R/eo_import_logs.R

In readosense: Imports Log and Data Files from Eosense Flux Chambers

#' imports log files from Eosense chambers
#' @param path folder in which the log files are located
#' @param colnames column names as defined in Eosense documentation
#' @param nb_ports number of ports
#' @param open status numbers indicating chamber is open
#' @param closed status numbers indicating chamber is closed
#' @param fully_closed status number indicating the chamber is fully closed
#' @return a dataframe with all the information from the logs and measurement id
#' @importFrom purrr map
#' @importFrom readr read_log
#' @importFrom tidyr pivot_longer
#' @importFrom dplyr arrange mutate case_when consecutive_id filter bind_rows
#' select distinct
#' @importFrom lubridate as_datetime round_date
#' @importFrom rlang .data
#' @export
#' @examples
#' path <- system.file("extdata/ex_logs", package = "readosense")
#' eo_import_logs(path)

eo_import_logs <- function(path,
                           closed = c(1:3),
                           open = 0,
                           fully_closed = 1,
                           colnames = c(
                             "port", "valvestatus", "chamberstatus",
                             "aux1", "aux2", "aux3", "aux4", "aux5",
                             "temperaturev", "pressure"
                           ),
                           nb_ports = 12) {


  # building col names
  seq_nb_ports <- seq_along(1:nb_ports)
  indices <- rep(seq_nb_ports, each = length(colnames))
  rep_colnames <- rep(colnames, times = nb_ports) |>
    paste(indices, sep = "_")
  log_colnames <- c(
    "epochtime",
    rep_colnames
  )

  chamber_log_read <- list.files(
    path = path,
    full.names = TRUE
  ) |>
    map(
      read_log,
      col_names = log_colnames,
      show_col_types = FALSE,
      .progress = TRUE
    ) |>
    bind_rows()

  # repeated colnames are normal
  chamber_log_all <- chamber_log_read |>
    pivot_longer(
      !c("epochtime"), names_to = c(".value", "variable"), names_sep = "_"
    ) |>
    filter(
      .data$port %in% seq_nb_ports # we filter out all the rows with port -1
    ) |>
    arrange(.data$epochtime) |> # just to be sure
    mutate( # without grouping
      chamber = case_when(
        .data$chamberstatus %in% closed ~ "open",
        .data$chamberstatus == open ~ "closed"
      ),
      change_id =
        consecutive_id(
          .data$port, .data$chamberstatus
        ), #detecting if same port but new measurement
      datetime = as_datetime(.data$epochtime), # we work in datetime
      datetime = round_date(.data$datetime)
    ) |>
    filter(
      .data$chamberstatus == fully_closed
    ) |>
    mutate(
      measurement_id =
        consecutive_id(
          .data$change_id
        ) # just getting rid of the missing id after filter
    ) |>
    select(!"variable") |>
    distinct(.data$datetime, .keep_all = TRUE) # some are doubled

  chamber_log_all
}