R: Extract Parts of a CTD Object

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

## Extract Parts of a CTD Object

### Description

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 'ctd'
    x[[i, j, ...]]

### Arguments

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

### 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.

### Details of the specialized `ctd` method

Some uses of `[[,ctd-method` involve direct retrieval of items within the `data` slot of the `ctd` object, while other uses involve calculations based on items in that `data` slot. For an example, all `ctd` objects should hold an item named `temperature` in the `data` slot, so for example `x[["temperature"]]` will retrieve that item. By contrast, `x[["sigmaTheta"]]` is taken to be a request to compute sigma[theta], and so it yields a call to `swTheta(x)` even if the `data` slot of `x` might happen to contain an item named `theta`. This can be confusing at first, but it tends to lead to fewer surprises in everyday work, for otherwise the user would be forced to check the contents of any `ctd` object under analysis, to determine whether that item will be looked up or computed. Nothing is lost in this scheme, since the data within the object are always accessible with `oceGetData`.

It should be noted that the accessor is set up to retrieve quantities in conventional units. For example, `read.ctd.sbe` is used on a `.cnv` file that stores pressure in psi, it will be stored in the same unit within the `ctd` object, but `x[["pressure"]]` will return a value that has been converted to decibars. (Users who need the pressure in PSI can use `x@data$pressure`.) Similarly, temperature is returned in the ITS-90 scale, with a conversion having been performed with `T90fromT68`, if the object holds temperature in IPTS-68. Again, temperature on the IPTS-68 scale is returned with `x@data$temperature`.

This preference for computed over stored quantities is accomplished by first checking for computed quantities, and then falling back to the general `[[` method if no match is found.

Some quantities are optionally computed. For example, some data files (e.g. the one upon which the `section` dataset is based) store `nitrite` along with the sum of nitrite and nitrate, the latter with name ``NO2+NO3``. In this case, e.g. `x[["nitrate"]]` will detect the setup, and subtract nitrite from the sum to yield nitrate.

Below is a list of computed quantities, or at least quantites that are typically not stored in data files. (This is a vague statement because Seabird software permits calculation of many of these and hence storage within `.cnv` files.)

- `CT` or `Conservative Temperature`: Conservative Temperature, computed with `gsw_CT_from_t` in the `gsw` package.

- `depth`: Depth in metres below the surface, computed with `swDepth(x)`.

- `N2`: Square of Brunt-Vaisala frequency, computed with `swN2(x)`.

- `potential temperature`: Potential temperature in the UNESCO formulation, computed with `swTheta(x)`. This is a synonym for `theta`.

- `Rrho`: Density ratio, computed with `swRrho(x)`.

- `SA` or `Absolute Salinity`: Absolute Salinity, computed with `gsw_SA_from_SP` in the `gsw` package.

- `sigmaTheta`: A form of potential density anomaly, computed with `swSigmaTheta(x)`.

- `sigma0` Equal to `sigmaTheta`, i.e. potential density anomaly referenced to a pressure of 0dbar, computed with `swSigma0(x)`.

- `sigma1`: Potential density anomaly referenced to a pressure of 1000dbar, computed with `swSigma1(x)`.

- `sigma2`: Potential density anomaly referenced to a pressure of 2000dbar, computed with `swSigma2(x)`.

- `sigma3`: Potential density anomaly referenced to a pressure of 3000dbar, computed with `swSigma3(x)`.

- `sigma4`: potential density anomaly referenced to a pressure of 4000dbar, computed with `swSigma4(x)`.

- `SP`: Salinity on the Practical Salinity Scale, which is `salinity` in the `data` slot.

- `spice`: a variable that is in some sense orthogonal to density, calculated with `swSpice(x)`.

- `SR`: Reference Salinity computed with `gsw_SR_from_SP` in the `gsw` package.

- `Sstar`: Preformed Salinity computed with `gsw_SR_from_SP` in the `gsw` package.

- `theta`: potential temperature in the UNESCO formulation, computed with `swTheta(x)`. This is a synonym for `potential temperature`.

- `z`: Vertical coordinate in metres above the surface, computed with `swZ(x)`.

### See Also

Other functions that extract parts of `oce` objects: `[[,adp-method`, `[[,adv-method`, `[[,amsr-method`, `[[,argo-method`, `[[,bremen-method`, `[[,cm-method`, `[[,coastline-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`

Other things related to `ctd` data: `[[<-,ctd-method`, `as.ctd`, `cnvName2oceName`, `ctd-class`, `ctdDecimate`, `ctdFindProfiles`, `ctdRaw`, `ctdTrim`, `ctd`, `handleFlags,ctd-method`, `plot,ctd-method`, `plotProfile`, `plotScan`, `plotTS`, `read.ctd.itp`, `read.ctd.odf`, `read.ctd.sbe`, `read.ctd.woce.other`, `read.ctd.woce`, `read.ctd`, `subset,ctd-method`, `summary,ctd-method`, `woceNames2oceNames`, `write.ctd`

### Examples

    data(ctd)
    head(ctd[["temperature"]])

[Package oce version 0.9-20 Index]