R: Methods for plotting models of dive phases

plotDiveModel-methods {diveMove} | R Documentation

## Methods for plotting models of dive phases

### Description

Methods for function `plotDiveModel`.

### Usage

    ## S4 method for signature 'diveModel,missing'
    plotDiveModel(x, diveNo)

    ## S4 method for signature 'numeric,numeric'
    plotDiveModel(x, y, times.s, depths.s, d.crit, a.crit,
                  diveNo=1, times.deriv, depths.deriv,
                  d.crit.rate, a.crit.rate)

    ## S4 method for signature 'TDRcalibrate,missing'
    plotDiveModel(x, diveNo)

### Arguments

`x` | A `diveModel` (diveMode,missing method), `numeric` vector of time step observations (numeric,numeric method), or `TDRcalibrate` object (TDRcalibrate,numeric method).
`diveNo` | integer representing the dive number selected for plotting.
`y` | numeric vector with depth observations at each time step.
`times.s` | numeric vector with time steps used to generate the smoothing spline (i.e. the knots, see `diveModel`).
`depths.s` | numeric vector with smoothed depth (see `diveModel`).
`d.crit` | integer denoting the index where descent ends in the observed time series (see `diveModel`).
`a.crit` | integer denoting the index where ascent begins in the observed time series (see `diveModel`).
`times.deriv` | numeric vector representing the time steps where the derivative of the smoothing spline was evaluated (see `diveModel`).
`depths.deriv` | numeric vector representing the derivative of the smoothing spline evaluated at `times.deriv` (see `diveModel`).
`d.crit.rate` | numeric scalar: vertical rate of descent corresponding to the quantile used (see `diveModel`).
`a.crit.rate` | numeric scalar: vertical rate of ascent corresponding to the quantile used (see `diveModel`).

### Methods

All methods produce a double panel plot. The top panel shows the depth against time, the cubic spline smoother, the identified descent and ascent phases (which form the basis for identifying the rest of the dive phases), while the bottom panel shows the first derivative of the smooth trace.

`signature(x = "diveModel", y = "missing")`

  Given a `diveModel` object and (possibly) the dive number that it corresponds to, the plot shows the model data.

`signature(x = "numeric", y = "numeric")`

  This is the main method, which requires all aspects of the model to be provided.

`signature(x = "TDRcalibrate", y = "missing")`

  Given a `TDRcalibrate` object and a dive number to extract from it, this method plots the observed data and the model. The intended use of this method is through `plotTDR` when `what="dive.model"`.

### Author(s)

Sebastian P. Luque spluque@gmail.com

### See Also

`diveModel`

### Examples

    ## Too long for checks
    ## Continuing the Example from '?calibrateDepth':
    utils::example("calibrateDepth", package="diveMove",
                   ask=FALSE, echo=FALSE, run.donttest=TRUE)

    ## 'diveModel' method
    dm <- getDiveModel(dcalib, 100)
    plotDiveModel(dm, diveNo=100)

    ## 'TDRcalibrate' method
    plotDiveModel(dcalib, diveNo=100)

[Package diveMove version 1.5.2 Index]