R: Class "diveModel" for representing a model for identifying...

diveModel-class {diveMove} | R Documentation

## Class "diveModel" for representing a model for identifying dive phases

### Description

Details of model used to identify the different phases of a dive.

### Slots

`label.matrix`

  Object of class `"matrix"`. A 2-column character matrix with row numbers matching each observation to the full `TDR` object, and a vector labelling the phases of each dive.

`model`

  Object of class `"character"`. A string identifying the specific model fit to dives for the purpose of dive phase identification. It should be one of ‘smooth.spline’ or ‘unimodal’.

`dive.spline`

  Object of class `"smooth.spline"`. Details of cubic smoothing spline fit (see `smooth.spline`).

`spline.deriv`

  Object of class `"list"`. A list with the first derivative of the smoothing spline (see `predict.smooth.spline`).

`descent.crit`

  Object of class `"numeric"`. The index of the observation at which the descent was deemed to have ended (from initial surface observation).

`ascent.crit`

  Object of class `"numeric"`. the index of the observation at which the ascent was deemed to have ended (from initial surface observation).

`descent.crit.rate`

  Object of class `"numeric"`. The rate of descent corresponding to the critical quantile used.

`ascent.crit.rate`

  Object of class `"numeric"`. The rate of ascent corresponding to the critical quantile used.

### Objects from the Class

Objects can be created by calls of the form `new("diveModel", ...)`.

‘diveModel’ objects contain all relevant details of the process to identify phases of a dive. Objects of this class are typically generated during depth calibration, using `calibrateDepth`, more specifically `.cutDive`.

### Author(s)

Sebastian P. Luque spluque@gmail.com

### See Also

`getDiveDeriv`, `plotDiveModel`

### Examples

    showClass("diveModel")

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

    ## Compare dive models for dive phase detection
    diveNo <- 255
    diveX <- as.data.frame(extractDive(dcalib, diveNo=diveNo))
    diveX.m <- cbind(as.numeric(row.names(diveX[-c(1, nrow(diveX)), ])),
                     diveX$depth[-c(1, nrow(diveX))],
                     diveX$time[-c(1, nrow(diveX))])

    ## calibrateDepth() default unimodal regression. Number of inner knots is
    ## either 10 or the number of samples in the dive, whichever is larger.
    (phases.uni <- diveMove:::.cutDive(diveX.m, smooth.par=0.2, knot.factor=20,
                                       dive.model="unimodal",
                                       descent.crit.q=0.01, ascent.crit.q=0))
    ## Smoothing spline model, using default smoothing parameter.
    (phases.spl <- diveMove:::.cutDive(diveX.m, smooth.par=0.2, knot.factor=20,
                                       dive.model="smooth.spline",
                                       descent.crit.q=0.01, ascent.crit.q=0))
    plotDiveModel(phases.spl,
                  diveNo=paste(diveNo, ", smooth.par=", 0.2, sep=""))
    plotDiveModel(phases.uni, diveNo=paste(diveNo))

[Package diveMove version 1.6.0 Index]