R: Extract Something From a ctd Object

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

## Extract Something From a ctd Object

### Description

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

### Arguments

`x` | a ctd 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

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 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 available using e.g. `ctd[[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 `[[`. 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 the names of things that can be inferred from the object's contents, e.g. `"SA"` is named in `dataDerived`, indicating that `argo[["SA"]]` is permitted (to compute Absolute Salinity).

- If `i` is `"conductivity"` without a second argument (e.g. `a[["conductivity"]]`) then the return value is the seawater electrical conductivity (if available or computable). 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.

- If `i` is `"CT"` or `"Conservative Temperature"` then Conservative Temperature, computed with `gsw::gsw_CT_from_t()`, is returned.

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

- If `i` is `"depth"` then the depth in metres below the surface, computed with swDepth`(x)`, is returned.

- If `i` is `"N2"` then the square of Brunt-Vaisala frequency, computed with swN2`(x)`, is returned.

- If `i` is `"potential temperature"` or `"theta"`, then potential temperature in the UNESCO formulation, computed with swTheta`(x)`, is returned.

- If `i` is `"Rrho"` then density ratio, computed with swRrho`(x)`, is returned.

- If `i` is `"SA"` or `"Absolute Salinity"` then Absolute Salinity, computed with `gsw::gsw_SA_from_SP()`, is returned. 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.

- If `i` is `"sigmaTheta"` then a form of potential density anomaly, computed with swSigmaTheta`(x)`, is returned.

- If `i` is `"sigma0"` then potential density anomaly referenced to a sea pressure of 0dbar (the surface), computed with swSigma0`(x)`, is returned.

- If `i` is `"sigma2"` then potential density anomaly referenced to a sea pressure of 1000dbar, computed with swSigma1`(x)`, is returned.

- If `i` is `"sigma2"` then potential density anomaly referenced to a sea pressure of 2000dbar, computed with swSigma2`(x)`, is returned.

- If `i` is `"sigma3"` then potential density anomaly referenced to a sea pressure of 3000dbar, computed with swSigma3`(x)`, is returned.

- If `i` is `"sigma4"` then potential density anomaly referenced to a sea pressure of 4000dbar, computed with swSigma4`(x)`, is returned.

- If `i` is `"SP"` then salinity on the Practical Salinity Scale, which is `salinity` in the `data` slot, is returned.

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

- If `i` is `"SR"` then Reference Salinity, computed with `gsw::gsw_SR_from_SP()`, is returned.

- If `i` is `"Sstar"` then Preformed Salinity, computed with `gsw::gsw_SR_from_SP()`, is returned. See `SA` for a note on longitude and latitude.

- If `i` is `"time"` then either vector of times or a single time, is returned, if available. 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 documentation of which explains how times are computed.

- If `i` is `"z"` then vertical coordinate in metres above the surface, computed with swZ`(x)`, is returned.

### 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.

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 (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.

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).

4. 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.

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.

6. 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`, `[[,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`, `[[,xbt-method`, `[[<-,adv-method`

Other things related to ctd data: `CTD_BCD2014666_008_1_DN.ODF.gz`, `[[<-,ctd-method`, `as.ctd()`, `cnvName2oceName()`, `ctd-class`, `ctd.cnv`, `ctdDecimate()`, `ctdFindProfiles()`, `ctdRaw`, `ctdRepair()`, `ctdTrim()`, `ctd_aml.csv`, `ctd`, `d200321-001.ctd`, `d201211_0011.cnv`, `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.odv()`, `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 1.7-2 Index]