R: Class to Store Hydrographic Section Data

section-class {oce} | R Documentation

## Class to Store Hydrographic Section Data

### Description

This class stores data from oceanographic section surveys.

### Details

Sections can be read with `read.section()` or created with `read.section()` or created from CTD objects by using `as.section()` or by adding a ctd station to an existing section with `sectionAddStation()`.

Sections may be sorted with `sectionSort()`, subsetted with `subset,section-method()`, smoothed with `sectionSmooth()`, and gridded with `sectionGrid()`. Gridded sections may be plotted with `plot,section-method()`.

Statistical summaries are provided by `summary,section-method()`, while overviews are provided by `show`.

The sample dataset `section()` contains data along WOCE line A03.

### Slots

`data`

  As with all `oce` objects, the `data` slot for `section` objects is a list containing the main data for the object.

`metadata`

  As with all `oce` objects, the `metadata` slot for `section` objects is a list containing information about the `data` or about the object itself. Examples that are of common interest include `stationId`, `longitude`, `latitude` and `time`.

`processingLog`

  As with all `oce` objects, the `processingLog` slot for `section` objects is a list with entries describing the creation and evolution of the object. The contents are updated by various `oce` functions to keep a record of processing steps. Object summaries and `processingLogShow()` both display the log.

### Modifying slot contents

Although the `[[<-` operator may permit modification of the contents of section objects (see `[[<-,section-method`), it is better to use `oceSetData()` and `oceSetMetadata()`, because those functions save an entry in the `processingLog` that describes the change.

### Retrieving slot contents

The full contents of the `data` and `metadata` slots of a section object may be retrieved in the standard R way using `slot()`. For example `slot(o,"data")` returns the `data` slot of an object named `o`, and similarly `slot(o,"metadata")` returns the `metadata` slot.

The slots may also be obtained with the `[[,section-method` operator, as e.g. `o[["data"]]` and `o[["metadata"]]`, respectively.

The `[[,section-method` operator can also be used to retrieve items from within the `data` and `metadata` slots. For example, `o[["temperature"]]` can be used to retrieve temperature from an object containing that quantity. The rule is that a named quantity is sought first within the object's `metadata` slot, with the `data` slot being checked only if `metadata` does not contain the item. This `[[` method can also be used to get certain derived quantities, if the object contains sufficient information to calculate them. For example, an object that holds (practical) salinity, temperature and pressure, along with longitude and latitude, has sufficient information to compute Absolute Salinity, and so `o[["SA"]]` will yield the calculated Absolute Salinity.

It is also possible to find items more directly, using `oceGetData()` and `oceGetMetadata()`, but neither of these functions can retrieve derived items.

### Author(s)

Dan Kelley

### See Also

Other classes provided by oce: `adp-class`, `adv-class`, `argo-class`, `bremen-class`, `cm-class`, `coastline-class`, `ctd-class`, `lisst-class`, `lobo-class`, `met-class`, `oce-class`, `odf-class`, `rsk-class`, `sealevel-class`, `topo-class`, `windrose-class`, `xbt-class`

Other things related to section data: `[[,section-method`, `[[<-,section-method`, `as.section()`, `handleFlags,section-method`, `initializeFlagScheme,section-method`, `plot,section-method`, `read.section()`, `sectionAddStation()`, `sectionGrid()`, `sectionSmooth()`, `sectionSort()`, `section`, `subset,section-method`, `summary,section-method`

### Examples

    library(oce)
    data(section)
    plot(section[['station', 1]])
    pairs(cbind(z=-section[["pressure"]],T=section[["temperature"]],S=section[["salinity"]]))
    ## T profiles for first few stations in section, at common scale
    par(mfrow=c(3,3))
    Tlim <- range(section[["temperature"]])
    ylim <- rev(range(section[["pressure"]]))
    for (stn in section[["station", 1:9]])
        plotProfile(stn, xtype='potential temperature', ylim=ylim, Tlim=Tlim)

[Package oce version 1.2-0 Index]