diveModel-class: Class "diveModel" for representing a model for identifying dive phases

Description

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

Arguments

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

Sebastian P. Luque spluque@gmail.com

Examples

Run this code

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))