R/count_sampleStatus.R

In USGS-R/sedReview: A package and shiny GUI for review of discrete water-quality sediment records and box coefficient exploration of data stored in the USGS NWIS system

#' count_sampleStatus. Counts of sample status (DQI_CD) by parameter
#' 
#' @description Returns counts of sample status (DQI_CD) by parameter for each site/WY or for multiple sites together
#' @param x A \code{dataframe} output from \code{get_localNWIS}
#' @param bySite Logical. Count by site if \code{TRUE} or for all sites if \code{FALSE}
#' @return A data.frame tabular summary of counts of sample status (DQI_CD) by parameter
#' @examples
#' data("exampleData",package="sedReview")
#' x <- exampleData
#' count_sampleStatusOut <- count_sampleStatus(x,bySite = TRUE)
#' @importFrom dplyr group_by
#' @importFrom dplyr summarise
#' @importFrom reshape2 dcast
#' @export
#' 


count_sampleStatus <- function(x, bySite = TRUE) {
  x <- x[c("UID","RECORD_NO","SITE_NO","STATION_NM","SAMPLE_START_DT","MEDIUM_CD","PARM_CD","PARM_NM","DQI_CD","RESULT_VA","WY")]
  x <- x[x$PARM_CD %in% c('80154','70331','91157','00530','91145','80225'),]
  x <- unique(x)
  
  if(bySite == TRUE){
  statusSum <- dplyr::summarise(dplyr::group_by(x,SITE_NO,STATION_NM,PARM_CD,PARM_NM,DQI_CD,WY),
                                N = length(RESULT_VA)
  )
  statusSum <- reshape2::dcast(statusSum,SITE_NO+STATION_NM+WY+PARM_CD+PARM_NM~DQI_CD,value.var = "N")
  
  } else {
    statusSum <- dplyr::summarise(dplyr::group_by(x,PARM_CD,PARM_NM,DQI_CD),
                                  N = length(RESULT_VA)
    )
    statusSum <- reshape2::dcast(statusSum,PARM_CD+PARM_NM~DQI_CD,value.var = "N")
  }
  
  statusSum[is.na(statusSum)] <- 0
  return(statusSum)
}