R/daily_data_table.R

In LimnoTech/SWMPrStorm: Organizing, and Analyzing Estuary Monitoring Data for Storm Events

#' daily_data_table
#'
#' @param var_in .xlsx with all required input variables defined (string).
#' @param data_path pathway to cdmo data folder (string).
#' @param storm_nm name of storm event (string).
#' @param storm_start YYYY-MM-DD HH:MM:SS start of storm event (string).
#' @param storm_end YYYY-MM-DD HH:MM:SS end of storm event (string).
#' @param wq_sites comma separated list of wq stations to plot. if left blank, all active stations from reserve will be plotted. (string).
#' @param met_sites comma separated list of met stations to plot. if left blank, all active stations from reserve will be plotted. (string).
#' @param keep_flags comma separated list of data quality flags that should be kept (string).
#' @param reserve 3 digit reserve code (string).
#' @param skip TRUE/FALSE. If TRUE, function will be skipped (string).
#' @param user_units User defined units. Set to "English" or "SI". Default CDMO data is in SI units. Not all parameters have common equivalent English units (e.g. concentrations), and therefore not all will be converted.
#'
#'
#' @return tables are generated and saved in /output/wq/data_table/ and /output/met/data_table/
#' @export
#'
#' @examples
#'
#' \dontrun{
#' #StormVariables.xlsx is a template variable input file saved in data/
#' vars_in <- 'data/StormTrackVariables.xlsx'
#' single_storm_track(var_in = vars_in)
#' }
daily_data_table <- function(var_in,
                            data_path = NULL,
                            storm_nm = NULL,
                            storm_start = NULL,
                            storm_end = NULL,
                            reserve = NULL,
                            wq_sites = NULL,
                            met_sites = NULL,
                            keep_flags = NULL,
                            skip = NULL,
                            user_units = NULL) {


  # ----------------------------------------------------------------------------
  # Define global variables
  # ----------------------------------------------------------------------------
  NERR.Site.ID_ <- rlang::sym('NERR.Site.ID')
  Station.Code_ <- rlang::sym('Station.Code')
  Status_ <- rlang::sym('Status')
  Station.Type_ <- rlang::sym('Station.Type')
  reserve_code_ <- rlang::sym('reserve_code')

  station_ <- rlang::sym('station')
  event_ <- rlang::sym('event')
  parameter_ <- rlang::sym('parameter')
  result_ <- rlang::sym('result')
  datetimestamp_ <- rlang::sym('datetimestamp')

  station_fac_ <- rlang::sym('station_fac')


  # ----------------------------------------------------------------------------
  # Read in Data
  # ----------------------------------------------------------------------------

  #a.  Read in the variable input template, var_in

  input_Parameters <- openxlsx::read.xlsx(var_in, sheet = "table_daily")
  input_Master <- openxlsx::read.xlsx(var_in, sheet = "MASTER")


  if(is.null(storm_nm)) storm_nm <- unlist(strsplit(input_Parameters[1,2],", "))
  if(is.null(storm_start)) storm_start <- unlist(strsplit(input_Parameters[2,2],", "))
  if(is.null(storm_end)) storm_end <- unlist(strsplit(input_Parameters[3,2],", "))
  if(is.null(reserve)) reserve <- if(is.na(input_Parameters[4,2])) {input_Master[1,2]} else {unlist(strsplit(input_Parameters[4,2],", "))}
  if(is.null(keep_flags)) keep_flags <- unlist(strsplit(input_Parameters[5,2],", "))
  if(is.null(skip)) skip <- input_Parameters[6,2]
  if(is.null(user_units)) user_units <- input_Parameters[7,2]
  if(is.null(data_path)) data_path <- 'data/cdmo'

  stations <- get('sampling_stations') %>%
    dplyr::filter(!! NERR.Site.ID_ %in% reserve) %>%
    dplyr::filter(!! Status_ == "Active")

  wq_sites <- stations %>%
    dplyr::filter(!! Station.Type_ == 1)
  wq_sites <- wq_sites$Station.Code

  met_sites <- stations %>%
    dplyr::filter(!! Station.Type_ == 0)
  met_sites <- met_sites$Station.Code


  ############## Tests #########################################################
  if(skip == "TRUE") {return(warning("skip set to 'TRUE', skipping compare_one_reserve_one_event"))}



  ########## WATER QUALITY #####################################################

  # ----------------------------------------------
  # Load water quality data ----------------------
  # ----------------------------------------------

  ## load, clean, and filter data
  data_type <- 'wq'

  ls_par <- lapply(wq_sites, SWMPr::import_local, path = data_path)
  ls_par <- lapply(ls_par, SWMPr::qaqc, qaqc_keep = keep_flags)
  names(ls_par) <- wq_sites

  ## convert dataset to user defined units (if "SI", no conversion will take place)
  ls_par <- SWMPrStorm::convert_units(ls_par, user_units)


