R/identify_walk_bouts_in_gps_and_accelerometry_data.R

In walkboutr: Generate Walk Bouts from GPS and Accelerometry Data

#' Identify walking bouts in GPS and accelerometry data:
#'
#' This function identifies walking bouts in GPS and accelerometry data.
#' It processes the GPS data and accelerometry counts to create walk bouts.
#'
#' @param gps_data A data frame containing GPS data
#' @param accelerometry_counts A data frame containing accelerometry counts
#' @param ... Additional arguments to be passed to the function
#' @param collated_arguments A list of collated arguments
#'
#' @returns A data frame containing identified walk bouts
#'
#' @export
identify_walk_bouts_in_gps_and_accelerometry_data <- function(gps_data, accelerometry_counts, ..., collated_arguments = NULL){
  collated_arguments <- collate_arguments(..., collated_arguments=collated_arguments)
  # complete_days <- generate_c_d()
  bouts <- process_accelerometry_counts_into_bouts(accelerometry_counts, collated_arguments=collated_arguments)
  # take out the complete days processing from identify bouts
  # merge on complete_days info
  gps_epochs <- process_gps_data_into_gps_epochs(gps_data, collated_arguments=collated_arguments)
  walk_bouts <- process_bouts_and_gps_epochs_into_walkbouts(bouts, gps_epochs, collated_arguments=collated_arguments)
  return(walk_bouts)
}



#' Summarize walking bouts:
#' This function summarizes walking bouts and calculates the median speed, complete day, non-wearing, bout start, and duration of each bout.
#'
#' @param walk_bouts A data frame containing identified walk bouts
#' @param ... Additional arguments to be passed to the function
#' @param collated_arguments A list of collated arguments
#'
#' @returns A data frame summarizing identified walk bouts
#'
#' @export
summarize_walk_bouts <- function(walk_bouts, ..., collated_arguments = NULL){
  bout <- median <- speed <- complete_day <- time <- bout_category <- NULL
  collated_arguments <- collate_arguments(..., collated_arguments=collated_arguments)

  summary_walk_bouts <- walk_bouts %>%
    dplyr::group_by(bout) %>%
    dplyr::filter(!is.na(bout)) %>%
    dplyr::summarise(
              median_speed = median(speed, na.rm=TRUE),
              complete_day = any(complete_day),
              bout_start = lubridate::as_datetime(
                min(as.numeric(time)), tz = "UTC"),
              duration =
                (max(as.numeric(time) + collated_arguments$epoch_length) -
                min(as.numeric(time)))/60,
              bout_category = (bout_category[1])
                )

  return(summary_walk_bouts)
}