cyphid (version 1.1)

get.all.breaks: Identify all breakpoints.

Description

This function divides chewing sequnces into individual cycles and identifies the phase transitions within each cycle.

Usage

get.all.breaks(dataset, CycleBreaks = NULL, window = NULL)

Arguments

dataset

A matrix of chewing sequences. Each column represents a single sequence.

CycleBreaks

A matrix of frame numbers used to force a sequence to break at predetermed locations. Each column represents the break points for a single sequence.

window

The frame limit for which no two cycle breaks can occur.

Value

This function returns 8 objects.

openbreaks

openbreaks, closebreaks, FCSC, and SOFO are matricies with one column for each sequence. Columns contain the frame numbers associated with either the open, close, FCSC, or SOFO loactions for each sequence.

closebreaks

see openbreaks

FCSC

see openbreaks

SOFO

see openbreaks

cyclemat

cyclemat is a matrix with one column for each cycle. Columns contain the displacement values for each cycle.

close.cycle

close.cycle, FCSC.cycle, SOFO.cycle is a vector with a value for each cycle. The values represent either the location of close, FCSC, or SOFO relative to the cycle.

FCSC.cycle

see close.cycle

SOFO.cycle

see close.cycle

Examples

# Run primary function for dividing sequences into cycles and cycles into phases
JawBreaks40 <- get.all.breaks(jaw, window=40)

# Check window based on cycle durations.
cycledurs <- get.cycle.durations(JawBreaks40$cyclemat)
win <- get.window(cycledurs)
win

# Rerun with modified window
JawBreaks27 <- get.all.breaks(jaw, window=27)

# Plot the output
plot(jaw[,1])
abline(v=JawBreaks27$openbreaks[,1])