summarize_PA: Compute physical activity summaries of minute level activity...

In martakarass/arcstats: Processing and Physical Activity Summaries of Minute Level Activity Data

Description

Compute physical activity summaries of minute level activity data.

Usage

summarize_PA(
  acc,
  acc_ts,
  wear_flag,
  valid_day_flag,
  sedentary_thresh = 1853,
  subset_minutes = NULL,
  exclude_minutes = NULL,
  in_bed_time = NULL,
  out_bed_time = NULL,
  adjust_out_colnames = TRUE
)

Arguments

acc	A numeric vector. A minute-level activity counts data vector. It is assumed to be in midnight-to-midnight format, meaning its vector length is a multiple of number of minutes in a full day (1440). See arcstats::midnight_to_midnight().
acc_ts	A POSIXct vector. Time of activity data collection, corresponding to acc in its original format (not: midnight-to-midnight).
wear_flag	An integer vector. It has value 1 if a minute belongs to a wear time-interval, value 0 if a minute belongs to a non-wear time-interval, and value NA to denote minutes before/after data collection started/finished. See arcstats::get_wear_flag().
valid_day_flag	An integer vector. It has value 1 if a minute belongs to a valid day, and 0 otherwise. See arcstats::get_valid_day_flag().
sedentary_thresh	A numeric scalar. If an activity count value falls below it then a corresponding minute is characterized as sedentary; otherwise, a corresponding minute is characterized as active. Default is 1853.
subset_minutes	Integer vector. Contains subset of a day's minutes within which activity summaries are to be computed. May take values from 1 (day's minute from 00:00 to 00:01) to 1440 (day's minute from 23:59 to 00:00). Default is NULL, i.e. no subset used (all day's minutes are used).
exclude_minutes	Integer vector. Contains subset of a day's minutes to be excluded from activity summaries computation. May take values from 1 (day's minute from 00:00 to 00:01) to 1440 (day's minute from 23:59 to 00:00). Default is NULL, i.e. no minutes excluded (all day's minutes are used).
in_bed_time	A POSIXct vector. An estimated in-bed time start. Together with a corresponding entry from out_bed_time vector, it defines a day-specific subset of "in bed time" minutes to be excluded from activity summaries computation. Default is NULL, i.e. no minutes excluded.
out_bed_time	A POSIXct vector. An estimated in-bed time end. Together with a corresponding entry from in_bed_time vector, it defines a day-specific subset of "in bed time" minutes to be excluded from activity summaries computation. Default is NULL, i.e. no minutes excluded.
adjust_out_colnames	A logical scalar. Whether or not to add an informative suffix to column names in the output data frame. This may happen in case any of the arguments: subset_minutes, or exclude_minutes, or in_bed_time and out_bed_time are set other than NULL. Default is TRUE.

Value

A data frame with physical activity summaries of minute level activity data. See README or vignette for summaries description.

Examples

## Read exemplary data
fpath_i <- system.file("extdata", extdata_fnames[1], package = "arcstats")
dat_i   <- as.data.frame(data.table::fread(fpath_i))
acc     <- dat_i$vectormagnitude
acc_ts  <- lubridate::ymd_hms(dat_i$timestamp)
## Get acc data vector in "midnight_to_midnight" format
acc <- midnight_to_midnight(acc, acc_ts)
## Get wear/non-wear flag
wear_flag <- get_wear_flag(acc)
## Get valid/non-valid day flag
valid_day_flag <- get_valid_day_flag(wear_flag)
## Impute missing data in acc data vector
acc_imputed <- impute_missing_data(acc, wear_flag, valid_day_flag)

## Example 1
## Summarize PA
summarize_PA(acc, acc_ts, wear_flag, valid_day_flag)

## Example 2
## Summarize PA within minutes range corresponding to 12:00 AM - 6:00 AM
subset_12am_6am <- 1 : (6 * 1440/24)
summarize_PA(acc, acc_ts, wear_flag, valid_day_flag, subset_minutes = subset_12am_6am)

## Example 3
## Summarize PA without (i.e., excluding) minutes range corresponding to 11:00 PM - 5:00 AM.
subset_11pm_5am <- c(
  (23 * 1440/24 + 1) : 1440,   ## 11:00 PM - midnight
  1 : (5 * 1440/24)            ## midnight - 5:00 AM
)
summarize_PA(acc, acc_ts, wear_flag, valid_day_flag, exclude_minutes = subset_11pm_5am)

martakarass/arcstats documentation built on Sept. 10, 2020, 5:29 a.m.