GGIR package - RDocumentation

Learn R Programming

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.

Copy Link

Version

Install

install.packages('GGIR')

Monthly Downloads

1,197

Version

3.3-9

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

September 12th, 2026

Functions in GGIR (3.3-9)

Checks myfun object before it is passed to applyExtfunction

Function to revise format of user-provided logs

Extract parameters from input and add them to params

create_test_acc_csv

Creates csv data file for testing purposes

apply_cosinor_IS_IV_Analyses

Apply Cosinor Analyses to time series

detect_nonwear_clipping

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

ShellDoc2Vignette

Extract Definition from Shell Documentation

createConfigFile

Creates Config File based on variables in function GGIR environment

Extract ID from file header object

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

applyExtFunction

Apply external function to acceleration data.

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

Generates vector of file names out of datadir input argument

Shell function for analysing an accelerometer dataset.

data.inspectfile

Example output from g.inspectfile

g.convert.part2.long

Convert part 2 report to long format

g.create.sp.mat

Converts sleep period information. Not intended for direct use

Aggregates event data as produced by external function

cosinor_IS_IV_Analyses

Apply cosinor anlaysis and extended cosinor analysis

correctOlderMilestoneData

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

g.fragmentation

Fragmentation metrics from time series.

g.extractheadervars

Extracts header variables from header object

filterNonwearNight

Filters short lasting nonwear during the night

g.analyse.perfile

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

Extract metrics from acceleration signals

Heuristic algorithms for sustiained inactivty bouts detection

Append GGIR milestone data from neighbouring or overlapping recordings

Generate report from milestone data produced by g.part4

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

Generate report from milestone data produced by g.part2

g.part5.lux_persegment

Extract key lux variables per segment of the data.

Check default parameters

g.intensitygradient

Intensity gradient calculation

g.part5.handle_lux_extremes

Check lux values for extremes and imputes or removes them

Metalong object as part of part 1 milestone data

Time series data.frame stored by part 5

Calculates IV and IS

function to estimate calibration error and make recommendation for addressing it

convertEpochData

convert external Epoch data to GGIR part 1 milestone data format

g.detecmidnight

Detect all midnights in a time series

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

Merge output from physical activity and sleep analysis into one report

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

g.part5.addfirstwake

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

create_test_sleeplog_csv

Creates csv sleeplog file for testing purposes

g.part5.onsetwaketiming

Identify wake and sleepperiod window timing

Extract M5 and L5 from time series

Example output from g.calibrate

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

function to calculate bouts from vector of binary classes

Perform temporal pattern analyses

g.part5_initialise_ts

Initialise time series data from for part 5

g.part5.savetimeseries

Saves part 5 time series to csv files

g.part3_alignIndexVectors

Aligns index vectors used inside g.part3_correct_guider

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

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

Extract start time of a measurement

Generate report from milestone data produced by g.part6

Wrapper function around function GGIR

markerButtonForRest

Improve the labelling of rest with marker button data

iso8601chartime2POSIX

Convert iso8601 timestamps to POSIX timestamp

Load default parameters

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.part4_extractid

Extracts ID from filename and finds matching rows in sleeplog

g.part5.wakesleepwindows

Label wake and sleepperiod window

Adds the sustained inactivity bout to the ts series.

g.part5.analyseRest

Analyse rest (internal function)

g.report.part5_dictionary

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

Generate report from milestone data produced by g.part5

inspect_binFile_brand

Identify the Device Brand from a Binary File

get_nw_clip_block_params

Set monitor brand specific parameters

identify_levels

Identifies levels of behaviour for g.part5 function.

get split names from filename

g.part5_analyseSegment

Analyses the time series per time segment for part 5

parametersVignette

Builds Section for Parameters Vignette

g.part3_correct_guider

Correct guider estimates

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

Load and clean sleeplog information

function to load and pre-process acceleration files

g.imputeTimegaps

Impute gaps in three axis raw accelerometer data

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.

Detects whether accelerometer is worn

getPart1BasicInfo

Get basic info form the part 1 milestone file

function to generate a plot for quality check purposes

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

g.part5.fixmissingnight

Fix missing night in part 4 output

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

sustiained inactivty bouts detection

Generic functiont to read large blocks of accelerometer data

g.part5.definedays

Fix missing night in part 4 output

Generate visualisation of time series produced by part 5.

g.readtemp_movisens

Reads the temperature from movisens files.

Read custom csv files with accelerometer data

part6AlignIndividuals

part6AlignIndividuals

get_starttime_weekday_truncdata

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

Generate sustiained inactivty bouts report

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

Checks whether datadir is a directory or a vector with filenames

getfolderstructure

Extracts folderstructure based on data directory.

Round numeric columns and replace NA/NaN values by blank

Check whether character timestamp is in iso8601 format.

Create plot of sustained inactivity bouts

write_epoch_parquet

Write flat epoch-level Parquet output

Append GGIR milestone data from neighbouring or overlapping recordings

write_dashboard_parquet

Write consolidated dashboard Parquet output

updateBlocksize

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

is_this_a_dst_night

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

part6PairwiseAggregation

part6PairwiseAggregation

Activity balance index (ABI)

Estimated self-similarity parameter

Detrended Fluctuation Analysis

POSIXtime2iso8601

Convert POSIX to iso8601 timestamp

A package to process multi-day raw accelerometer data

CalcSleepRegularityIndex

Calculates Sleep Regularity Index

Heuristic Algorithms estimating SPT window.