GGIR configuration parameters"

In GGIR: Raw Accelerometer Data Analysis

knitr::include_graphics("GGIR-MASTERLOGO-RGB.png")

See also complementary vignettes on: General introduction to GGIR, Cut-points, Day segment analyses, Embedding externalf unctions, and Reading ad-hoc csv file formats.

The GGIR shell function takes the input arguments and groups them into parameter objects. The first section below displays all optional GGIR input argument names, the GGIR part (1, 2, 3, 4 and/or 5) they are used in, and the parameter object they are stored in. As you will see, a few parameters are not part of any parameter object because they are direct arguments of the GGIR shell function.

In the second section of this vignette you will find a description and default value for all the arguments.

Input arguments/parameters overview

| Argument (parameter) | Used in GGIR part | Parameter object | |-----------------------------|-------------------|--------------------------| | datadir | 1, 2, 4, 5 | not in parameter objects | | f0 | 1, 2, 3, 4, 5 | not in parameter objects | | f1 | 1, 2, 3, 4, 5 | not in parameter objects | | windowsizes | 1, 5 | params_general | | desiredtz | 1, 2, 3, 4, 5 | params_general | | overwrite | 1, 2, 3, 4, 5 | params_general | | do.parallel | 1, 2, 3, 5 | params_general | | maxNcores | 1, 2, 3, 5 | params_general | | myfun | 1, 2, 3 | not in parameter objects | | outputdir | 1 | not in parameter objects | | studyname | 1 | not in parameter objects | | chunksize | 1 | params_rawdata | | do.enmo | 1 | params_metrics | | do.lfenmo | 1 | params_metrics | | do.en | 1 | params_metrics | | do.bfen | 1 | params_metrics | | do.hfen | 1 | params_metrics | | do.hfenplus | 1 | params_metrics | | do.mad | 1 | params_metrics | | do.anglex | 1 | params_metrics | | do.angley | 1 | params_metrics | | do.angle | 1 | params_metrics | | do.enmoa | 1 | params_metrics | | do.roll_med_acc_x | 1 | params_metrics | | do.roll_med_acc_y | 1 | params_metrics | | do.roll_med_acc_z | 1 | params_metrics | | do.dev_roll_med_acc_x | 1 | params_metrics | | do.dev_roll_med_acc_y | 1 | params_metrics | | do.dev_roll_med_acc_z | 1 | params_metrics | | do.lfen | 1 | params_metrics | | do.lfx | 1 | params_metrics | | do.lfy | 1 | params_metrics | | do.lfz | 1 | params_metrics | | do.hfx | 1 | params_metrics | | do.hfy | 1 | params_metrics | | do.hfz | 1 | params_metrics | | do.bfx | 1 | params_metrics | | do.bfy | 1 | params_metrics | | do.bfz | 1 | params_metrics | | do.zcx | 1 | params_metrics | | do.zcy | 1 | params_metrics | | do.zcz | 1 | params_metrics | | do.neishabouricounts | 1 | params_metrics | | actilife_LFE | 1 | params_metrics | | lb | 1 | params_metrics | | hb | 1 | params_metrics | | n | 1 | params_metrics | | do.cal | 1 | params_rawdata | | spherecrit | 1 | params_rawdata | | minloadcrit | 1 | params_rawdata | | printsummary | 1 | params_rawdata | | print.filename | 1 | params_general | | backup.cal.coef | 1 | params_rawdata | | rmc.noise | 1 | params_rawdata | | rmc.dec | 1 | params_rawdata | | rmc.firstrow.acc | 1 | params_rawdata | | rmc.firstrow.header | 1 | params_rawdata | | rmc.col.acc | 1 | params_rawdata | | rmc.col.temp | 1 | params_rawdata | | rmc.col.time | 1 | params_rawdata | | rmc.unit.acc | 1 | params_rawdata | | rmc.unit.temp | 1 | params_rawdata | | rmc.origin | 1 | params_rawdata | | rmc.header.length | 1 | params_rawdata | | mc.format.time | 1 | params_rawdata | | rmc.bitrate | 1 | params_rawdata | | rmc.dynamic_range | 1 | params_rawdata | | rmc.unsignedbit | 1 | params_rawdata | | rmc.desiredtz | 1 | params_rawdata | | rmc.sf | 1 | params_rawdata | | rmc.headername.sf | 1 | params_rawdata | | rmc.headername.sn | 1 | params_rawdata | | rmc.headername.recordingid | 1 | params_rawdata | | rmc.header.structure | 1 | params_rawdata | | rmc.check4timegaps | 1 | params_rawdata | | rmc.col.wear | 1 | params_rawdata | | rmc.doresample | 1 | params_rawdata | | imputeTimegaps | 1 | params_rawdata | | selectdaysfile | 1, 2 | params_cleaning | | dayborder | 1, 2, 5 | params_general | | dynrange | 1 | params_rawdata | | configtz | 1 | params_general | | minimumFileSizeMB | 1 | params_rawdata | | interpolationType | 1 | params_rawdata | | expand_tail_max_hours | deprecated | params_general | | recordingEndSleepHour | 1 | params_general | | maxRecordingInterval | 1 | params_general | | nonwear_approach | 1 | params_general | | dataFormat | 1 | params_general | | extEpochData_dateformat | 1 | params_general | | metadatadir | 2, 3, 4, 5 | not in parameter objects | | minimum_MM_length.part5 | 5 | params_cleaning | | strategy | 2, 5 | params_cleaning | | hrs.del.start | 2, 5 | params_cleaning | | hrs.del.end | 2, 5 | params_cleaning | | maxdur | 2, 5 | params_cleaning | | max_calendar_days | 2 | params_cleaning | | includedaycrit | 2 | params_cleaning | | nonWearEdgeCorrection | 2 | params_cleaning | | L5M5window | 2 | params_247 | | M5L5res | 2, 5 | params_247 | | winhr | 2, 5 | params_247 | | qwindow | 2 | params_247 | | qlevels | 2 | params_247 | | ilevels | 2 | params_247 | | mvpathreshold | 2 | params_phyact | | boutcriter | 2 | params_phyact | | ndayswindow | 2 | params_cleaning | | idloc | 2, 4 | params_general | | do.imp | 2 | params_cleaning | | storefolderstructure | 2, 4, 5 | params_output | | epochvalues2csv | 2 | params_output | | do.part2.pdf | 2 | params_output | | mvpadur | 2 | params_phyact | | window.summary.size | 2 | params_247 | | bout.metric | 2, 5 | params_phyact | | closedbout | 2 | params_phyact | | IVIS_windowsize_minutes | 2 | params_247 | | IVIS_epochsize_seconds | 2 | params_247 | | IVIS.activity.metric | 2 | params_247 | | iglevels | 2, 5 | params_247 | | TimeSegments2ZeroFile | 2 | params_cleaning | | qM5L5 | 2 | params_247 | | MX.ig.min.dur | 2 | params_247 | | qwindow_dateformat | 2 | params_247 | | anglethreshold | 3 | params_sleep | | timethreshold | 3 | params_sleep | | acc.metric | 3, 5 | params_general | | ignorenonwear | 3 | params_sleep | | constrain2range | 3 | params_sleep | | do.part3.pdf | 3 | params_output | | sensor.location | 3, 4 | params_general | | HASPT.algo | 3 | params_sleep | | HASIB.algo | 3 | params_sleep | | Sadeh_axis | 3 | params_sleep | | longitudinal_axis | 3 | params_sleep | | HASPT.ignore.invalid | 3 | params_sleep | | loglocation | 4, 5 | params_sleep | | colid | 4 | params_sleep | | coln1 | 4 | params_sleep | | possible_nap_window | 5 | params_sleep | | possible_nap_dur | 5 | params_sleep | | do.visual | 4 | params_output | | outliers.only | 4 | params_output | | excludefirstlast | 4 | params_cleaning | | criterror | 4 | params_output | | includenightcrit | 4 | params_cleaning | | relyonguider | 4 | params_sleep | | relyonsleeplog | 4 | not in parameter objects | | relyonguider_SleepEfficiency| 4 | params_sleep | | def.noc.sleep | 4 | params_sleep | | data_cleaning_file | 4, 5 | params_cleaning | | excludefirst.part4 | 4 | params_cleaning | | excludelast.part4 | 4 | params_cleaning | | sleepwindowType | 4 | params_cleaning | | excludefirstlast.part5 | 5 | params_cleaning | | boutcriter.mvpa | 5 | params_phyact | | boutcriter.in | 5 | params_phyact | | boutcriter.lig | 5 | params_phyact | | threshold.lig | 5 | params_phyact | | threshold.mod | 5 | params_phyact | | threshold.vig | 5 | params_phyact | | boutdur.mvpa | 5 | params_phyact | | boutdur.in | 5 | params_phyact | | boutdur.lig | 5 | params_phyact | | save_ms5rawlevels | 5 | params_output | | part5_agg2_60seconds | 5 | params_general | | includedaycrit.part5 | 5 | params_cleaning | | frag.metrics | 5 | params_phyact | | LUXthresholds | 5 | params_247 | | LUX_cal_constant | 5 | params_247 | | LUX_cal_exponent | 5 | params_247 | | LUX_day_segments | 5 | params_247 | | timewindow | 5 | params_output | | save_ms5raw_format | 5 | params_output | | save_ms5raw_without_invalid | 5 | params_output | | do.sibreport | 5 | params_output | | visualreport_without_invalid| visualreport | params_output | | dofirstpage | visualreport | params_output | | visualreport | visualreport | params_output | | viewingwindow | visualreport | params_output |

