diveMove (version 1.4.1)

bout-misc: Fit a Broken Stick Model on Log Frequency Data for identification of bouts of behaviour

Description

Application of methods described by Sibly et al. (1990) and Mori et al. (2001) for the identification of bouts of behaviour.

Usage

boutfreqs(x, bw, method=c("standard", "seq.diff"), plot=TRUE, ...)
boutinit(lnfreq, x.break, plot=TRUE, ...)
labelBouts(x, bec, bec.method=c("standard", "seq.diff"))
logit(p)
unLogit(logit)

Arguments

x

numeric vector on which bouts will be identified based on “method”. For labelBouts it can also be a matrix with different variables for which bouts should be identified.

bw

numeric scalar: bin width for the histogram.

method, bec.method

character: method used for calculating the frequencies: “standard” simply uses x, while “seq.diff” uses the sequential differences method.

plot

logical, whether to plot results or not.

...

For boutfreqs, arguments passed to hist (must exclude breaks and include.lowest); for boutinit, arguments passed to plot (must exclude type).

lnfreq

data.frame with components lnfreq (log frequencies) and corresponding x (mid points of histogram bins).

x.break

vector of length 1 or 2 with x value(s) defining the break(s) point(s) for broken stick model, such that x < x.break[1] is 1st process, and x >= x.break[1] & x < x.break[2] is 2nd one, and x >= x.break[2] is 3rd one.

bec

numeric vector or matrix with values for the bout ending criterion which should be compared against the values in x for identifying the bouts.

p

numeric vector of proportions (0-1) to transform to the logit scale.

logit

numeric scalar: logit value to transform back to original scale.

Value

boutfreqs returns a data frame with components lnfreq containing the log frequencies and x, containing the corresponding mid points of the histogram. Empty bins are excluded. A plot (histogram of input data) is produced as a side effect if argument plot is TRUE. See the Details section.boutinit returns a list with as many elements as the number of processes implied by x.break (i.e. length(x.break) + 1). Each element is a vector of length two, corresponding to a and lambda, which are starting values derived from broken stick model. A plot is produced as a side effect if argument plot is TRUE.labelBouts returns a numeric vector sequentially labelling each row or element of x, which associates it with a particular bout.unLogit and logit return a numeric vector with the (un)transformed arguments.

Details

This follows the procedure described in Mori et al. (2001), which is based on Sibly et al. 1990. Currently, only a two process model is supported.

boutfreqs creates a histogram with the log transformed frequencies of x with a chosen bin width and upper limit. Bins following empty ones have their frequencies averaged over the number of previous empty bins plus one.

boutinit fits a "broken stick" model to the log frequencies modelled as a function of x (well, the midpoints of the binned data), using chosen value(s) to separate the two or three processes.

labelBouts labels each element (or row, if a matrix) of x with a sequential number, identifying which bout the reading belongs to. The bec argument needs to have the same dimensions as x to allow for situations where bec within x.

logit and unLogit are useful for reparameterizing the negative maximum likelihood function, if using Langton et al. (1995).

References

Langton, S.; Collett, D. and Sibly, R. (1995) Splitting behaviour into bouts; a maximum likelihood approach. Behaviour 132, 9-10.

Luque, S.P. and Guinet, C. (2007) A maximum likelihood approach for identifying dive bouts improves accuracy, precision, and objectivity. Behaviour, 144, 1315-1332.

Mori, Y.; Yoda, K. and Sato, K. (2001) Defining dive bouts using a sequential differences analysis. Behaviour, 2001 138, 1451-1466.

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

See Also

bouts2.nls, bouts.mle. These include an example for labelBouts.

Examples

## Using the Example from '?diveStats':
utils::example("diveStats", package="diveMove",
               ask=FALSE, echo=FALSE)
postdives <- tdrX.tab$postdive.dur[tdrX.tab$phase.no == 2]
## Remove isolated dives
postdives <- postdives[postdives < 2000]
lnfreq <- boutfreqs(postdives, bw=0.1, method="seq.diff", plot=FALSE)
boutinit(lnfreq, 50)

## See ?bouts.mle for labelBouts() example