Raw Accelerometer Data Analysis


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Documentation for package ‘GGIR’ version 2.6-0

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GGIR-package A package to process multi-day raw accelerometer data
applyExtFunction Apply external function to acceleration data.
CalcSleepRegularityIndex Calculates Sleep Regularity Index
chartime2iso8601 Convert character timestamps to iso8601 timestamp
check_myfun Checks myfun object before it is passed to applyExtfunction
check_params Check default parameters
createConfigFile Creates Config File based on variables in g.shell.GGIR environment
create_test_acc_csv Creates csv data file for testing purposes
create_test_sleeplog_csv Creates csv sleeplog file for testing purposes
data.calibrate Example output from g.calibrate
data.getmeta Example output from g.getmeta
data.inspectfile Example output from g.inspectfile
datadir2fnames Generates vector of file names out of datadir input argument
extract_params Extract parameters from input and add them to params
g.abr.day.names Abbreviates daynames to numbers, needed for report generation in g.plot5
g.analyse Function to analsyse meta-data generated by g.getmeta and g.impute
g.analyse.avday 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.analyse.perfile Function supports g.analyse. Not intended for direct use by user.
g.applymetrics Extract metrics from acceleration signals
g.binread 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.calibrate function to estimate calibration error and make recommendation for addressing it
g.conv.actlog Function to read activity log and make it useful for the rest of GGIR.
g.convert.part2.long Convert part 2 report to long format
g.create.sp.mat Converts sleep period information. Not intended for direct use
g.createcoordinates Create coordinates for g.plot
g.cwaread Function to read .cwa-format files as produced by the accelerometer named 'Axivity'
g.detecmidnight Detect all midnights in a time series
g.dotorcomma Assesses whether decimals in fileheader are stored with comma or dot separated decimals
g.downsample Downsample a vector of numeric values at three time resolutions
g.extractheadervars Extracts header variables from header object
g.fragmentation Fragmentation metrics from time series.
g.getbout function to calculate bouts from vector of binary classes
g.getidfromheaderobject Extracts participant identifier from header object
g.getM5L5 Extract M5 and L5 from time series
g.getmeta Function to extract meta-data (features) from data in accelerometer file
g.getstarttime Extract start time of a measurement
g.impute 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
g.imputeTimegaps Impute gaps in three axis raw accelerometer data
g.inspectfile function to inspect accelerometer file for brand, sample frequency and header
g.intensitygradient Intensity gradient calculation
g.IVIS Calculates IV and IS
g.loadlog Load and clean sleeplog information
g.part1 function to load and pre-process acceleration files
g.part2 function to analyse and summarize pre-processed output from g.part1
g.part3 Detection of sustained inactivity periods as needed for sleep detection in g.part4.
g.part4 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.part5 Merge output from physical activity and sleep analysis into one report
g.part5.addfirstwake Adds first wake if it is missing in part 4 output.
g.part5.addsib Adds the sustained inactivity bout to the ts series.
g.part5.classifyNaps Classify Naps from identified sustained inactivty bouts
g.part5.definedays Fix missing night in part 4 output
g.part5.fixmissingnight Fix missing night in part 4 output
g.part5.handle_lux_extremes Check lux values for extremes and imputes or removes them
g.part5.lux_persegment Extract key lux variables per segment of the data.
g.part5.onsetwaketiming Identify wake and sleepperiod window timing
g.part5.savetimeseries Saves oart 5 time series to csv files
g.part5.wakesleepwindows Label wake and sleepperiod window
g.plot function to generate a plot for quality check purposes
g.plot5 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.
g.readaccfile Generic functiont to read large blocks of accelerometer data
g.readtemp_movisens Reads the temperature from movisens files.
g.report.part2 Generate report from milestone data produced by g.part2
g.report.part4 Generate report from milestone data produced by g.part4
g.report.part5 Generate report from milestone data produced by g.part5
g.shell.GGIR Shell function for analysing an accelerometer dataset.
g.sib.det sustiained inactivty bouts detection
g.sib.plot Create plot of sustained inactivity bouts
g.sib.sum sustiained inactivty bouts detection
g.sibreport Generate sustiained inactivty bouts report
g.wavread function to read .wav files as produced by the accelerometer named 'Axivity'
g.weardec Detects whether accelerometer is worn
getFirstTimestamp Extract first timestamp from GENEActiv file
getfolderstructure Extracts folderstructure based on data directory.
getStartEnd Generate start and end time of a day
getStartEndNumeric Generate start and end page of a day
get_nw_clip_block_params Set monitor brand specific parameters
get_starttime_weekday_meantemp_truncdata Get starttime (adjusted), weekday, mean temp, and adjust data accordingly.
GGIR A package to process multi-day raw accelerometer data
HASIB Heuristic algorithms for sustiained inactivty bouts detection
HASPT Heuristic Algorithms estimating SPT window.
identify_levels Identifies levels of behaviour for g.part5 function.
is.ISO8601 Check whether character timestamp is in iso8601 format.
isfilelist Checks whether datadir is a directory or a vector with filenames
ismovisens Checks whether the files to process are collected with movisens accelerometers.
iso8601chartime2POSIX Convert iso8601 timestamps to POSIX timestamp
is_this_a_dst_night Check whether the night starting on a calendar date has DST.
load_params Load default parameters
numUnpack Simple function using Rcpp
parseGT3Xggir Parse activity samples from a GT3X file with batch loading
POSIXtime2iso8601 Convert POSIX to iso8601 timestamp
read.gt3x_ggir Read GT3X
read.myacc.csv Read custom csv files with accelerometer data
resample Simple function using Rcpp
updateBlocksize Update blocksize of data to be read depending on available memory.