R: Class to Store Echosounder Data

echosounder-class {oce}

R Documentation

Class to Store Echosounder Data

Description

This class stores echosounder data. Echosounder objects may be read with read.echosounder(), summarized with summary,echosounder-method(), and plotted with plot,echosounder-method(). The findBottom() function infers the ocean bottom from tracing the strongest reflector from ping to ping.

Details

An infrequently updated record of the instrument position, in timeSlow, longitudeSlow and latitudeSlow. These are used in plotting maps with plot,echosounder-method().
An interpolated record of the instrument position, in time, longitude, and latitude. Linear interpolation is used to infer the longitude and latitude from the variables listed above.
depth, vector of depths of echo samples (measured positive downwards in the water column). This is calculated from the inter-sample time interval and the sound speed provided as the soundSpeed argument to read.echosounder(), so altering the value of the latter will alter the echosounder plots provided by plot,echosounder-method().
The echosounder signal amplitude a, a matrix whose number of rows matches the length of time, etc., and number of columns equal to the length of depth. Thus, for example, a[100,] represents the depth-dependent amplitude at the time of the 100th ping.
A matrix named b exists for dual-beam and split-beam cases. For dual-beam data, this is the wide-beam data, whereas a is the narrow-beam data. For split-beam data, this is the x-angle data.
A matrix named c exists for split-beam data, containing the y-angle data.
In addition to these matrices, ad-hoc calculated matrices named Sv and TS may be accessed as explained in the next section.

Slots

data: As with all oce objects, the data slot for echosounder objects is a list containing the main data for the object.
metadata: As with all oce objects, the metadata slot for echosounder objects is a list containing information about the data or about the object itself.
processingLog: As with all oce objects, the processingLog slot for echosounder 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 echosounder objects (see [[<-,echosounder-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 echosounder 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 [[,echosounder-method operator, as e.g. o[["data"]] and o[["metadata"]], respectively.

The [[,echosounder-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