---
title: "GGIR configuration parameters"
output:
   html_document:
    toc : true
    number_sections: true
    toc_depth: 3
    toc_float: true #by turning this on, the table of contents moves to the left of the page.
urlcolor: blue
vignette: >
  %\VignetteIndexEntry{GGIR configuration parameters}
  \usepackage[utf8]{inputenc}
  %\VignetteEngine{knitr::rmarkdown}
---

```{r, echo=FALSE, out.width = "60%", out.extra='style="border: 0; padding:20px"'}
knitr::include_graphics("GGIR-MASTERLOGO-RGB.png")
```

See also complementary vignettes on:
[General introduction to GGIR](https://cran.r-project.org/package=GGIR/vignettes/GGIR.html), [Cut-points](https://CRAN.R-project.org/package=GGIR/vignettes/CutPoints.html), [Day segment analyses](https://CRAN.R-project.org/package=GGIR/vignettes/TutorialDaySegmentAnalyses.html), [Embedding externalf unctions](https://CRAN.R-project.org/package=GGIR/vignettes/ExternalFunction.html), and [Reading ad-hoc csv file formats](https://CRAN.R-project.org/package=GGIR/vignettes/readmyacccsv.html).

The GGIR
[shell function](https://cran.r-project.org/package=GGIR/vignettes/GGIR.html#23_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](#default-argument-values) 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           |
| 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_timeformat     | 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, 5              | 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            |
| sep_reports                 | 2, 4, 5           | params_output            |
| dec_reports                 | 2, 4, 5           | params_output            |
| sep_config                  | 1, 2, 3, 4, 5     | params_output            |
| dec_config                  | 1, 2, 3, 4, 5     | params_output            |
| mvpadur                     | 2                 | params_phyact            |
| 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             |
| ignorenonwear               | 3                 | params_sleep             |
| HDCZA_threshold             | 3                 | params_sleep             |
| acc.metric                  | 3, 5              | params_general           |
| 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                 | deprecated               |
| sleepefficiency.metric      | 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](https://CRAN.R-project.org/package=GGIR/GGIR.pdf).

## 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"))`


```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```


```{r, echo=FALSE, out.width = "60%", out.extra='style="border: 0; padding:20px"'}
knitr::include_graphics("GGIR-MASTERLOGO-RGB.png")
```
