summarize_actigraphy: Summarize Actigraphy Data

In muschellij2/SummarizedActigraphy: Coerce 'Actigraphy' to Summarized Experiments

Summarize Actigraphy Data

Description

Summarize Actigraphy Data

Usage

summarize_daily_actigraphy(
  x,
  unit = "1 min",
  fix_zeros = TRUE,
  fill_in = TRUE,
  trim = FALSE,
  verbose = TRUE,
  calculate_mims = FALSE,
  calculate_ac = FALSE,
  flag_data = TRUE,
  ensure_all_time = TRUE,
  flags = NULL,
  ...
)

summarise_daily_actigraphy(
  x,
  unit = "1 min",
  fix_zeros = TRUE,
  fill_in = TRUE,
  trim = FALSE,
  verbose = TRUE,
  calculate_mims = FALSE,
  calculate_ac = FALSE,
  flag_data = TRUE,
  ensure_all_time = TRUE,
  flags = NULL,
  ...
)

summarize_actigraphy(
  x,
  unit = "1 min",
  .fns = list(mean = mean, median = median),
  verbose = TRUE,
  ...
)

collapse_daily_actigraphy(
  x,
  .fns = list(mean = function(x) mean(x, na.rm = TRUE), median = function(x) median(x,
    na.rm = TRUE)),
  verbose = TRUE
)

summarise_actigraphy(
  x,
  unit = "1 min",
  .fns = list(mean = mean, median = median),
  verbose = TRUE,
  ...
)

Arguments

x	an AccData object. If 'x' is a character, then read_actigraphy will be run
unit	units to group the data to take the statistic over
fix_zeros	Should fix_zeros be run before calculating the measures?
fill_in	if fix_zeros = TRUE, should the zeros be filled in with the last observation carried forward?
trim	if fix_zeros = TRUE, should the time course be trimmed for zero values at the beginning and the end of the time course? observation carried forward?
verbose	print diagnostic messages
calculate_mims	Should MIMS units be calculated? Passed to calculate_measures
calculate_ac	Should Activity Counts from the activityCounts package be calculated?
flag_data	Should [SummarizedActigraphy::flag_qc()] be run? It will be executed after fix_zeros before any measure calculation
ensure_all_time	if TRUE, then all times from the first to last times will be in the output, even if data during that time was not in the input
flags	the flags to calculate, passed to [SummarizedActigraphy::flag_qc()]
...	Additional arguments to pass to read_actigraphy
.fns	Functions to apply to each of the selected columns. See across

Value

A tsibble object, with 86400 rows, with one row for each second of the day '24*60*60'.

Examples

path = system.file("extdata",
"TAS1H30182785_2019-09-17.gt3x",
package = "SummarizedActigraphy")

x = read_actigraphy(path)

options(digit.secs = 2)

fixed = fix_zeros(x)
daily = summarize_daily_actigraphy(fixed, fix_zeros = FALSE)
average_day = collapse_daily_actigraphy(daily)
## Not run: 
  average_day = summarize_actigraphy(fixed, fix_zeros = FALSE)
  if (requireNamespace("ggplot2", quietly = TRUE)) {
    library(magrittr)
    average_day %>%
      ggplot(aes(x = time, y = ai_mean)) +
      geom_line()

    average_day %>%
      ggplot(aes(x = time, y = ai_median)) +
      geom_line()
  }

## End(Not run)

muschellij2/SummarizedActigraphy documentation built on April 9, 2024, 8:32 a.m.