Man pages for GGIR
Raw Accelerometer Data Analysis
| appendRecords | Append GGIR milestone data from neighbouring or overlapping... |
| applyCosinorAnalyses | Apply Cosinor Analyses to time series |
| applyExtFunction | Apply external function to acceleration data. |
| CalcSleepRegularityIndex | Calculates Sleep Regularity Index |
| check_log | Function to revise format of user-provided logs |
| checkMilestoneFolders | Checks for existence of folders to process |
| check_myfun | Checks myfun object before it is passed to applyExtfunction |
| check_params | Check default parameters |
| convertEpochData | convert external Epoch data to GGIR part 1 milestone data... |
| correctOlderMilestoneData | Corrects milestone data from g.part1 generated in older GGIR... |
| cosinorAnalyses | Apply cosinor anlaysis and extended cosinor analysis |
| createConfigFile | Creates Config File based on variables in function GGIR... |
| 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 |
| datadir2fnames | Generates vector of file names out of datadir input argument |
| data.getmeta | Example output from g.getmeta |
| data.inspectfile | Example output from g.inspectfile |
| data.metalong | Metalong object as part of part 1 milestone data |
| data.ts | Time series data.frame stored by part 5 |
| detect_nonwear_clipping | Detect non-wear and clipping time in the raw accelerometer... |
| extractID | Extract ID from file header object |
| extract_params | Extract parameters from input and add them to params |
| g.abr.day.names | Abbreviates daynames to numbers, needed for report generation... |
| g.analyse | Function to analsyse meta-data generated by g.getmeta and... |
| g.analyse.avday | Function supports g.analyse. Not intended for direct use by... |
| g.analyse.perday | Function supports g.analyse. Not intended for direct use by... |
| g.analyse.perfile | Function supports g.analyse. Not intended for direct use by... |
| g.applymetrics | Extract metrics from acceleration signals |
| g.calibrate | function to estimate calibration error and make... |
| g.conv.actlog | Function to read activity log and make it useful for the rest... |
| g.convert.part2.long | Convert part 2 report to long format |
| g.create.sp.mat | Converts sleep period information. Not intended for direct... |
| g.detecmidnight | Detect all midnights in a time series |
| g.dotorcomma | Assesses whether decimals in fileheader are stored with comma... |
| getfolderstructure | Extracts folderstructure based on data directory. |
| get_nw_clip_block_params | Set monitor brand specific parameters |
| get_starttime_weekday_truncdata | Get starttime (adjusted), weekday, and adjust data... |
| 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... |
| g.getstarttime | Extract start time of a measurement |
| GGIR | Shell function for analysing an accelerometer dataset. |
| GGIR-package | A package to process multi-day raw accelerometer data |
| g.impute | Function to identify invalid periods in the meta-data as... |
| g.imputeTimegaps | Impute gaps in three axis raw accelerometer data |
| g.inspectfile | function to inspect accelerometer file for brand, sample... |
| 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.part3 | Detection of sustained inactivity periods as needed for sleep... |
| g.part4 | Labels detected sustained inactivity periods by g.part3 as... |
| g.part4_extradctid | Extracts ID from filename and finds matching rows in sleeplog |
| g.part5 | Merge output from physical activity and sleep analysis into... |
| 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.analyseRest | Analyse rest (internal function) |
| g.part5_analyseSegment | Analyses the time series per time segment for part 5 |
| 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_initialise_ts | Initialise time series data from for part 5 |
| g.part5.lux_persegment | Extract key lux variables per segment of the data. |
| g.part5.ontsetwaketiming | Identify wake and sleepperiod window timing |
| g.part5.savetimeseries | Saves part 5 time series to csv files |
| g.part5.wakesleepwindows | Label wake and sleepperiod window |
| g.part6 | Perform temporal pattern analyses |
| g.plot | function to generate a plot for quality check purposes |
| g.plot5 | Generate user-friendly visual report. The first part of the... |
| 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.report.part5_dictionary | Generate data dictionary for reports from milestone data... |
| g.report.part6 | Generate report from milestone data produced by g.part6 |
| 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.sibreport | Generate sustiained inactivty bouts report |
| g.sib.sum | sustiained inactivty bouts detection |
| g.weardec | Detects whether accelerometer is worn |
| HASIB | Heuristic algorithms for sustiained inactivty bouts detection |
| HASPT | Heuristic Algorithms estimating SPT window. |
| identify_levels | Identifies levels of behaviour for g.part5 function. |
| isfilelist | Checks whether datadir is a directory or a vector with... |
| is.ISO8601 | Check whether character timestamp is in iso8601 format. |
| ismovisens | Checks whether the files to process are collected with... |
| 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 |
| part6AlignIndividuals | part6AlignIndividuals |
| part6PairwiseAggregation | part6PairwiseAggregation |
| 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... |
