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.
g.part3(metadatadir=c(), f0, f1, myfun=c(),
params_sleep = c(), params_metrics = c(), params_output = c(), params_general = c(),
...)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.
File index to start with (default = 1). Index refers to the filenames sorted in increasing order
File index to finish with (defaults to number of files available)
External function object to be applied to raw data. See details applyExtFunction.
See details
List, see g.part1.
List, see g.part1
List, see g.part1
To ensure compatibility with R scripts written for older GGIR versions, the user can also provide parameters listed in the params_ objects as direct argument.
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
GGIR comes with many processing parameters, which have been thematically grouped in parameter objects (R list). By running print(load_params()) you can see the default values of all the parameter objects. When g.part 3 is used via g.shell.GGIR you have the option to specifiy a configuration file, which will overrule the default parameter values. Further, as user you can set parameter values as input argument to both g.part3 and g.shell.GGIR. Directly specified argument overrule the configuration file and default values.
See the GGIR package vignette for a more elaborate overview of parameter objects and their usage across GGIR.
The parameter objects used by GGIR part 3 (g.part3) that are no already discussed in g.part1 or g.part2 are:
A list of parameters used to configure the sleep analysis as performend in GGIR part 3 and 4.
Boolean. If TRUE then sleep onset and waking time are defined based on timestamps derived from the guider. If participants were instructed NOT to wear the accelerometer during waking hours then set to TRUE, in all other scenarios set to FALSE (default).
Do not use, now replaced by argument relyonguider. Values provided to argument relyonsleeplog will be passed on to argument relyonguider to not preserve functionality of old R scripts.
Numeric. The time window during which sustained inactivity will be assumed to represent sleep, e.g. def.noc.sleep=c(21,9). This is only used if no sleep log entry is available. If def.noc.sleep is left blank 'def.noc.sleep=c()' then the 12 hour window centred at the least active 5 hours of the 24 hour period will be used instead. Here, L5 is hardcoded and will not change by changing argument winhr in function g.part2. If def.noc.sleep is filled with a single integer, e.g. def.noc.sleep=c(1) then the window will be detected with based on built in algorithms. See argument HASPT.algo from HASPT for specifying which of those algorithms to use.
Character to indicate type of sleeplog, default "SPT". Set to "TimeInBed" if sleep log recorded time in bed to enable calculation of sleep latency and sleep efficiency.
Number of nights for which sleep log information should be available. It assumes that this is constant within a study. If sleep log information is missing for certain nights then leave these blank.
Character. Path to csv file with sleep log information. See package vignette for how to format this file.
Numeric. Column number in the sleep log spreadsheet in which the participant ID code is stored (default = 1)
Numeric. Column number in the sleep log spreadsheet where the onset of the first night starts
Boolean. Should the participant identifier as stored in the sleeplog be interpretted as a number (TRUE=default) or character (FALSE)?
Boolean, see g.sib.sum
Boolean, Whether or not to constrain the range of threshold used in the diary free sleep period time window detection
Boolean, see HASPT
Character, character to indicate what heuristic algorithm to use for detecting the SPT window, see HASPT
Character, character to indicate what heuristic algorithm to use for detecting the sustained inactivity bouts (SIB), see HASIB
Character, character to indicate which axis to use for the Sadeh1994 algorithm, and other algortihms that related on count-based Actigraphy such as Galland2012.
Character, g.loadlog
Character, see g.part5.classifyNaps
Integer to indicate which axis is the longitudinal axis. If not provided function will estimate longitudinal axis. Only used when sensor.location="hip" or HASPT.algo="HorAngle".
Numeric, Angle threshold (degrees) for sustained inactivity periods detection, default = 5
Numeric, 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)
Numeric, see g.part5.classifyNaps
Numeric, see g.part5.classifyNaps
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
van Hees VT, Sabia S, et al. (2018) Estimating sleep parameters using an accelerometer without sleep diary. Scientific Reports.
# NOT RUN {
# }
# 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)
# }
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