Heuristic Algorithms estimating SPT window.
A package to process multi-day raw accelerometer data
Convert POSIX to iso8601 timestamp
Apply external function to acceleration data.
Append GGIR milestone data from neighbouring or overlapping recordings
Apply Cosinor Analyses to time series
Creates csv sleeplog file for testing purposes
Creates csv data file for testing purposes
Extract Definition from Shell Documentation
Shell function for analysing an accelerometer dataset.
Checks myfun object before it is passed to applyExtfunction
Calculates Sleep Regularity Index
Heuristic algorithms for sustiained inactivty bouts detection
Calculates IV and IS
Function to revise format of user-provided logs
Extract ID from file header object
Generates vector of file names out of datadir input
argument
convert external Epoch data to GGIR part 1 milestone data format
correctOlderMilestoneData
Corrects milestone data from g.part1 generated in older GGIR versions
Creates Config File based on variables in function GGIR environment
Extract parameters from input and add them to params
Apply cosinor anlaysis and extended cosinor analysis
Check default parameters
Example output from g.calibrate
Metalong object as part of part 1 milestone data
Converts sleep period information. Not intended for direct use
Detect non-wear and clipping time in the raw accelerometer data
function to estimate calibration error and make recommendation for addressing it
Example output from g.getmeta
Extract metrics from acceleration signals
Example output from g.inspectfile
Function to read activity log and make it useful for the rest of GGIR.
Abbreviates daynames to numbers, needed for report generation in
g.plot5
Convert part 2 report to long format
Time series data.frame stored by part 5
Detect all midnights in a time series
Function supports g.analyse. Not intended for direct use by user.
Function supports g.analyse. Not intended for direct use by user.
Impute gaps in three axis raw accelerometer data
function to inspect accelerometer file for brand, sample frequency and header
Function to extract meta-data (features) from data in accelerometer file
function to calculate bouts from vector of binary classes
Fragmentation metrics from time series.
Extracts header variables from header object
Function supports g.analyse. Not intended for direct use by user.
Function to analsyse meta-data generated by g.getmeta and g.impute
Extract M5 and L5 from time series
Assesses whether decimals in fileheader are stored with comma
or dot separated decimals
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
Extract start time of a measurement
Load and clean sleeplog information
Merge output from physical activity and sleep analysis into one report
Intensity gradient calculation
Adds first wake if it is missing in part 4 output.
Identify wake and sleepperiod window timing
function to load and pre-process acceleration files
Extracts ID from filename and finds matching rows in sleeplog
Detection of sustained inactivity periods as needed for sleep detection
in g.part4.
Labels detected sustained inactivity periods by g.part3 as either
part of the Sleep Period Time window or not
Saves part 5 time series to csv files
Adds the sustained inactivity bout to the ts series.
Analyse rest (internal function)
function to analyse and summarize pre-processed output from g.part1
Generate report from milestone data produced by g.part2
Label wake and sleepperiod window
Fix missing night in part 4 output
g.part5.handle_lux_extremes
Check lux values for extremes and imputes or removes them
Fix missing night in part 4 output
Generate report from milestone data produced by g.part4
Classify Naps from identified sustained inactivty bouts
Analyses the time series per time segment for part 5
Perform temporal pattern analyses
Extract key lux variables per segment of the data.
Initialise time series data from for part 5
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
Update blocksize of data to be read depending on available memory.
sustiained inactivty bouts detection
Reads the temperature from movisens files.
Create plot of sustained inactivity bouts
get_starttime_weekday_truncdata
Get starttime (adjusted), weekday, and adjust data accordingly.
Generic functiont to read large blocks of accelerometer data
part6AlignIndividuals
part6PairwiseAggregation
Extracts folderstructure based on data directory.
Load default parameters
Generate report from milestone data produced by g.part6
Wrapper function around function GGIR
function to generate a plot for quality check purposes
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.
Set monitor brand specific parameters
Detects whether accelerometer is worn
Builds Section for Parameters Vignette
sustiained inactivty bouts detection
Generate sustiained inactivty bouts report
Checks whether datadir is a directory or a vector with
filenames
Check whether the night starting on a calendar date has DST.
Identifies levels of behaviour for g.part5 function.
Check whether character timestamp is in iso8601 format.
Read custom csv files with accelerometer data
Round numeric columns and replace NA/NaN values by blank
Convert iso8601 timestamps to POSIX timestamp
Checks whether the files to process are collected with movisens accelerometers.