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

In arctools: Processing and Physical Activity Summaries of Minute Level Activity Data

Compute 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,
  subset_weekdays = 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 arctools::midnight_to_midnight().
acc_ts	A POSIXct vector. Time of activity data collection, corresponding to acc in its original format (not: midnight-to-midnight). We strongly recommended to use lubridate::ymd_hms() function to create acc_ts (see Examples below).
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 arctools::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 arctools::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).
subset_weekdays	Integer vector. Specfies days of a week within which activity summaries are to be computed. Takes values between 1 (Sunday) to 7 (Saturday). Default is NULL, i.e.no subset used (all days of a week 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 = "arctools")
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)

arctools documentation built on Nov. 11, 2022, 1:05 a.m.