g.part5: Merge output from physical activity and sleep analysis into...

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

Description

Function to merge the output from g.part2 and g.part4 into one report enhanced with profiling of sleep and physical activity stratified across intensity levels and based on bouted periods as well as non-bouted periods.

Usage

g.part5(datadir=c(),metadatadir=c(),f0=c(),f1=c(),strategy=1,maxdur=7,
hrs.del.start=0,hrs.del.end =0,
loglocation= c(),excludefirstlast=FALSE,windowsizes=c(5,900,3600),
boutcriter.mvpa=0.8,boutcriter.in=0.9,boutcriter.lig=0.8,
storefolderstructure=FALSE,threshold.lig = c(40),threshold.mod = c(100),
threshold.vig = c(400),timewindow=c("MM","WW"),boutdur.mvpa = c(1,5,10),
boutdur.in = c(10,20,30),boutdur.lig = c(1,5,10),winhr = 5,
M5L5res = 10,overwrite=FALSE,desiredtz="Europe/London",bout.metric=4)

Arguments

datadir	Directory where the accelerometer files are stored or list of accelerometer filenames and directories
metadatadir	Directory that holds a folders '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)
strategy	how to deal with knowledge about study protocol. value = 1 means select data based on hrs.del.start, hrs.del.end, and maxdur. Value = 2 makes that only the data between the first midnight and the last midnight is used for imputation, see g.impute
maxdur	how many DAYS after start of experiment did experiment definitely stop? (set to zero if unknown = default), see g.impute
hrs.del.start	how many HOURS after start of experiment did wearing of monitor start?, see g.impute
hrs.del.end	how many HOURS before the end of the experiment did wearing of monitor definitely end?, see g.impute
loglocation	Location of the spreadsheet (csv) with sleep log information. The spreadsheet needs to have the following structure: one column for participant id, and then followed by alternatingly one column for onset time and one column for waking time. Timestamps are to be stored without date as in 18:20:00. If onset corresponds to lights out or intention to fall asleep, then it is the end-users responsibility to account for this in the interpretation of the results.
excludefirstlast	If TRUE then the first and last night of the measurement are ignored for the sleep assessment.
windowsizes	see g.getmeta
boutcriter.mvpa	A number between 0 and 1 and defines what fraction of a bout needs to be above the mvpathreshold
boutcriter.in	A number between 0 and 1 and defines what fraction of a bout needs to be below the light threshold
boutcriter.lig	A number between 0 and 1 and defines what fraction of a bout needs to be between the light and moderage threshold
storefolderstructure	Store folder structure of the accelerometer data
threshold.lig	Threshold for light physical activity to separate inactivity from light. Value can be one number or an array of multiple numbers, e.g. threshold.lig =c(30,40). If multiple numbers are entered then analysis will be repliced for each combination of threshold values. Threshold is applied to the first metric in the milestone data, so if you have only specified do.ENMO == TRUE then it will be applied to ENMO.
threshold.mod	Threshold for moderate physical activity to separate light from moderate. Value can be one number or an array of multiple numbers, e.g. threshold.mod =c(100,110). If multiple numbers are entered then analysis will be repliced for each ombination of threshold values. Threshold is applied to the first metric in the milestone data, so if you have only specified do.ENMO == TRUE then it will be applied to ENMO.
threshold.vig	Threshold for vigorous physical activity to separate moderate from vigorous. Value can be one number or an array of multiple numbers, e.g. threshold.mod =c(400,500). If multiple numbers are entered then analysis will be repliced for each combination of threshold values. Threshold is applied to the first metric in the milestone data, so if you have only specified do.ENMO == TRUE then it will be applied to ENMO.
timewindow	Timewindow over which summary statistics are derived. Value can be "MM" (midnight to midnight), "WW" (waking time to waking time), or both c("MM","WW").
boutdur.mvpa	Durations of mvpa bouts in minutes to be extracted. The default values is c(1,5,10) and will start with the identification of 10 minute bouts, followed by 5 minute bouts in the rest of the data, and followed by 1 minute bouts in the rest of the data.
boutdur.in	Durations of inactivty bouts in minutes to be extracted. Inactivity bouts are detected in the segments of the data which were not labelled as sleep or MVPA bouts. The default duration values is c(10,20,30), this will start with the identification of 30 minute bouts, followed by 20 minute bouts in the rest of the data, and followed by 10 minute bouts in the rest of the data.
boutdur.lig	Durations of light activty bouts in minutes to be extracted. Light activity bouts are detected in the segments of the data which were not labelled as sleep, MVPA, or inactivity bouts. The default duration values is c(1,5,10), this will start with the identification of 10 minute bouts, followed by 5 minute bouts in the rest of the data, and followed by 1 minute bouts in the rest of the data.
M5L5res	resoltion of L5 and M5 analysis in minutes (default: 10 minutes)
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
bout.metric	See documnetion in g.getbout and
winhr	see g.getmeta

Value

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

Author(s)

Vincent T van Hees <[e-mail]>

References

• This function has not been described in a scientific journal yet

Examples

## Not run: 
metadatadir = "C:/myfolder/meta"
g.part5(metadatadir=metadatadir)

## End(Not run)

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