R/formMWRacc.R

In massbays-tech/MassWateR: Quality Control and Analysis of Massachusetts Water Quality Data

#' Format data quality objective accuracy data
#'
#' @param accdat input data fram
#'
#' @details This function is used internally within \code{\link{readMWRacc}} to format the input data for downstream analysis.  The formatting includes:
#' 
#' \itemize{
#'   \item Minor formatting for units: For conformance to WQX, e.g., ppt is changed to ppth, s.u. is changed to NA in \code{uom}
#'   \item Convert Parameter: All parameters are converted to \code{Simple Parameter} in \code{\link{paramsMWR}} as needed
#'   \item Remove unicode: Remove or replace unicode characters with those that can be used in logical expressions in \code{\link{qcMWRacc}}, e.g., replace \eqn{\geq} with \eqn{>=}
#'   \item Convert limits to numeric: Convert \code{MDL} and \code{UQL} columns to numeric
#' }
#' 
#' @return A formatted data frame of the data quality objectives file for accuracy
#' 
#' @export
#'
#' @examples
#' accpth <- system.file('extdata/ExampleDQOAccuracy.xlsx', package = 'MassWateR')
#' 
#' accdat <- readxl::read_excel(accpth, na = c('NA', ''))
#' accdat <- dplyr::mutate(accdat, dplyr::across(-c(`Value Range`), ~ dplyr::na_if(.x, 'na')))
#' 
#' formMWRacc(accdat)
formMWRacc <- function(accdat){
  
  # convert ph s.u. to NA, salinity ppt to ppth 
  out <- accdat %>% 
    dplyr::mutate(
      uom = trimws(uom),
      uom = gsub('^ppt$', 'ppth', uom),
      uom = ifelse(Parameter == 'pH' & uom == 's.u.', NA_character_, uom)
    )

  # convert all parameters to simple
  out <- out %>% 
    dplyr::mutate( 
      `Parameter` = ifelse(
        `Parameter` %in% paramsMWR$`WQX Parameter`, 
        paramsMWR$`Simple Parameter`[match(`Parameter`, paramsMWR$`WQX Parameter`)], 
        `Parameter`
        ),
      dplyr::across(-c(Parameter, uom, MDL, UQL), function(x) gsub('\u00b1', '', x)),
      dplyr::across(-c(Parameter, uom, MDL, UQL), function(x) gsub('\u2264', '<=', x)),
      dplyr::across(-c(Parameter, uom, MDL, UQL), function(x) gsub('\u2265', '>=', x)), 
      dplyr::across(c(MDL, UQL), as.numeric)
    )
  
  return(out)
  
}