R/readNWISqw.r

In usgs/dataRetrieval: Retrieval Functions for USGS and EPA Hydrologic and Water Quality Data

#' Raw Data Import for USGS NWIS QW Data
#'
#' Imports data from NWIS web service. This function gets the data from here: \url{https://nwis.waterdata.usgs.gov/nwis/qwdata}
#' A list of parameter codes can be found here: \url{https://nwis.waterdata.usgs.gov/nwis/pmcodes/}
#' A list of statistic codes can be found here: \url{https://nwis.waterdata.usgs.gov/nwis/help/?read_file=stat&format=table}
#'
#' @details Valid parameter code groups are "All," or group codes:
#'\tabular{ll}{
#'Code \tab Description\cr
#'INF \tab Information \cr
#'PHY \tab Physical \cr
#'INM \tab Inorganics, Major, Metals (major cations) \cr
#'INN \tab Inorganics, Major, Non-metals (major anions) \cr
#'NUT \tab Nutrient \cr
#'MBI \tab Microbiological \cr
#'BIO \tab Biological \cr
#'IMN \tab Inorganics, Minor, Non-metals \cr
#'IMM \tab Inorganics, Minor, Metals \cr
#'TOX \tab Toxicity \cr
#'OPE \tab Organics, pesticide \cr
#'OPC \tab Organics, PCBs \cr
#'OOT \tab Organics, other \cr
#'RAD \tab Radiochemical \cr
#'SED \tab Sediment \cr
#'POP \tab Population/community \cr
#'}
#'If more than one parameter group is requested, only sites that data for all requested groups are returned.
#'
#' @param siteNumbers character of USGS site numbers.  This is usually an 8 digit number
#' @param parameterCd character that contains the code for a parameter
#' group, or a character vector of 5-digit parameter codes. See \bold{Details}.
#' @param startDate character starting date for data retrieval in the form YYYY-MM-DD. Default is "" which indicates
#' retrieval for the earliest possible record. Date arguments are always specified in local time.
#' @param endDate character ending date for data retrieval in the form YYYY-MM-DD. Default is "" which indicates
#' retrieval for the latest possible record. Date arguments are always specified in local time.
#' @param expanded logical defaults to \code{TRUE}. If \code{TRUE}, retrieves additional information. Expanded data includes
#' remark_cd (remark code), result_va (result value), val_qual_tx (result value qualifier code), meth_cd (method code),
#' dqi_cd (data-quality indicator code), rpt_lev_va (reporting level), and rpt_lev_cd (reporting level type). If \code{FALSE},
#' only returns remark_cd (remark code) and result_va (result value). Expanded = \code{FALSE} will not give
#' sufficient information for unbiased statistical analysis.
#' @param reshape logical, reshape the expanded data. If \code{TRUE}, then return a wide data frame with all water-quality in a single row for each sample. 
#' If \code{FALSE} (default), then return a long data frame with each water-quality result in a single row. This
#' argument is only applicable to expanded data. Data requested using \code{expanded=FALSE} is always returned in the wide format.
#' @param tz character to set timezone attribute of dateTime. Default is "UTC", and converts the 
#' date times to UTC, properly accounting for daylight savings times based on the data's provided tz_cd column.
#' Possible values to provide are "America/New_York","America/Chicago", "America/Denver","America/Los_Angeles",
#' "America/Anchorage", as well as the following which do not use daylight savings time: "America/Honolulu",
#' "America/Jamaica","America/Managua","America/Phoenix", and "America/Metlakatla". See also  \code{OlsonNames()} 
#' for more information on time zones.
#' @keywords data import USGS web service
#' @return A data frame with at least the following columns:
#' \tabular{lll}{
#' Name \tab Type \tab Description \cr
#' agency_cd \tab character \tab The NWIS code for the agency reporting the data\cr
#' site_no \tab character \tab The USGS site number \cr
#' sample_dt \tab Date \tab The date the sample was collected \cr 
#' sample_tm \tab character \tab The reported sample collection time \cr
#' startDateTime \tab POSIXct \tab Combining sample_dt and sample_tm, a date/time column is created, and converted into UTC 
#' (unless the tz argument specifies a different time zone)\cr
#' endDateTime \tab POSIXct \tab If any sample_end_dt and sample_end_dt exist, this column is created similar to startDateTime\cr
#' }
#' 
#' Further columns will be included depending on the requested output format (expanded = TRUE or FALSE).
#' Columns that end in "_reported" are the originally reported timezones, 
#' but the "tz_cd" column defines the timezone of any POSIXct columns.
#' 
#' There are also several useful attributes attached to the data frame:
#' \tabular{lll}{
#' Name \tab Type \tab Description \cr
#' url \tab character \tab The url used to generate the data \cr
#' queryTime \tab POSIXct \tab The time the data was returned \cr
#' comment \tab character \tab Header comments from the RDB file \cr
#' siteInfo \tab data frame \tab A data frame containing information on the requested sites \cr
#' variableInfo \tab data frame \tab A data frame containing information on the requested parameters \cr
#' }
#' @export
#' @seealso \code{\link{readWQPdata}}, \code{\link{whatWQPsites}}, 
#' \code{\link{readWQPqw}}, \code{\link{constructNWISURL}}
#' @examples
#' site_ids <- c('04024430','04024000')
#' startDate <- '2010-01-01'
#' endDate <- ''
#' parameterCd <- c('34247','30234','32104','34220')
#' \donttest{
#' rawNWISqwData <- readNWISqw(site_ids,parameterCd,startDate,endDate)
#' rawNWISqwDataReshaped <- readNWISqw(site_ids,parameterCd,
#'           startDate,endDate,reshape=TRUE)
#' parameterCd <- "all"
#' rawNWISall <- readNWISqw(site_ids,parameterCd,
#'           startDate,endDate)
#' pgroup <- c("NUT")
#' rawNWISNutrients <- readNWISqw(site_ids,pgroup,
#'           startDate,endDate)
#' groups <- c("NUT","OPE")
#' rawNWISNutOpe <- readNWISqw(site_ids,groups,
#'           startDate,endDate) 
#' rawNWISOpe <- readNWISqw(site_ids,"OPE",
#'           startDate,endDate) 
#'          } 
readNWISqw <- function (siteNumbers,parameterCd,startDate="",endDate="",
                        expanded=TRUE,reshape=FALSE,tz="UTC"){  
  
