R/read_importfib.R

In tbep-tech/tbeptools: Data and Indicators for the Tampa Bay Estuary Program

#' Load local water quality file for Fecal Indicator Bacteria (FIB)
#'
#' @inheritParams read_importepc
#' @param all logical indicating if all stations with FIB data are returned, default is \code{TRUE}, see details
#'
#' @return A \code{data.frame} of formatted FIB data.
#'
#' @details Loads the "RWMDataSpreadsheet" worksheet from the file located at \code{xlsx}.  The file is downloaded from \url{https://epcbocc.sharepoint.com/:x:/s/Share/EYXZ5t16UlFGk1rzIU91VogBa8U37lh8z_Hftf2KJISSHg?e=8r1SUL&download=1}.  The files can be viewed at \url{https://epcbocc.sharepoint.com/:f:/s/Share/EiypSSYdsEFCi84Sv_6-t7kBUYaXiIqN0B1n2w57Z_V3kQ?e=NdZQcU}.
#'
#' Returns FIB data including E. coli, Enterococcus, Fecal Coliform, and Total Coliform concentrations and waterbody class (freshwater as 1 or 3F, marine as 2 or 3M) for stations and sample dates.
#'
#' Values are returned for E. coli (\code{ecoli}), Enterococcus (\code{entero}), Fecal Coliform (\code{fcolif}), and Total Coliform (\code{totcol}).  Values shown are # of colonies per 100 mL of water (\code{#/100mL}). Qualifier columns for each are also returned with the \code{_q} suffix. Qualifier codes can be interpreted from the source spreadsheet.
#'
#' Concentrations noted with \code{<} or \code{>} in the raw data are reported as is, with only the numeric value shown.  Samples with this notation can be determined from the qualifier columns.
#'
#' If \code{all = FALSE}, only stations with AreaName in the source data as Hillsborough River, Hillsborough River Tributary, Alafia River, Alafia River Tributary, Lake Thonotosassa, Lake Thonotosassa Tributary, and Lake Roberta.
#'
#' @export
#'
#' @concept read
#'
#' @seealso \code{\link{read_formfib}}
#'
#' @examples
#' \dontrun{
#' # file path
#' xlsx <- '~/Desktop/RWMDataSpreadsheet_ThroughCurrentReportMonth.xlsx'
#'
#' # load and assign to object
#' fibdata <- read_importfib(xlsx, download_latest = T)
#'
#' }
read_importfib <- function(xlsx, download_latest = FALSE, na = c('', 'NULL'), all = TRUE){

  # download data
  rawdat <- read_importepc(xlsx, download_latest = download_latest, na = na)

  # format
  out <- read_formfib(rawdat, all = all)

  return(out)

}