DataShrink {mMARCH.AC}

Annotating the merged data for all accelerometer files in the GGIR output

Description

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

Usage

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
)

Arguments

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 module2. Default is 7 days.

QChours.alpha

number Minimum required number of valid hours in day specific analysis as a quality control step in module2. 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 module1. 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 module 5-7. Defaut is NULL, which makes all accelerometer files will be used in module 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.

Value

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

Nmissday

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) at the night. This is a night-level varialbe.

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 module5-7.