adjust_bout_summaries: Apply wear time residual adjustment to the output of bout...

In paulhibbing/PBpatterns: Analyze Patterns of Physical Behavior

Apply wear time residual adjustment to the output of bout summary methods

Description

Applies to output from the *_summary methods of analyze_bouts, in conjunction with information from summarize_weartime

Usage

adjust_bout_summaries(d, verbose = FALSE)

Arguments

d	the output of to adjust
verbose	logical. Print updates to console

Value

The original d, with extra columns (adj_*) reflecting residual adjustments on relevant variables

Examples

## Set up the data

  data(example_data, package = "PBpatterns")

  valid_indices <- c(
    654:1454, 1917:2837, 3499:4266, 5216:5632,
    6340:7119, 7704:8555, 9118:10077
  )

  example_data$Timestamp <- seq(
    as.POSIXlt(Sys.Date()), by = "1 min", length.out = nrow(example_data)
  )

  example_data$is_wear <- TRUE

  example_data$intensity <- cut(
    example_data$PAXINTEN,
    c(-Inf, 101, 760, Inf),
    c("SB", "LPA", "MVPA"),
    right = FALSE
  )

  example_data$valid_index <- 1:nrow(example_data) %in% valid_indices

## Set up the analysis (It needs to have more than one data
## point, so we will stratify by PAXDAY for illustration)

  weartime_info <- purrr::map_df(
    split(example_data, example_data$PAXDAY),
    ~ summarize_weartime(.x, "is_wear", "Timestamp", .x$valid_index)
  )

  sb_bouts <- purrr::map_df(
    split(example_data, example_data$PAXDAY),
     ~ analyze_bouts(
       .x$intensity, "SB", "SB_summary",
       is_wear = .x$is_wear,
       valid_indices = .x$valid_index,
       epoch_length_sec = 60
     )
  )

  mvpa_bouts <- purrr::map_df(
    split(example_data, example_data$PAXDAY),
    ~ analyze_bouts(
      .x$intensity, "MVPA", "MVPA_summary",
      is_wear = .x$is_wear,
      valid_indices = .x$valid_index,
      epoch_length_sec = 60
      )
  )

  d <- merge(weartime_info, sb_bouts)

  d <- merge(d, mvpa_bouts)

## Run the analysis

  adjust_bout_summaries(d)

paulhibbing/PBpatterns documentation built on Feb. 17, 2024, 5:34 a.m.