ctd-class {oce} | R Documentation

## Class to store hydrographic data

### Description

Class to store hydrographic data such as measured with a CTD (conductivity, temperature, depth) instrument.

### Methods

Consider an object named `ctd`.

Accessing metadata.

Metadata (contained in the S4 slot named `metadata`) may be retrieved or set by name, `ctd[["longitude"]] <- ctd[["longitude"]] + 1` corrects a one-degree error.

Accessing measured data.

Column data may be accessed by name, e.g. `ctd[["salinity"]]`, `ctd[["temperature"]]`, `ctd[["pressure"]]`, etc.

Temperature is stored in the ITS-90 scale within the object, but the IPTS-68 value can be accessed with e.g. `ctd[["temperature68"]]`, and this must be done in using various seawater functions, e.g. the density function `swRho`, if the UNESCO formulation is being requested.

The TEOS-10 notation for these quantities also works, with `ctd[["SP"]]`, `ctd[["t"]]` and `ctd[["p"]]` returning identical values to those returned for the longer names.

After the names listed above have been checked, the remaining names in the `data` slot are checked using `pmatch`, so that e.g. `ctd[["sal"]]` will recover practical `salinity`, `ctd[["sc"]]` will recover `scan` (if it exists), etc.

Accessing derived data.

Depth is accessed with e.g. `ctd[["depth"]]`, while its negative, the vertical coordinate, is accessed with e.g. `ctd[["z"]]`; note that these are calculated using `swDepth` and `swZ`, and that any values that may have been read in a data file are ignored.

Potential temperature defined according to UNESCO-1980 is calculated with `ctd[["theta"]]` or `ctd[["potential temperature"]]`. Salinity is retrieved with `ctd[["S"]]` or `ctd[["salinity"]]`.

Conservative Temperature defined according to TEOS-2010 is calculated with `ctd[["CT"]]` or `ctd[["conservative temperature"]]`. Absolute salinity is calculated with `ctd[["SA"]]` or `ctd[["absolute salinity"]]`. Note that the salinity calculation requires a latitude and longitude, and if the `ctd` object lacks those data, the values 300E and 30N will be used as a default.

The square of buoyancy frequency is retrieved with `ctd[["N2"]]` or `swN2`, density ratio with `ctd[["Rrho"]]` and spiciness with `ctd[["spice"]]`.

Assigning values.

Items stored in the object may be altered with e.g. `ctd[["salinity"]] <- rep(35,10)`. For obvious reasons, this does not work with derived quantities such as conservative temperature, etc.

Overview of contents.

The `show` method (e.g. `show(ctd)`) displays information about the object.

### Author(s)

Dan Kelley

### See Also

A file containing CTD profile data may be read with `read.ctd`, and a CTD object can also be created with `as.ctd`. See `read.ctd` for references on data formats used in CTD files.

Statistical summaries are provided by `summary.ctd`, while `show` displays an overview.

CTD objects may be plotted with `plot.ctd`, which does much of its work by calling `plotProfile` or `plotTS`, both of which can also be called by the user, to get fine control over the plots.

A CTD profile can be isolated from a larger record with `ctdTrim`, a task made easier when `plotScan` is used to examine the results. Towyow data can be split up into sets of profiles (ascending or descending) with `ctdFindProfiles`. CTD data may be smoothed and/or cast onto specified pressure levels with `ctdDecimate`.

Low-level manipulation may be done with functions such as `ctdAddColumn` and `ctdUpdateHeader`. Additionally, many of the contents of CTD objects may be altered with the `[[]]` scheme discussed above, and skilled users may also manipulate the contents directly.

[Package oce version 0.9-18 Index]