R: Extract Something From a CTD Object

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

## Extract Something From a CTD Object

### Description

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

### Usage

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

### Arguments

`x` | An `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

A two-step process is used to try to find the requested information. First, a class-specific function tries to find it, but if that fails, then a general function is used (see next section).

### 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 values of `i` and, optionally, `j`. The work proceeds in steps, by testing a sequence of possible conditions in sequence.

1. 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.

2. 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"]]` (note the space), then just the expression is returned, and if it ends in `" scale"`, then just the scale is returned.

3. 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.

4. If `i` is `"sigmaTheta"`, then the value of `swSigmaTheta(x)` is returned. Similarly, `"sigma0"` returns `swSigma0(x)` and `"spice"` returns `swSpice(x)`. Note that these relate to seawater properties and only make sense for certain object types.

5. 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, without the issuance of a warning or error message. (This silent operation is employed so that `[[` will behave like the normal R version.)

### 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. (To get pressure in PSI, use `x[["pressurePSI"]]`.) 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.

The list given below provides notes on some quantities that are, or may be, computed.

- `conductivity` without a second argument (e.g. `a[["conductivity"]]`) returns the value stored in the object. However, if a second argument is given, and it is string specifying a unit, then conversion is made to that unit. The permitted units are: either `""` or `"ratio"` (for ratio), `"uS/cm"`, `"mS/cm"` and `"S/m"`. The calculations are based on the definition of conductivity ratio as the ratio between measured conductivity and the standard value 4.2914 S/m.

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

- `density`: seawater density, computed with `swRho(x)`. (Note that it may be better to call that function directly, to gain control of the choice of equation of state, etc.)

- `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. The calculation involves location as well as measured water properties. If the object `x` does not containing information on the location, then 30N and 60W is used for the calculation, and a warning is generated.

- `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` or `spiciness0`: a variable that is in some sense orthogonal to density, calculated with `swSpice(x)`. Note that this is defined differently for `eos="unesco"` and `eos="gsw"`.

- `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. See `SA` for a note on longitude and latitude.

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

- `time`: returns either a vector of times, a single time, or `NULL`. A vector is returned if `time` is present in the `data` slot, or if a time can be inferred from other entries in the `data` slot (some of which, such as the common `timeS`, also employ `startTime` within the `metadata` slot). A single value is returned if the dataset only has information on the start time (which is stored as `startTime` within the `metadata` slot. If it is impossible to determine the sampling time, then `NULL` is returned. These time variants occur, in the present version of oce, only for data read by `read.ctd.sbe`, the documention of which explains how times are computed.

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

### Author(s)

Dan Kelley

### 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`, `[[,landsat-method`, `[[,lisst-method`, `[[,lobo-method`, `[[,met-method`, `[[,oce-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`, `initialize,ctd-method`, `initializeFlagScheme,ctd-method`, `oceNames2whpNames`, `oceUnits2whpUnits`, `plot,ctd-method`, `plotProfile`, `plotScan`, `plotTS`, `read.ctd.itp`, `read.ctd.odf`, `read.ctd.sbe`, `read.ctd.woce.other`, `read.ctd.woce`, `read.ctd`, `setFlags,ctd-method`, `subset,ctd-method`, `summary,ctd-method`, `woceNames2oceNames`, `woceUnit2oceUnit`, `write.ctd`

### Examples

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

[Package oce version 1.1-1 Index]