  pgrp <- c("INF", "PHY", "INM", "INN", "NUT", "MBI", "BIO", "IMM", "IMN", "TOX",
                           "OPE", "OPC", "OOT", "RAD", "XXX", "SED", "POP")

  if(any(parameterCd == "all") | any(parameterCd == "All") ){
    
    siteNumbers <- paste(siteNumbers, collapse=",")
    url <- paste0("https://nwis.waterdata.usgs.gov/nwis/qwdata?multiple_site_no=", siteNumbers,
           "&sort_key=site_no&group_key=NONE&inventory_output=0",
           "&begin_date=", startDate, "&end_date=", endDate,
           "&TZoutput=0",
           "&radio_parm_cds=all_parm_cds&qw_attributes=0&format=rdb",
           "&qw_sample_wide=0&rdb_qw_attributes=expanded&date_format=YYYY-MM-DD",
           "&rdb_compression=value&list_of_search_criteria=multiple_site_no")
  } else if (all(parameterCd %in% pgrp)){
    siteNumbers <- paste(siteNumbers, collapse=",")
    groups <- paste(parameterCd, collapse=",")
    url <- paste0("https://nwis.waterdata.usgs.gov/nwis/qwdata?multiple_site_no=", siteNumbers,
                  "&sort_key=site_no&group_key=NONE&inventory_output=0",
                  "&begin_date=", startDate, "&end_date=", endDate,
                  "&TZoutput=0&param_group=", groups,
                  "&qw_attributes=0&format=rdb",
                  "&qw_sample_wide=0&rdb_qw_attributes=expanded&date_format=YYYY-MM-DD",
                  "&rdb_compression=value&list_of_search_criteria=multiple_site_no")

