bouts3NLS: Fit mixture of 3 Poisson Processes to Log Frequency data

In diveMove: Dive analysis and calibration

Description

Functions to model a mixture of 3 random Poisson processes to histogram-like data of log frequency vs interval mid points. This follows Sibly et al. (1990) method, adapted for a three-process model by Berdoy (1993).

Usage

bouts3.nlsFUN(x, a1, lambda1, a2, lambda2, a3, lambda3)
bouts3.nls(lnfreq, start, maxiter)
bouts3.nlsBEC(fit)
plotBouts3.nls(fit, lnfreq, bec.lty, ...)

Arguments

x	numeric vector with values to model.
a1, lambda1, a2, lambda2, a3, lambda3	numeric: parameters from the mixture of Poisson processes.
lnfreq	data.frame with named components lnfreq (log frequencies) and corresponding x (mid points of histogram bins).
start, maxiter	Arguments passed to nls.
fit	nls object.
bec.lty	Line type specification for drawing the BEC reference line.
...	Arguments passed to plot.default.

Details

bouts3.nlsFUN is the function object defining the nonlinear least-squares relationship in the model. It is not meant to be used directly, but is used internally by bouts3.nls.

bouts3.nls fits the nonlinear least-squares model itself.

bouts3.nlsBEC calculates the BEC from a list object, as the one that is returned by nls, representing a fit of the model. plotBouts3.nls plots such an object.

Value

bouts3.nlsFUN returns a numeric vector evaluating the mixture of 3 Poisson process.

bouts3.nls returns an nls object resulting from fitting this model to data.

bouts3.nlsBEC returns a number corresponding to the bout ending criterion derived from the model.

plotBouts3.nls plots the fitted model with the corresponding data.

Author(s)

Sebastian P. Luque [e-mail]

References

Sibly, R.; Nott, H. and Fletcher, D. (1990) Splitting behaviour into bouts. Animal Behaviour 39, 63-69.

Berdoy, M. (1993) Defining bouts of behaviour: a three-process model. Animal Behaviour 46, 387-396.

See Also

bouts.mle for a better approach; boutfreqs; boutinit

Examples

## Using the Example from '?diveStats':
utils::example("diveStats", package="diveMove",
               ask=FALSE, echo=FALSE)
## Postdive durations
postdives <- tdrX.tab$postdive.dur
postdives.diff <- abs(diff(postdives))
## Remove isolated dives
postdives.diff <- postdives.diff[postdives.diff < 4000]

## Construct histogram
lnfreq <- boutfreqs(postdives.diff, bw=0.1, plot=FALSE)

startval <- boutinit(lnfreq, c(50, 400))
## Drop names by wrapping around as.vector()
startval.l <- list(a1=as.vector(startval[[1]]["a"]),
                   lambda1=as.vector(startval[[1]]["lambda"]),
                   a2=as.vector(startval[[2]]["a"]),
                   lambda2=as.vector(startval[[2]]["lambda"]),
                   a3=as.vector(startval[[3]]["a"]),
                   lambda3=as.vector(startval[[3]]["lambda"]))

## Fit the 3 process model
bout.fit <- bouts3.nls(lnfreq, start=startval.l, maxiter=500)
summary(bout.fit)
plotBouts(bout.fit)

## Estimated BEC
bec3(bout.fit)

diveMove documentation built on May 2, 2019, 4:47 p.m.