Arguments/parameters description {#default-argument-values}

All information as shown below has been auto-generated and is identical to the information provided in the GGIR package pdf manual.

GGIR function input arguments

mode {-}

r format(GGIR::ShellDoc2Vignette("mode"))

datadir {-}

r format(GGIR::ShellDoc2Vignette("datadir"))

outputdir {-}

r format(GGIR::ShellDoc2Vignette("outputdir"))

studyname {-}

r format(GGIR::ShellDoc2Vignette("studyname"))

f0 {-}

r format(GGIR::ShellDoc2Vignette("f0"))

f1 {-}

r format(GGIR::ShellDoc2Vignette("f1"))

do.report {-}

r format(GGIR::ShellDoc2Vignette("do.report"))

configfile {-}

r format(GGIR::ShellDoc2Vignette("configfile"))

myfun {-}

r format(GGIR::ShellDoc2Vignette("myfun"))

General Parameters

r format(GGIR::parametersVignette("general"))

Raw Data Parameters

r format(GGIR::parametersVignette("rawdata"))

Metrics Parameters

r format(GGIR::parametersVignette("metrics"))

Cleaning Parameters

r format(GGIR::parametersVignette("cleaning"))

Sleep Parameters

r format(GGIR::parametersVignette("sleep"))

Physical activity Parameters

r format(GGIR::parametersVignette("phyact"))

24/7 Parameters

r format(GGIR::parametersVignette("247"))

Output Parameters

r format(GGIR::parametersVignette("output"))

knitr::opts_chunk$set(echo = TRUE)

knitr::include_graphics("GGIR-MASTERLOGO-RGB.png")

GGIR documentation built on Oct. 17, 2023, 1:12 a.m.