R/load-agd-settings.R

In chms: Accelerometer Processing Methods for Cycle 7 of the CHMS

#' @title Load the `settings` table from an ActiGraph `.agd` file.
#' @description This function loads the `settings` table from an ActiGraph
#' `.agd` file.
#' @param file Required: a length-one character vector representing the full
#' path to an `.agd` file.
#' @return Returns a tibble of the `settings` table in a wide shape.
#' @examples
#' # Initialize agd_worker R6 class
#' agd_data <- agd_worker$new(
#'   id = "jane-canuck",
#'   age = 10,
#'   agd_lfe = system.file("extdata", "jane-canuck-lfe.agd", package = "chms"),
#'   agd_nml = system.file("extdata", "jane-canuck-nml.agd", package = "chms"),
#'   epoch_length = 15,
#'   day_max = 3,
#'   sleep_algo = "barreira",
#'   non_wear_algo = "barreira"
#' )
#'
#' # Load ActiGraph settings
#' dt <- load_agd_settings(agd_data$args$agd_lfe)
#' @export

load_agd_settings <- function(file) {
  # Connect to database
  connection <- DBI::dbConnect(
    drv = RSQLite::SQLite(),
    dbname = file
  )

  # Close connection to database on exit
  on.exit(expr = DBI::dbDisconnect(conn = connection), add = TRUE)

  # Get settings table
  settings <- connection |>
    dplyr::tbl(dplyr::sql("SELECT * FROM settings")) |>
    dplyr::collect(n = Inf) |>
    dplyr::distinct(
      settingName,
      settingValue
    ) |>
    tidyr::pivot_wider(
      names_from = "settingName",
      values_from = "settingValue"
    ) |>
    dplyr::mutate(
      dplyr::across(
        .cols = startdatetime:downloaddatetime,
        .fns = ~ (as.numeric(.x) / 1e7) |>
          as.POSIXct(origin = "0001-01-01 00:00:00", tz = "UTC")
      ),
      time_zone = suppressWarnings(lubridate::tz(startdatetime)),
      dplyr::across(
        .cols = startdatetime:downloaddatetime,
        .fns = ~ format(
          x = .x,
          format = "%Y-%m-%d %H:%M:%S %Z"
        )
      )
    )

  # Exit
  settings
}