  } else {
    url <- constructNWISURL(siteNumbers,
                            parameterCd,
                            startDate,
                            endDate,"qw",expanded=expanded)    
  }

  data <- importRDB1(url,asDateTime=TRUE, tz = tz)
  
  url <- attr(data, "url")
  comment <- attr(data, "comment")
  queryTime <- attr(data, "queryTime")
  header <- attr(data, "headerInfo")
  
  if(reshape){
    if(expanded){
      columnsToMelt <- c("agency_cd","site_no","sample_dt","sample_tm",
                         "sample_end_dt","sample_end_tm","sample_start_time_datum_cd","tm_datum_rlbty_cd",
                         "parm_cd","startDateTime","endDateTime","coll_ent_cd", "medium_cd","project_cd",
                         "aqfr_cd","tu_id","body_part_id", "hyd_cond_cd", "samp_type_cd",
                         "hyd_event_cd","sample_lab_cm_tx","tz_cd","startDateTime","endDateTime",
                         "sample_start_time_datum_cd_reported","sample_end_time_datum_cd_reported")
      measureCols <- names(data)[!(names(data) %in% columnsToMelt)]
      columnsToMelt <- names(data)[(names(data) %in% columnsToMelt)]
      dataWithPcodes <- data[data$parm_cd != "",]
      if(sum(data$parm_cd == "") > 0){
        warning("Some or all data returned without pCodes, those data will not be included in reshape")
      }
      original_start_dates <- dataWithPcodes$startDateTime
      original_end_dates <- dataWithPcodes$endDateTime
      
      parameterCd <- unique(dataWithPcodes$parm_cd)
      idcols <- names(dataWithPcodes)[!(names(dataWithPcodes) %in% c(measureCols,"parm_cd"))]

      dataWithPcodes[,idcols] <- lapply(dataWithPcodes[,idcols], function(x) as.factor(x))
      dataWithPcodes[,idcols] <- lapply(dataWithPcodes[,idcols], function(x) addNA(x))

      wide2 <- stats::reshape(dataWithPcodes, 
                              idvar = idcols,
                              timevar = "parm_cd",
                              v.names = measureCols,
                              direction = "wide")
      names(wide2) <- gsub("\\.","_",names(wide2))
      idcols_factors <- idcols[unname(sapply(wide2[idcols], class) == "factor")]
      idcols_dates <- idcols[grep("_dt",idcols)]
      
      wide2[,idcols_factors] <- sapply(wide2[,idcols_factors], as.character)
      wide2[,idcols_dates] <- lapply(wide2[,idcols_dates], as.Date)
      other_dates <- names(wide2)[grep("_dt",names(wide2))]
      other_dates <- other_dates[!(other_dates %in% idcols_dates)]
      wide2[,other_dates] <- lapply(wide2[,other_dates], function(x) as.Date(strptime(x, format = "%Y%m%d")))
      if("startDateTime" %in% names(wide2)){
        wide2[,"startDateTime"] <- as.POSIXct(wide2[,"startDateTime"], tz = attr(original_start_dates, "tzone"))
      }
      if("endDateTime" %in% names(wide2)){
        wide2[,"endDateTime"] <- as.POSIXct(wide2[,"endDateTime"], tz = attr(original_end_dates, "tzone"))
      }
      
      data <- wide2
    } else {
      warning("Reshape can only be used with expanded data. Reshape request will be ignored.")
    }
  } else {
    parameterCd <- unique(data$parm_cd)
  }
  
  if(exists("siteNumbers") &&  all(!(is.na(siteNumbers))) & length(siteNumbers) > 0){
    siteInfo <- readNWISsite(siteNumbers)
    if(nrow(data) > 0){
      siteInfo <- merge(x = unique(data[,c("agency_cd","site_no")]), 
                        y = siteInfo,
                        by=c("agency_cd","site_no"), 
                        all.x = TRUE)
    }
    attr(data, "siteInfo") <- siteInfo    
  }
  
  if(exists("parameterCd") && all(!is.na(parameterCd)) & length(parameterCd) > 0){
    parameterCd <- parameterCd[parameterCd != ""]
    varInfo <- readNWISpCode(parameterCd)
    attr(data, "variableInfo") <- varInfo
  }
  
  attr(data, "statisticInfo") <- NULL
  
  attr(data, "url") <- url
  attr(data, "comment") <- comment
  attr(data, "queryTime") <- queryTime
  attr(data, "header") <- header
  
  return (data)

}