), then the other is returned. The same is done for code 252 (ice) and code 251 (rain).

### Value

In all cases, the returned value is a matrix with with `NA` values inserted at locations where the raw data equal `as.raw(251:255)`, as explained in “Details”.

### Details of the general method

If the specialized method produces no matches, the following generalized method is applied. As with the specialized method, the procedure hinges first on the value of `i`.

First, a check is made as to whether `i` names one of the standard `oce` slots, and returns the slot contents if so. Thus, `x[["metadata"]]` will retrieve the `metadata` slot, while `x[["data"]]` and `x[["processingLog"]]` return those slots.

Next, 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"]]`, then just the expression is returned, and if it ends in `" scale"`, then just the scale is returned.

Next, 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 none of the preceding conditions are met, a check is done to see if the `metadata` slot contains an item with the provided name, and that is returned, if so. A direct match is required for this condition.

Finally, the `data` slot is checked to see if it contains an item with the name indicated by `i`. In this case, a partial match will work; this is accomplished by using `pmatch`.

If none of the above-listed conditions holds, then `NULL` is returned.

### Author(s)

Dan Kelley

### See Also

Other functions that extract parts of `oce` objects: `[[,adp-method`, `[[,adv-method`, `[[,argo-method`, `[[,bremen-method`, `[[,cm-method`, `[[,coastline-method`, `[[,ctd-method`, `[[,echosounder-method`, `[[,g1sst-method`, `[[,gps-method`, `[[,ladp-method`, `[[,lisst-method`, `[[,lobo-method`, `[[,met-method`, `[[,odf-method`, `[[,rsk-method`, `[[,sealevel-method`, `[[,section-method`, `[[,tidem-method`, `[[,topo-method`, `[[,windrose-method`, `[[<-,adv-method`

### Examples

    ## Not run:
    # Show a daytime SST image, along with an indication of whether
    # the NA values are from rain.
    library(oce)
    earth <- read.amsr("f34_20160102v7.2.gz")
    fclat <- subset(earth , 35 <= latitude & latitude <= 55)
    fc <- subset(fclat , -70 <= longitude & longitude <= -30)
    par(mfrow=c(2,1))
    plot(fc, "SSTDay")
    rainy <- fc[["SSTDay", "raw"]] == as.raw(0xfb)
    lon <- fc[["longitude"]]
    lat <- fc[["latitude"]]
    asp <- 1 / cos(pi*mean(lat)/180)
    imagep(lon, lat, rainy, asp=asp)
    mtext("red: too rainy to sense SSTDay")

    ## End(Not run)

[Package oce version 0.9-20 Index]