  # filter timeframes

  evts <- data.frame()
  for(i in 1:length(storm_nm)) {

    evt <- dplyr::bind_rows(ls_par, .id = 'station')
    evt <- subset(evt, subset = c(as.POSIXct(storm_start[i]), as.POSIXct(storm_end[i])))
    evt$event <- storm_nm[i]

    evts <- dplyr::bind_rows(evts, evt)

  }

  # reformat, add reserve name
  dat <- evts %>% dplyr::relocate(!! event_) %>%
    dplyr::left_join(stations %>%
                       dplyr::select(!! NERR.Site.ID_, !! Station.Code_) %>%
                       dplyr::rename("reserve_code" = !! NERR.Site.ID_, "station" = !! Station.Code_)) %>%
    dplyr::relocate(!! event_, !! reserve_code_)


  # combine data.frames into one and tidy
  dat_tidy <- tidyr::pivot_longer(dat, 5:length(names(dat)), names_to = 'parameter', values_to = 'result') %>%
    dplyr::mutate(date = as.Date(!! datetimestamp_))

  # ----------------------------------------------
  # Single Event Comparison, Single Reserves ---
  # ----------------------------------------------

  summary <- dat_tidy %>%
    dplyr::group_by(!! event_, !! parameter_, !! station_, date) %>%
    tidyr::drop_na(!! result_) %>%
    dplyr::summarise(min = min(!! result_, na.rm = T)
                     , max = max(!! result_, na.rm = T)
                     , mean = mean(!! result_, na.rm = T)
                     , median = stats::median(!! result_, na.rm = T))

  # add readable station names
  summary$station_name <- sapply(summary$station, SWMPrExtension::title_labeler)

  # # add factors for spatial filtering
  # summary$station_fac <- factor(summary$station, levels = wq_sites)
  #
  # # re-sort the table using factors
  # summary <- summary %>% arrange(., parameter, station_fac)

  # write table
  tbl_ttl <- paste('output/wq/data_table/daily_data_table_wq_', user_units, "_", storm_nm, '_', paste0(reserve, collapse = "_"), '.csv', sep = '')
  utils::write.csv(summary, file = tbl_ttl, quote = F, row.names = F)


  ########## Meteorological #####################################################


  # ----------------------------------------------
  # Load meteorological data ----------------------
  # ----------------------------------------------

  ## load, clean, and filter data
  data_type <- 'met'

  ls_par <- lapply(met_sites, SWMPr::import_local, path = data_path)
  ls_par <- lapply(ls_par, SWMPr::qaqc, qaqc_keep = keep_flags)
  names(ls_par) <- met_sites

  ## convert dataset to user defined units (if "SI", no conversion will take place)
  ls_par <- SWMPrStorm::convert_units(ls_par, user_units)

  ## add in precip intensity
  ls_par <- lapply(ls_par, function(x) {x$intensprcp <- x$totprcp * 4; x}) # unit/15-min to unit/hr

  # filter timeframes

  evts <- data.frame()
  for(i in 1:length(storm_nm)) {

    evt <- dplyr::bind_rows(ls_par, .id = 'station')
    evt <- subset(evt, subset = c(as.POSIXct(storm_start[i]), as.POSIXct(storm_end[i])))
    evt$event <- storm_nm[i]

    evts <- dplyr::bind_rows(evts, evt)

  }

  # reformat, add reserve name
  dat <- evts %>% dplyr::relocate(!! event_) %>%
    dplyr::left_join(stations %>%
                       dplyr::select(!! NERR.Site.ID_, !! Station.Code_) %>%
                       dplyr::rename("reserve_code" = !! NERR.Site.ID_, "station" = !! Station.Code_)) %>%
    dplyr::relocate(!! event_, !! reserve_code_)

  # combine data.frames into one and tidy
  dat_tidy <- tidyr::pivot_longer(dat, 5:length(names(dat)), names_to = 'parameter', values_to = 'result') %>%
    dplyr::mutate(date = as.Date(!! datetimestamp_))

  # ----------------------------------------------
  # Single Event Comparison, One Reserves ---
  # ----------------------------------------------


  total_nalist <- c("atemp", "bp", "intensprcp", "maxwspd", "rh", "sdwdir", "wdir", "wspd")

  summary <- dat_tidy %>%
    dplyr::group_by(!! event_,!! parameter_, !! station_, date) %>%
    tidyr::drop_na(!! result_) %>%
    dplyr::summarise(min = min(!! result_, na.rm = T)
                     , max = max(!! result_, na.rm = T)
                     , mean = mean(!! result_, na.rm = T)
                     , median = stats::median(!! result_, na.rm = T)
                     , total = sum(!! result_, na.rm = T)) %>%
    dplyr::mutate(total = dplyr::case_when(!! parameter_ %in% total_nalist == FALSE ~ total))



  # add readable station names
  summary$station_name <- sapply(summary$station, SWMPrExtension::title_labeler)



  # write table
  tbl_ttl <- paste('output/met/data_table/daily_data_table_met_', user_units, "_", storm_nm, '_', paste0(reserve, collapse = "_"), '.csv', sep = '')
  utils::write.csv(summary, file = tbl_ttl, quote = F, row.names = F)


}