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

1,581

Version

2.7-1

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

May 30th, 2022

Functions in GGIR (2.7-1)

chartime2iso8601

Convert character timestamps to iso8601 timestamp

POSIXtime2iso8601

Convert POSIX to iso8601 timestamp

Heuristic algorithms for sustiained inactivty bouts detection

Check default parameters

Checks myfun object before it is passed to applyExtfunction

applyExtFunction

Apply external function to acceleration data.

Heuristic Algorithms estimating SPT window.

Shell function for analysing an accelerometer dataset.

Extract parameters from input and add them to params

Calculates IV and IS

create_test_acc_csv

Creates csv data file for testing purposes

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

function to estimate calibration error and make recommendation for addressing it

data.inspectfile

Example output from g.inspectfile

cosinorAnalyses

Apply cosinor anlaysis and extended cosinor analysis

Example output from g.getmeta

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

Extract start time of a measurement

g.part5.classifyNaps

Classify Naps from identified sustained inactivty bouts

Example output from g.calibrate

g.extractheadervars

Extracts header variables from header object

g.fragmentation

Fragmentation metrics from time series.

g.intensitygradient

Intensity gradient calculation

Generates vector of file names out of datadir input argument

Load and clean sleeplog information

create_test_sleeplog_csv

Creates csv sleeplog file for testing purposes

g.part5.definedays

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.

function to generate a plot for quality check purposes

getFirstTimestamp

Extract first timestamp from GENEActiv file

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

g.abr.day.names

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

createConfigFile

Creates Config File based on variables in function GGIR environment

identify_levels

Identifies levels of behaviour for g.part5 function.

Generate start and end time of a day

Check whether character timestamp is in iso8601 format.

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

g.imputeTimegaps

Impute gaps in three axis raw accelerometer data

Downsample a vector of numeric values at three time resolutions

A package to process multi-day raw accelerometer data

CalcSleepRegularityIndex

Calculates Sleep Regularity Index

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

Read custom csv files with accelerometer data

g.convert.part2.long

Convert part 2 report to long format

g.analyse.perfile

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

Extract metrics from acceleration signals

Extract M5 and L5 from time series

function to load and pre-process acceleration files

function to calculate bouts from vector of binary classes

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

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

g.part5.wakesleepwindows

Label wake and sleepperiod window

g.part5.savetimeseries

Saves oart 5 time series to csv files

sustiained inactivty bouts detection

Adds the sustained inactivity bout to the ts series.

g.part5.addfirstwake

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

Generic functiont to read large blocks of accelerometer data

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

g.analyse.perday

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

g.create.sp.mat

Converts sleep period information. Not intended for direct use

g.detecmidnight

Detect all midnights in a time series

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

g.getidfromheaderobject

Extracts participant identifier from header object

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

g.part4_extractid

Extracts ID from filename and finds matching rows in sleeplog

Generate sustiained inactivty bouts report

Simple function using Rcpp

Merge output from physical activity and sleep analysis into one report

Generate report from milestone data produced by g.part4

Generate report from milestone data produced by g.part2

Round numeric columns and replace NA/NaN values by blank

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

updateBlocksize

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

get_starttime_weekday_meantemp_truncdata

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

g.readtemp_movisens

Reads the temperature from movisens files.

g.createcoordinates

Create coordinates for g.plot

Generate report from milestone data produced by g.part5

Parse activity samples from a GT3X file with batch loading

getfolderstructure

Extracts folderstructure based on data directory.

sustiained inactivty bouts detection

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

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

Create plot of sustained inactivity bouts

iso8601chartime2POSIX

Convert iso8601 timestamps to POSIX timestamp

Wrapper function around function GGIR

getStartEndNumeric

Generate start and end page of a day

get_nw_clip_block_params

Set monitor brand specific parameters

g.part5.handle_lux_extremes

Check lux values for extremes and imputes or removes them

g.part5.fixmissingnight

Fix missing night in part 4 output

Load default parameters

Simple function using Rcpp

g.part5.lux_persegment

Extract key lux variables per segment of the data.

Checks whether datadir is a directory or a vector with filenames

Detects whether accelerometer is worn

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

g.part5.onsetwaketiming

Identify wake and sleepperiod window timing

is_this_a_dst_night

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