# Raw Accelerometer Data Analysis

## Documentation for package ‘GGIR’ version 2.9-0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

GGIR-package | A package to process multi-day raw accelerometer data
applyExtFunction | Apply external function to acceleration data.
CalcSleepRegularityIndex | Calculates Sleep Regularity Index
check_myfun | Checks myfun object before it is passed to applyExtfunction
check_params | Check default parameters
correctOlderMilestoneData | Corrects milestone data from g.part1 generated in older GGIR versions
cosinorAnalyses | Apply cosinor anlaysis and extended cosinor analysis
createConfigFile | Creates Config File based on variables in function 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 | Deprecated, internally replaced by function readGenea from the GGIRread package
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.cwaread | Deprecated, internally replaced by function readAxivity from the GGIRread package
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.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 | Wrapper function around function GGIR
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
getfolderstructure | Extracts folderstructure based on data directory.
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 | Shell function for analysing an accelerometer dataset.
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
parametersVignette | Builds Section for Parameters Vignette
POSIXtime2iso8601 | Convert POSIX to iso8601 timestamp
read.myacc.csv | Read custom csv files with accelerometer data
ShellDoc2Vignette | Extract Definition from Shell Documentation
tidyup_df | Round numeric columns and replace NA/NaN values by blank
updateBlocksize | Update blocksize of data to be read depending on available memory.