R/checkMWRsites.R

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

#' Check site metadata file
#'
#' @param sitdat input data frame
#'
#' @details This function is used internally within \code{\link{readMWRsites}} to run several checks on the input data for completeness and conformance to WQX requirements
#' 
#' The following checks are made: 
#' \itemize{
#'  \item Column name spelling: Should be the following: Monitoring Location ID, Monitoring Location Name, Monitoring Location Latitude, Monitoring Location Longitude, Location Group
#'  \item Columns present: All columns from the previous check should be present
#'  \item Missing longitude or latitude: No missing entries in Monitoring Location Latitude or Monitoring Location Longitude
#'  \item Non-numeric latitude values: Values entered in Monitoring Location Latitude must be numeric
#'  \item Non-numeric longitude values: Values entered in Monitoring Location Longitude must be numeric
#'  \item Positive longitude values: Values in Monitoring Location Longitude must be negative
#'  \item Missing Location ID: No missing entries for Monitoring Location ID
#' }
#' 
#' @return \code{sitdat} is returned as is if no errors are found, otherwise an informative error message is returned prompting the user to make the required correction to the raw data before proceeding. 
#' 
#' @export
#'
#' @examples
#' library(dplyr)
#' 
#' sitpth <- system.file('extdata/ExampleSites.xlsx', package = 'MassWateR')
#' 
#' sitdat <- readxl::read_excel(sitpth, na = c('NA', 'na', ''))
#'     
#' checkMWRsites(sitdat)
checkMWRsites <- function(sitdat){
  
  message('Running checks on site metadata...\n')

  # globals
  colnms <- c("Monitoring Location ID", "Monitoring Location Name", "Monitoring Location Latitude", 
              "Monitoring Location Longitude", "Location Group")
  
  # check field names
  msg <- '\tChecking column names...'
  nms <- names(sitdat) 
  chk <- nms %in% colnms
  if(any(!chk)){
    tochk <- nms[!chk]
    stop(msg, '\n\tPlease correct the column names or remove: ', paste(tochk, collapse = ', '), call. = FALSE)
  }
  message(paste(msg, 'OK'))
  
  # check all fields are present
  msg <- '\tChecking all required columns are present...'
  nms <- names(sitdat)
  chk <- colnms %in% nms
  if(any(!chk)){
    tochk <- colnms[!chk]
    stop(msg, '\n\tMissing the following columns: ', paste(tochk, collapse = ', '), call. = FALSE)
  }
  message(paste(msg, 'OK'))
  
  # checking for missing lat/lon
  msg <- '\tChecking for missing latitude or longitude values...'
  chk <- sitdat %>% 
    dplyr::select(`Monitoring Location Latitude`, `Monitoring Location Longitude`) %>% 
    apply(1, function(x) !anyNA(x))
  if(any(!chk)){
    rws <- which(!chk)
    stop(msg, '\n\tMissing latitude or longitude in row(s) ', paste(rws, collapse = ', '), call. = FALSE)
  }
  message(paste(msg, 'OK'))
  
  # check for non-numeric latitude
  msg <- '\tChecking for non-numeric values in latitude...'
  typ <- sitdat$`Monitoring Location Latitude`
  chk <- !is.na(suppressWarnings(as.numeric(typ)))
  if(any(!chk)){
    rws <- which(!chk)
    tochk <- unique(typ[!chk])
    stop(msg, '\n\tNon-numeric entries in Monitoring Location Latitude found: ', paste(tochk, collapse = ', '), ' in row(s) ', paste(rws, collapse = ', '), call. = FALSE)
  }
  message(paste(msg, 'OK'))
  
  # check for non-numeric longitude
  msg <- '\tChecking for non-numeric values in longitude...'
  typ <- sitdat$`Monitoring Location Longitude`
  chk <- !is.na(suppressWarnings(as.numeric(typ)))
  if(any(!chk)){
    rws <- which(!chk)
    tochk <- unique(typ[!chk])
    stop(msg, '\n\tNon-numeric entries in Monitoring Location Longitude found: ', paste(tochk, collapse = ', '), ' in row(s) ', paste(rws, collapse = ', '), call. = FALSE)
  }
  message(paste(msg, 'OK'))
  
  # positive values in lon
  msg <- '\tChecking for positive values in longitude...'
  typ <- sitdat$`Monitoring Location Longitude`
  chk <- typ <= 0
  if(any(!chk)){
    rws <- which(!chk)
    tochk <- unique(typ[!chk])
    stop(msg, '\n\tPositive Monitoring Location Longitude found in row(s) ', paste(rws, collapse = ', '), call. = FALSE)
  }
  message(paste(msg, 'OK'))
  
  # missing location id
  msg <- '\tChecking for missing entries for Monitoring Location ID...'
  chk <- sitdat$`Monitoring Location ID`
  chk <- !is.na(chk)
  if(any(!chk)){
    rws <- which(!chk)
    stop(msg, '\n\tMissing Monitoring Location ID in row(s) ', paste(rws, collapse = ', '), call. = FALSE)
  }
  message(paste(msg, 'OK'))
  
  message('\nAll checks passed!')
  
  return(sitdat)
  
}