R/determine_position.R

In neonSoilFlux: Compute Soil Carbon Fluxes for the National Ecological Observatory Network Sites

#' @title Internal function to determine the depth of a measurement

#' @author
#' John Zobitz \email{zobitz@augsburg.edu}

#' @description
#' Given a NEON measurement data frame and measurement depth, pull out the measurement depth for a measurement - because it may vary in time based on if a sensor is replaced.
#'
#' @param input_positions Required. Input vector of measurements depths
#' @param input_measurement Required. Input vector of measurements.


#' @return A data frame that reports the measurement depth for and associated environmental measurement.


determine_position <- function(input_positions, input_measurement) {

  # changelog and author contributions / copyrights
  #   John Zobitz (2024-01-17)
  #     original creation



  .data = NULL  # Appease R CMD Check

  # Define %within% so we can use here
  `%within%` <- lubridate::`%within%`

    position_data <- input_positions |>
    dplyr::mutate(dplyr::across(.cols = .data[["positionStartDateTime"]]:.data[["positionEndDateTime"]], .fns = ~ as.POSIXct(.x,
      format = "%Y-%m-%dT%H:%M:%S", # format time
      tz = "UTC"
    ))) |>
    dplyr::mutate(dplyr::across(.cols = .data[["positionStartDateTime"]]:.data[["positionEndDateTime"]], .fns = ~ dplyr::if_else(is.na(.x), Sys.time(), .x))) |>
    dplyr::mutate(measurement_interval = lubridate::interval(.data[["positionStartDateTime"]], .data[["positionEndDateTime"]])) |>
    tidyr::separate_wider_delim(cols = .data[["HOR.VER"]], names = c("horizontalPosition", "verticalPosition"), delim = ".") |>
    dplyr::group_by(.data[["horizontalPosition"]],.data[["verticalPosition"]]) |>
    tidyr::nest() |>
    dplyr::rename(position_info = .data[["data"]]) |>
    dplyr::mutate(n_levels = purrr::map_dbl(.x = .data[["position_info"]], .f = ~ nrow(.x))) # Test to see if we have multiple measurement levels - then we need to check


  out_measurement <- input_measurement |>
    dplyr::group_by(.data[["horizontalPosition"]],.data[["verticalPosition"]],.data[["startDateTime"]]) |>
    tidyr::nest() |>
    dplyr::rename(measurement_info = .data[["data"]]) |>
    dplyr::inner_join(position_data, by = c("horizontalPosition", "verticalPosition")) |>
    dplyr::mutate(position_info = purrr::pmap(
      .l = list(.data[["n_levels"]], .data[["startDateTime"]],.data[["position_info"]]),
      .f = function(levels, startDateTime, position_info) {
        (


          if (levels == 1) {
            return(position_info)
          } else {
            new_info <- position_info |>
              dplyr::filter(startDateTime  %within% .data[["measurement_interval"]])

            return(new_info)
          })
      }
    )) |>
    dplyr::mutate(zOffset = purrr::map_dbl(.x = .data[["position_info"]], .f = ~ purrr::pluck(.x, "zOffset"))) |>
    dplyr::select(-tidyselect::all_of(c("n_levels","position_info"))) |>
    tidyr::unnest(cols = c(.data[["measurement_info"]]))

  return(out_measurement)
}