g.getbout: function to calculate bouts from vector of binary classes

In ucl-cls/mcs-acc: Raw Accelerometer Data Analysis

Description

To detect bouts of behaviour in time series. The function is used by g.analyse

Usage

g.getbout(x,boutduration,boutcriter=0.8,closedbout=FALSE,bout.metric=1,ws3=5)

Arguments

x	vector of zeros and/or ones to be screened for bouts of ones
boutduration	duration of bout in epochs
boutcriter	Minimum percentage of boutduration for which the epoch values are expected to meet the threshold criterium
closedbout	TRUE if you want breaks in bouts to be counted towards time spent in bouts (argument only active for bout.metric 1 and 2)
bout.metric	If value=1 the code uses the MVPA bout definition as has been available since 2014 (see papers by Sabia AJE 2014 and da Silva IJE 2014). Here, the algorithm looks for 10 minute windows in which more than XX percent of the epochs are above mvpathreshold, and then counts the entire window as mvpa. If value=2 the code looks for a group or groups of epochs with a value above mvpathreshold that span a time window of at least mvpadur minutes in which more than boutcriter percent of the epochs are above the threshold. The motivation for the defition 1 was: A person who spends 10 minutes in MVPA with a 2 minute break in the middle is equally active as a person who spends 8 minutes in MVPA without taking a break. Therefore, both should be counted equal and counted as 10 minute MVPA bout. The motivation for the definition 2 is: not counting breaks towards MVPA simplifies interpretation and still counts the two persons in the example as each others equal. If value=3, using sliding window across the data to test bout criteria per window and do not allow for breaks of 1 minute or longer. If value=4, same as 3 but also requires the first and last epoch to require the threshold criteria.
ws3	epoch length in seconds, only needed for bout.metric =3, because it needs to measure how many epochs equal 1 minute breaks

Value

x	Vector with binary numbers indicator where bouts where detected
boutcount	Vector with binary numbers indicator where bouts where detected and counted towards time spent in bouts, see argument closedbout for clarification

Author(s)

Vincent T van Hees <[e-mail]>

Examples

y = g.getbout(x=round(runif(1000,0.4,1)),boutduration = 120,boutcriter=0.9,
    closedbout=FALSE,bout.metric=3,ws3=5)

ucl-cls/mcs-acc documentation built on May 3, 2019, 2:22 p.m.