Extract Something From a ctd 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 '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" then swSpice() is called to compute a quantity that is in some sense orthogonal to density on a T-S diagram. This is done by calling swSpice() with the eos argument set to "unesco". In an earlier version of oce, [[ could be provided with a second argument to yield a return value for "spiciness", a variable that is described in the next item. On 2024-02-14, this possibility was removed because it could lead to user confusion and non-reproducible code. To get spiciness, use [["spiciness0"]].
If i is "spiciness0", "spiciness1" or "spiciness2", then the return value comes from the Gibbs SeaWater formulation of a variable that is in some sense orthogonal to density on a T-S diagram. The numbers refer to the reference pressure, in units of 1000 dbar. These results are computed with gsw::gsw_spiciness0(), etc.
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.

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

data(ctd)
head(ctd[["temperature"]])
#> [1] 14.22109 14.22649 14.22509 14.22219 14.22669 14.23318