GGIR package - RDocumentation

Learn R Programming

Getting started:

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

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

1,581

Version

3.2-0

License

Apache License (== 2.0) | 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

February 20th, 2025

Functions in GGIR (3.2-0)

Detrended Fluctuation Analysis

Estimated self-similarity parameter

POSIXtime2iso8601

Convert POSIX to iso8601 timestamp

A package to process multi-day raw accelerometer data

Activity balance index (ABI)

Shell function for analysing an accelerometer dataset.

CalcSleepRegularityIndex

Calculates Sleep Regularity Index

Heuristic Algorithms estimating SPT window.

Heuristic algorithms for sustiained inactivty bouts detection

apply_cosinor_IS_IV_Analyses

Apply Cosinor Analyses to time series

checkMilestoneFolders

Checks for existence of folders to process

Append GGIR milestone data from neighbouring or overlapping recordings

Checks myfun object before it is passed to applyExtfunction

ShellDoc2Vignette

Extract Definition from Shell Documentation

Function to revise format of user-provided logs

Check default parameters

create_test_sleeplog_csv

Creates csv sleeplog file for testing purposes

Aggregates event data as produced by external function

convertEpochData

convert external Epoch data to GGIR part 1 milestone data format

Metalong object as part of part 1 milestone data

Example output from g.getmeta

create_test_acc_csv

Creates csv data file for testing purposes

applyExtFunction

Apply external function to acceleration data.

createConfigFile

Creates Config File based on variables in function GGIR environment

data.inspectfile

Example output from g.inspectfile

Example output from g.calibrate

Calculates IV and IS

filterNonwearNight

Filters short lasting nonwear during the night

g.extractheadervars

Extracts header variables from header object

detect_nonwear_clipping

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

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

Time series data.frame stored by part 5

Extract parameters from input and add them to params

g.convert.part2.long

Convert part 2 report to long format

Generates vector of file names out of datadir input argument

g.fragmentation

Fragmentation metrics from time series.

Extract ID from file header object

g.detecmidnight

Detect all midnights in a time series

function to calculate bouts from vector of binary classes

g.create.sp.mat

Converts sleep period information. Not intended for direct use

Extract M5 and L5 from time series

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

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

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

Extract start time of a measurement

Extract metrics from acceleration signals

g.analyse.perfile

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

Merge output from physical activity and sleep analysis into one report

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

g.intensitygradient

Intensity gradient calculation

g.part5.addfirstwake

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

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

g.analyse.perday

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

Adds the sustained inactivity bout to the ts series.

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

cosinor_IS_IV_Analyses

Apply cosinor anlaysis and extended cosinor analysis

g.part5.definedays

Fix missing night in part 4 output

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

g.part5.classifyNaps

Classify Naps from identified sustained inactivty bouts

Perform temporal pattern analyses

g.part5.savetimeseries

Saves part 5 time series to csv files

correctOlderMilestoneData

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

g.part5.analyseRest

Analyse rest (internal function)

g.part5.fixmissingnight

Fix missing night in part 4 output

g.part5_analyseSegment

Analyses the time series per time segment for part 5

function to estimate calibration error and make recommendation for addressing it

g.part5_initialise_ts

Initialise time series data from for part 5

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

Generate report from milestone data produced by g.part4

Load and clean sleeplog information

g.part5.handle_lux_extremes

Check lux values for extremes and imputes or removes them

g.imputeTimegaps

Impute gaps in three axis raw accelerometer data

g.part5.wakesleepwindows

Label wake and sleepperiod window

get_nw_clip_block_params

Set monitor brand specific parameters

get_starttime_weekday_truncdata

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

g.report.part5_dictionary

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

function to generate a plot for quality check purposes

function to load and pre-process acceleration files

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

g.part4_extractid

Extracts ID from filename and finds matching rows in sleeplog

g.readtemp_movisens

Reads the temperature from movisens files.

Generate report from milestone data produced by g.part2

part6PairwiseAggregation

part6PairwiseAggregation

Read custom csv files with accelerometer data

iso8601chartime2POSIX

Convert iso8601 timestamps to POSIX timestamp

Generate report from milestone data produced by g.part5

Generate sustiained inactivty bouts report

Detects whether accelerometer is worn

g.part5.lux_persegment

Extract key lux variables per segment of the data.

g.part5.onsetwaketiming

Identify wake and sleepperiod window timing

Wrapper function around function GGIR

Load default parameters

Generate report from milestone data produced by g.part6

sustiained inactivty bouts detection

Checks whether datadir is a directory or a vector with filenames

identify_levels

Identifies levels of behaviour for g.part5 function.

getfolderstructure

Extracts folderstructure based on data directory.

sustiained inactivty bouts detection

Round numeric columns and replace NA/NaN values by blank

Create plot of sustained inactivity bouts

parametersVignette

Builds Section for Parameters Vignette

part6AlignIndividuals

part6AlignIndividuals

updateBlocksize

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

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.

Check whether character timestamp is in iso8601 format.

Generic functiont to read large blocks of accelerometer data

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

Generate visualisation of time series produced by part 5.

is_this_a_dst_night

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