GGIR package - RDocumentation

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Getting started:

The package vignette and this short tutorial video provide an introduction to GGIR, including: How it can be installed, Key software features, and where to get help.

Contribution guidelines:

We always welcome contributions to the package. If you want to contribute to the development of GGIR, have a look at the contribution guidelines.

Images usaged

The copyright of the GGIR logo as contained in the file vignettes/GGIR-MASTERLOGO-RGB.png lies with Accelting (Almere, The Netherlands), please contact v.vanhees@accelting.com to ask for permission to use this logo.

All other images in this repository are released under the Creative Commons Attribution 4.0 International (CC BY 4.0) license.

Research notice

Please note that this repository is participating in a study into sustainability of open source projects. Data will be gathered about this repository for approximately the next 12 months, starting from June 2021.

Data collected will include number of contributors, number of PRs, time taken to close/merge these PRs, and issues closed.

For more information, please visit the informational page or download the participant information sheet.

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Version

Install

install.packages('GGIR')

Monthly Downloads

1,775

Version

2.5-0

License

LGPL (>= 2.0, < 3) | file LICENSE

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/wadpac/GGIR/

Homepage

https://groups.google.com/forum/#!forum/RpackageGGIR

Maintainer

Vincent T van Hees

Last Published

October 26th, 2021

Functions in GGIR (2.5-0)

createConfigFile

Creates Config File based on variables in g.shell.GGIR environment

POSIXtime2iso8601

Convert POSIX to iso8601 timestamp

Heuristic Algorithms estimating SPT window.

Checks myfun object before it is passed to applyExtfunction

applyExtFunction

Apply external function to acceleration data.

chartime2iso8601

Convert character timestamps to iso8601 timestamp

A package to process multi-day raw accelerometer data

CalcSleepRegularityIndex

Calculates Sleep Regularity Index

Heuristic algorithms for sustiained inactivty bouts detection

create_test_sleeplog_csv

Creates csv sleeplog file for testing purposes

g.create.sp.mat

Converts sleep period information. Not intended for direct use

function to estimate calibration error and make recommendation for addressing it

Generates vector of file names out of datadir input argument

function to read binary files as produced by the accelerometer named 'Genea', not to be confused with the 'GENEActiv' (see package GENEAread for this)

g.fragmentation

Fragmentation metrics from time series.

g.extractheadervars

Extracts header variables from header object

Calculates IV and IS

g.abr.day.names

Abbreviates daynames to numbers, needed for report generation in g.plot5

Function to read activity log and make it useful for the rest of GGIR.

function to analsyse meta-data generated by g.getmeta and g.impute

g.convert.part2.long

Convert part 2 report to long format

g.createcoordinates

Create coordinates for g.plot

Example output from g.calibrate

Extract metrics from acceleration signals

g.analyse.perfile

Function supports g.analyse. Not intended for direct use by user.

data.inspectfile

Example output from g.inspectfile

Example output from g.getmeta

g.part4_extractid

Extracts ID from filename and finds matching rows in sleeplog

create_test_acc_csv

Creates csv data file for testing purposes

g.part5.onsetwaketiming

Identify wake and sleepperiod window timing

Merge output from physical activity and sleep analysis into one report

g.part5.savetimeseries

Saves oart 5 time series to csv files

Extract M5 and L5 from time series

function to calculate bouts from vector of binary classes

function to load and pre-process acceleration files

function to extract meta-data (features) from data in accelerometer file

g.getidfromheaderobject

Extracts participant identifier from header object

function to analyse and summarize pre-processed output from g.part1

Extract start time of a measurement

g.readtemp_movisens

Reads the temperature from movisens files.

Generate report from milestone data produced by g.part4

function to identify invalid periods in the meta-data as generated by g.getmeta and to impute these invalid periods with the average of similar timepoints on other days of the measurement

Function supports g.analyse. Not intended for direct use by user.

Generate report from milestone data produced by g.part5

g.analyse.perday

Function supports g.analyse. Not intended for direct use by user.

g.part5.handle_lux_extremes

Check lux values for extremes and imputes or removes them

Create plot of sustained inactivity bouts

Generate sustiained inactivty bouts report

sustiained inactivty bouts detection

g.part5.lux_persegment

Extract key lux variables per segment of the data.

get_starttime_weekday_meantemp_truncdata

Get starttime (adjusted), weekday, mean temp, and adjust data accordingly.

get_nw_clip_block_params

Set monitor brand specific parameters

Checks whether datadir is a directory or a vector with filenames

Checks whether the files to process are collected with movisens accelerometers.

function to read .wav files as produced by the accelerometer named 'Axivity'

Generate report from milestone data produced by g.part2

Detection of sustained inactivity periods as needed for sleep detection in g.part4.

Function to read .cwa-format files as produced by the accelerometer named 'Axivity'

Assesses whether decimals in fileheader are stored with comma or dot separated decimals

g.detecmidnight

Detect all midnights in a time series

getFirstTimestamp

Extract first timestamp from GENEActiv file

Check whether character timestamp is in iso8601 format.

Detects whether accelerometer is worn

is_this_a_dst_night

Check whether the night starting on a calendar date has DST.

function to inspect accelerometer file for brand, sample frequency and header

Downsample a vector of numeric values at three time resolutions

g.intensitygradient

Intensity gradient calculation

Load and clean sleeplog information

g.part5.definedays

Fix missing night in part 4 output

Labels detected sustained inactivity periods by g.part3 as either part of the Sleep Period Time window or not

g.part5.wakesleepwindows

Label wake and sleepperiod window

function to generate a plot for quality check purposes

Simple function using Rcpp

getStartEndNumeric

Generate start and end page of a day

Read custom csv files with accelerometer data

Generate start and end time of a day

Extract metrics from acceleration signals

g.part5.fixmissingnight

Fix missing night in part 4 output

Generate user-friendly visual report. The first part of the report summarizes important daily metrics in bar plot format. The second part of the report shows the raw data and annotations in 24-hr periods. Angle-z is shown with sleep annotations during the SPT (sleep period time) window. ENMO is shown with daytime inactivity and PA (physical activity) annotations in the lower section of each 24-hr plot. The PA annotations are based on a 10 minute bout metric and 80 of a 10 minute bout of MVPA. Vigorous PA is a short window of time above threshold.vig that is part of a bout of MVPA. Light PA is a short window of time above threshold.lig that is part of a bout of light PA.

Generic functiont to read large blocks of accelerometer data

g.part5.addfirstwake

Adds first wake if it is missing in part 4 output.

getfolderstructure

Extracts folderstructure based on data directory.

identify_levels

Identifies levels of behaviour for g.part5 function.

Adds the sustained inactivity bout to the ts series.

updateBlocksize

Update blocksize of data to be read depending on available memory.

Shell function for analysing an accelerometer dataset.

sustiained inactivty bouts detection

iso8601chartime2POSIX

Convert iso8601 timestamps to POSIX timestamp

Simple function using Rcpp