R: Class "TDRcalibrate" for dive analysis

TDRcalibrate-class {diveMove} | R Documentation

## Class "TDRcalibrate" for dive analysis

### 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.

[Package diveMove version 1.5.2 Index]