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. |