DataShrink: Annotating the merged data for all accelerometer files in the...
In postGGIR: Data Processing after Running 'GGIR' for Accelerometer Data

Annotating the merged ENMO/ANGLEZ data by adding some descriptive variables such as number of valid days and missing pattern.

DataShrink(
  studyname,
  outputdir,
  workdir,
  QCdays.alpha = 7,
  QChours.alpha = 16,
  summaryFN = "../summary/part24daysummary.info.csv",
  epochIn = 5,
  epochOut = 60,
  useIDs.FN = NULL,
  RemoveDaySleeper = FALSE,
  trace = FALSE,
  Step = 1
)

`studyname`	`character` Specify the study name that used in the output file names
`outputdir`	`character` Directory where the GGIR output was stored.
`workdir`	`character` Directory where the output needs to be stored. Note that this directory must exist.
`QCdays.alpha`	`number` Minimum required number of valid days in subject specific analysis as a quality control step in part2. Default is 7 days.
`QChours.alpha`	`number` Minimum required number of valid hours in day specific analysis as a quality control step in part2. Default is 16 hours.
`summaryFN`	`character` Filename with or without directory for sample information in CSV format, which includes summary description of each accelerometer file. Some description will be extracted and merged into the ENMO/ANGLEZ data.
`epochIn`	`number` Epoch size to which acceleration was averaged (seconds) in GGIR output. Defaut is 5 seconds.
`epochOut`	`number` Epoch size to which acceleration was averaged (seconds) in part1. Defaut is 60 seconds.
`useIDs.FN`	`character` Filename with or without directory for sample information in CSV format, which inclues "filename" and "duplicate" in the headlines at least. If duplicate="remove", the accelerometer files will not be used in the data analysis of part 5-7. Defaut is NULL, which makes all accelerometer files will be used in part 5-7.
`RemoveDaySleeper`	`logical` Specify if the daysleeper nights are removed from the calculation of number of valid days for each subject. Default is FALSE.
`trace`	`logical` Specify if the intermediate results is printed when the function was executed. Default is FALSE.
`Step`	`number` Specify which of the varaible need to be cleaned. For example, Step = 1 for the "anglez" variable, and Step = 2 for the "enmo" variable.

Files were written to the specified sub-directory, named as flag_ALL_studyname_ENMO.data.Xs.csv and flag_ALL_studyname_ANGLEZ.data.Xs.csv, which Xs is the epoch size to which acceleration was averaged (seconds) in GGIR output. This excel file includs the following columns,

`filename`	accelerometer file name
`Date`	date recored from the GGIR part2.summary file
`id`	IDs recored from the GGIR part2.summary file
`calender_date`	date in the format of yyyy-mm-dd
`N.valid.hours`	number of hours with valid data recored from the part2_daysummary.csv file in the GGIR output
`N.hours`	number of hours of measurement recored from the part2_daysummary.csv file in the GGIR output
`weekday`	day of the week-Day of the week
`measurementday`	day of measurement-Day number relative to start of the measurement
`newID`	new IDs defined as the user-defined function of filename2id(), e.g. substrings of the filename
`Nmiss_c9_c31`	number of NAs from the 9th to 31th column in the part2_daysummary.csv file in the GGIR output
`missing`	"M" indicates missing for an invalid day, and "C" indicates completeness for a valid day
`Ndays`	number of days of measurement
`ith_day`	rank of the measurementday, for example, the value is 1,2,3,4,-3,-2,-1 for measurementday = 1,...,7
`Nmiss`	number of missing (invalid) days
`Nnonmiss`	number of non-missing (valid) days
`misspattern`	indicators of missing/nonmissing for all measurement days at the subject level
`RowNonWear`	number of columnns in the non-wearing matrix
`NonWearMin`	number of minutes of non-wearing
`Nvalid.day`	number of valid days with/without removing daysleeper nights; It is equal to Nnonmiss when RemoveDaySleeper=FALSE.
`daysleeper`	If 0 then the person is a nightsleeper (sleep period did not overlap with noon) if value=1 then the person is a daysleeper (sleep period did overlap with noon).
`remove16h7day`	indicator of a key qulity control output. If remove16h7day=1, the day need to be removed. If remove16h7day=0, the day need to be kept.
`duplicate`	If duplicate="remove", the accelerometer files will not be used in the data analysis of part5-7.