g.part3: Detection of sustained inactivity periods as needed for sleep...

In PeteJWatson/ggircal: Raw Accelerometer Data Analysis

Description

Function called by g.shell.GGIR. It estimates the sustained inactivity periods in each day, which are used as input for g.part4 which then labels them as nocturnal sleep or day time sustained inactivity periods. Typical users should work with function g.shell.GGIR only.

Usage

g.part3(metadatadir=c(),f0,f1,anglethreshold = 5,timethreshold = 5,acc.metric="ENMO",
  ignorenonwear=FALSE,overwrite=FALSE,desiredtz="Europe/London",constrain2range=TRUE,
  do.part3.pdf=TRUE)

Arguments

metadatadir	Directory that holds a folder 'meta' and inside this a folder 'basic' which contains the milestone data produced by g.part1. The folderstructure is normally created by g.part1 and g.shell.GGIR will recognise what the value of metadatadir is.
f0	File index to start with (default = 1). Index refers to the filenames sorted in increasing order
f1	File index to finish with (defaults to number of files available)
anglethreshold	Angle threshold (degrees) for sustained inactivity periods detection, default = 5
timethreshold	Time threshold (minutes) for sustained inactivity periods detection, default = 5. This can be specified as multiple thresholds, each of which will be implemented. For example, timethreshold = c(5,10)
acc.metric	Which one of the metrics do you want to consider to analyze L5. The metric of interest need to be calculated in M (see g.part1)
ignorenonwear	If TRUEE then ignore detected monitor non-wear periods to avoid confusion between monitor non-wear time and sustained inactivity (default = TRUE)
overwrite	Overwrite previously generated milestone data by this function for this particular dataset? If FALSE then it will skip the previously processed files (default = FALSE).
desiredtz	See g.getmeta
constrain2range	Whether or not to constrain the range of threshold used in the diary free Sleep period time window detection
do.part3.pdf	Whether to generate a pdf for part 3 (default is TRUE). Turning this off could speed up the processing.

Value

The function provides no values, it only ensures that other functions are called and that their output is stored in .RData files.

• night nightnumber

• definition definition of sustained inactivity. For example, T10A5 refers to 10 minute window and a 5 degree angle (see paper for further explaination).

• start.time.day timestamp when the day started

• nsib.periods number of sustained inactivity bouts

• tot.sib.dur.hrs total duration of all sustained inactivity bouts

• fraction.night.invalid fraction of the night for which accelerometer data was invalid, e.g. monitor not worn

• sib.period number of sustained inactivity period

• sib.onset.time onset time of sustained inactivity period

• sib.end.time end time of sustained inactivity period

Author(s)

Vincent T van Hees <[e-mail]>

References

• van Hees VT, Sabia S, et al. (2015) A novel, open access method to assess sleep duration using a wrist-worn accelerometer, PLoS ONE, November 2015

Examples

## Not run: 
metadatadir = "C:/myfolder/meta" # assumes that there is a subfolder in
# metadatadir named 'basic' containing the output from g.part1
g.part3(metadatadir=metadatadir,anglethreshold=5,timethreshold=5,overwrite=FALSE)

## End(Not run)

PeteJWatson/ggircal documentation built on Nov. 24, 2021, 11:14 a.m.