Class "TDRcalibrate" for dive analysis

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Description

This class holds information produced at various stages of dive analysis. Methods are provided for extracting data from each slot.

Details

This is perhaps the most important class in diveMove, as it holds all the information necessary for calculating requested summaries for a TDR.

Objects from the Class

Objects can be created by calls of the form new("TDRcalibrate", ...). The objects of this class contain information necessary to divide the record into sections (e.g. dry/water), dive/surface, and different sections within dives. They also contain the parameters used to calibrate speed and criteria to divide the record into phases.

Slots

call:

Object of class call.

The matched call to the function that created the object.

tdr:

Object of class TDR.

This slot contains the time, zero-offset corrected depth, and possibly a data frame. If the object is also of class "TDRspeed", then the data frame might contain calibrated or uncalibrated speed. See readTDR and the accessor function getTDR for this slot.

gross.activity:

Object of class ‘list’.

This slot holds a list of the form returned by .detPhase, composed of 4 elements. It contains a vector (named phase.id) numbering each major activity phase found in the record, a factor (named activity) labelling each row as being dry, wet, or trivial wet activity. These two elements are as long as there are rows in tdr. This list also contains two more vectors, named begin and end: one with the beginning time of each phase, and another with the ending time; both represented as POSIXct objects. See .detPhase.

dive.activity:

Object of class data.frame.

This slot contains a data.frame of the form returned by .detDive, with as many rows as those in tdr, consisting of three vectors named: dive.id, which is an integer vector, sequentially numbering each dive (rows that are not part of a dive are labelled 0), dive.activity is a factor which completes that in activity above, further identifying rows in the record belonging to a dive. The third vector in dive.activity is an integer vector sequentially numbering each postdive interval (all rows that belong to a dive are labelled 0). See .detDive, and getDAct to access all or any one of these vectors.

dive.phases:

Object of class ‘factor’. This slot is a factor that labels each row in the record as belonging to a particular phase of a dive. It has the same form as the “phase.labels” component of the list returned by .labDivePhase.

dive.models:

Object of class ‘list’. This slot contains the details of the process of dive phase identification for each dive. It has the same form as the dive.models component of the list returned by .labDivePhase. It has as many components as there are dives in the TDR object, each of them of class diveModel.

dry.thr:

Object of class ‘numeric’ the temporal criteria used for detecting dry periods that should be considered as wet.

wet.thr:

Object of class ‘numeric’ the temporal criteria used for detecting periods wet that should not be considered as foraging time.

dive.thr:

Object of class ‘numeric’ the criteria used for defining a dive.

speed.calib.coefs:

Object of class ‘numeric’ the intercept and slope derived from the speed calibration procedure. Defaults to c(0, 1) meaning uncalibrated speeds.

Author(s)

Sebastian P. Luque spluque@gmail.com

See Also

TDR for links to other classes in the package. TDRcalibrate-methods for the various methods available.

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