GGIR package - RDocumentation

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Getting started:

The package documentation provides extensive documentation on GGIR and its functionalities.

Getting help:

For guidance on how to seek help see this page.

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.

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Version

Install

install.packages('GGIR')

Monthly Downloads

1,343

Version

3.3-8

License

Apache License (== 2.0) | file LICENSE

Issues

Pull Requests

Stars

Forks

Repository

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

Homepage

https://wadpac.github.io/GGIR/

Maintainer

Vincent T van Hees

Last Published

July 24th, 2026

Functions in GGIR (3.3-8)

Shell function for analysing an accelerometer dataset.

Extract M5 and L5 from time series

Heuristic algorithms for sustiained inactivty bouts detection

correctOlderMilestoneData

Corrects milestone data from g.part1 generated in older GGIR versions

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

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

Calculates IV and IS

convertEpochData

convert external Epoch data to GGIR part 1 milestone data format

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

Generate report from milestone data produced by g.part5

Generates vector of file names out of datadir input argument

cosinor_IS_IV_Analyses

Apply cosinor anlaysis and extended cosinor analysis

filterNonwearNight

Filters short lasting nonwear during the night

detect_nonwear_clipping

Detect non-wear and clipping time in the raw accelerometer data

Time series data.frame stored by part 5

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

Metalong object as part of part 1 milestone data

get_starttime_weekday_truncdata

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

sustiained inactivty bouts detection

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

Read custom csv files with accelerometer data

g.analyse.perfile

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

Extract metrics from acceleration signals

getfolderstructure

Extracts folderstructure based on data directory.

g.analyse.perday

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

Append GGIR milestone data from neighbouring or overlapping recordings

g.extractheadervars

Extracts header variables from header object

g.part3_alignIndexVectors

Aligns index vectors used inside g.part3_correct_guider

g.fragmentation

Fragmentation metrics from time series.

g.part5.definedays

Fix missing night in part 4 output

g.part3_correct_guider

Correct guider estimates

get_nw_clip_block_params

Set monitor brand specific parameters

function to load and pre-process acceleration files

g.imputeTimegaps

Impute gaps in three axis raw accelerometer data

Load and clean sleeplog information

Load default parameters

iso8601chartime2POSIX

Convert iso8601 timestamps to POSIX timestamp

markerButtonForRest

Improve the labelling of rest with marker button data

parametersVignette

Builds Section for Parameters Vignette

A package to process multi-day raw accelerometer data

Detrended Fluctuation Analysis

POSIXtime2iso8601

Convert POSIX to iso8601 timestamp

Activity balance index (ABI)

Heuristic Algorithms estimating SPT window.

CalcSleepRegularityIndex

Calculates Sleep Regularity Index

Estimated self-similarity parameter

applyExtFunction

Apply external function to acceleration data.

ShellDoc2Vignette

Extract Definition from Shell Documentation

Append GGIR milestone data from neighbouring or overlapping recordings

Add split names to output object in g.part4 and g.part5

Aggregates event data as produced by external function

Function to revise format of user-provided logs

checkMilestoneFolders

Checks for existence of folders to process

build_epoch_table

Build a flat epoch table from ms5.outraw time series

Example output from g.getmeta

create_test_acc_csv

Creates csv data file for testing purposes

createConfigFile

Creates Config File based on variables in function GGIR environment

Checks myfun object before it is passed to applyExtfunction

Check default parameters

apply_cosinor_IS_IV_Analyses

Apply Cosinor Analyses to time series

data.inspectfile

Example output from g.inspectfile

g.abr.day.names

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

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

create_test_sleeplog_csv

Creates csv sleeplog file for testing purposes

function to estimate calibration error and make recommendation for addressing it

Example output from g.calibrate

g.create.sp.mat

Converts sleep period information. Not intended for direct use

Extract parameters from input and add them to params

Extract ID from file header object

g.convert.part2.long

Convert part 2 report to long format

g.detecmidnight

Detect all midnights in a time series

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

function to calculate bouts from vector of binary classes

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

g.intensitygradient

Intensity gradient calculation

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

Extract start time of a measurement

g.part4_extractid

Extracts ID from filename and finds matching rows in sleeplog

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

g.part5.analyseRest

Analyse rest (internal function)

Adds the sustained inactivity bout to the ts series.

g.part5_analyseSegment

Analyses the time series per time segment for part 5

g.part5.onsetwaketiming

Identify wake and sleepperiod window timing

g.part5.wakesleepwindows

Label wake and sleepperiod window

g.part5.savetimeseries

Saves part 5 time series to csv files

g.report.part5_dictionary

Generate data dictionary for reports from milestone data produced by g.part5

Generate report from milestone data produced by g.part2

Generate report from milestone data produced by g.part4

g.part5.fixmissingnight

Fix missing night in part 4 output

Merge output from physical activity and sleep analysis into one report

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

g.part5.lux_persegment

Extract key lux variables per segment of the data.

g.part5.handle_lux_extremes

Check lux values for extremes and imputes or removes them

g.part5.addfirstwake

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

Generic functiont to read large blocks of accelerometer data

g.readtemp_movisens

Reads the temperature from movisens files.

getPart1BasicInfo

Get basic info form the part 1 milestone file

Detects whether accelerometer is worn

sustiained inactivty bouts detection

Generate report from milestone data produced by g.part6

Check whether character timestamp is in iso8601 format.

Wrapper function around function GGIR

is_this_a_dst_night

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

Create plot of sustained inactivity bouts

Generate sustiained inactivty bouts report

Checks whether datadir is a directory or a vector with filenames

updateBlocksize

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

Round numeric columns and replace NA/NaN values by blank

part6AlignIndividuals

part6AlignIndividuals

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

g.part5_initialise_ts

Initialise time series data from for part 5

identify_levels

Identifies levels of behaviour for g.part5 function.

inspect_binFile_brand

Identify the Device Brand from a Binary File

Generate visualisation of time series produced by part 5.

write_dashboard_parquet

Write consolidated dashboard Parquet output

part6PairwiseAggregation

part6PairwiseAggregation

write_epoch_parquet

Write flat epoch-level Parquet output

Perform temporal pattern analyses

get split names from filename