R/read_sediment_trap_data.R

In FRBCesab/forcis: An R Client to Access the FORCIS Database

#' @rdname read_data
#' @export

read_sediment_trap_data <- function(
    path = ".", version = options()$"forcis_version", 
    check_for_update = options()$"check_for_update") {
  
  ## Check args ----
  
  check_if_character(path)
  check_version(version)
  
  
  ## Check/set version ----
  
  version <- set_version(version, ask = FALSE)
  
  
  ## Check local database ----
  
  path <- file.path(path, "forcis-db", paste0("version-", version))
  
  if (!dir.exists(path)) {
    stop("The directory '", path, "' does not exist. Please check the ",
         "argument 'path' or use the function 'download_forcis_db()'.",
         call. = FALSE)
  }
  
  
  ## Check file ----
  
  file_name <- list.files(path, pattern = sediment_trap_filename())
  
  if (!length(file_name)) {
    stop("The Sediment trap dataset does not exist. Please use the function ", 
         "'download_forcis_db()'.", call. = FALSE)
  }
  
  
  ## Check for update ----
  
  if (is.null(check_for_update)) {
    check_for_update <- TRUE
  }
  
  if (check_for_update) {
    if (version != get_latest_version()) {
      message("A newer version of the FORCIS database is available. Use ", 
              "'download_forcis_db(version = NULL)' to download it.")
    }  
  }
  
  
  ## Read data ----
  
  file_name <- list.files(path, pattern = sediment_trap_filename())
  
  data <- vroom::vroom(file.path(path, file_name), delim = ";",
                       altrep = FALSE, show_col_types = FALSE)
  
  data <- as.data.frame(data)
  
  data <- add_data_type(data, "Sediment trap")
  
  
  ## Check and convert columns ----
  
  taxa_columns <- get_species_names(data)
  
  for (i in seq_len(length(taxa_columns))) {
    
    data[ , taxa_columns[i]] <- as.numeric(data[ , taxa_columns[i]])
  }
  
  data
}