From 6bf6d275167a0ffe78a1c9a808a8f02e2a95bc32 Mon Sep 17 00:00:00 2001
From: Laura DeCicco <ldecicco@usgs.gov>
Date: Fri, 1 Aug 2014 16:52:22 -0500
Subject: [PATCH] Getting rid of duplicate code. Using getRawQWData instead.
---
R/getWQPData.r | 90 ++++++++++++--------------------------------------
1 file changed, 21 insertions(+), 69 deletions(-)
diff --git a/R/getWQPData.r b/R/getWQPData.r
index 582ebeea..b1995775 100644
--- a/R/getWQPData.r
+++ b/R/getWQPData.r
@@ -1,8 +1,8 @@
#' Data Import from Water Quality Portal
#'
-#' Imports data from Water Quality Portal web service. This function gets the data from here: \url{http://www.waterqualitydata.us}. This function is more general than getQWData
+#' Imports data from Water Quality Portal web service. This function gets the data from: \url{http://www.waterqualitydata.us}. This function is more general than getQWData
#' because it allows for other agencies rather than the USGS. Therefore, the 5-digit parameter code cannot be used.
-#' Instead, this function uses characteristicName. A complete list can be found here \url{http://www.waterqualitydata.us/Codes/Characteristicname}
+#' Instead, this function uses characteristicName. A complete list can be found here
#'
#' @param siteNumber string site number. If USGS, it should be in the form :'USGS-XXXXXXXXX...'
#' @param characteristicName string
@@ -16,77 +16,29 @@
#' @import RCurl
#' @examples
#' # These examples require an internet connection to run
-#' getWQPData('USGS-01594440','Chloride', '', '')
-#' getWQPData('WIDNR_WQX-10032762','Specific conductance', '', '')
+#' Chloride <- getWQPData('USGS-01594440','Chloride', '', '')
+#' SC <- getWQPData('WIDNR_WQX-10032762','Specific conductance', '', '')
+#' NWIS_Cl <- getWQPData('USGS-04024000','30234', '', '')
getWQPData <- function(siteNumber,characteristicName,StartDate,EndDate,interactive=TRUE){
-
-# require(RCurl)
-
- StartDate <- formatCheckDate(StartDate, "StartDate", interactive=interactive)
- EndDate <- formatCheckDate(EndDate, "EndDate", interactive=interactive)
- dateReturn <- checkStartEndDate(StartDate, EndDate, interactive=interactive)
- StartDate <- dateReturn[1]
- EndDate <- dateReturn[2]
-
- if (nzchar(StartDate)){
- StartDate <- format(as.Date(StartDate), format="%m-%d-%Y")
- }
- if (nzchar(EndDate)){
- EndDate <- format(as.Date(EndDate), format="%m-%d-%Y")
+ retval <- getRawQWData(siteNumber=siteNumber,
+ ParameterCd=characteristicName,
+ StartDate=StartDate,
+ EndDate=EndDate,
+ interactive=interactive)
+ #Check for pcode:
+ if(all(nchar(characteristicName) == 5)){
+ suppressWarnings(pCodeLogic <- all(!is.na(as.numeric(characteristicName))))
+ } else {
+ pCodeLogic <- FALSE
}
-
- characteristicName <- URLencode(characteristicName)
-
- baseURL <- "http://www.waterqualitydata.us/Result/search?siteid="
- url <- paste(baseURL,
- siteNumber,
- "&characteristicName=",
- characteristicName, # to get multi-parameters, use a semicolen
- "&startDateLo=",
- StartDate,
- "&startDateHi=",
- EndDate,
- "&countrycode=US&mimeType=tsv",sep = "")
- h <- basicHeaderGatherer()
- doc <- getURI(url, headerfunction = h$update)
- numToBeReturned <- as.numeric(h$value()["Total-Result-Count"])
-
- suppressWarnings(retval <- read.delim(url, header = TRUE, quote="\"", dec=".", sep='\t', colClasses=c('character'), fill = TRUE))
-
- qualifier <- ifelse((retval$ResultDetectionConditionText == "Not Detected" |
- retval$ResultDetectionConditionText == "Detected Not Quantified" |
- retval$ResultMeasureValue < retval$DetectionQuantitationLimitMeasure.MeasureValue),"<","")
-
- correctedData<-ifelse((nchar(qualifier)==0),retval$ResultMeasureValue,retval$DetectionQuantitationLimitMeasure.MeasureValue)
- test <- data.frame(retval$CharacteristicName)
-
- # test$dateTime <- as.POSIXct(strptime(paste(retval$ActivityStartDate,retval$ActivityStartTime.Time,sep=" "), "%Y-%m-%d %H:%M:%S"))
- test$dateTime <- as.Date(retval$ActivityStartDate, "%Y-%m-%d")
-
- originalLength <- nrow(test)
-
- if (!is.na(numToBeReturned)){
- if(originalLength != numToBeReturned) warning(numToBeReturned, " sample results were expected, ", originalLength, " were returned")
-
- test$qualifier <- qualifier
- test$value <- as.numeric(correctedData)
-
- test <- test[!is.na(test$dateTime),]
- newLength <- nrow(test)
- if (originalLength != newLength){
- numberRemoved <- originalLength - newLength
- warningMessage <- paste(numberRemoved, " rows removed because no date was specified", sep="")
- warning(warningMessage)
- }
-
- colnames(test)<- c("CharacteristicName","dateTime","qualifier","value")
- data <- reshape(test, idvar="dateTime", timevar = "CharacteristicName", direction="wide")
- data$dateTime <- format(data$dateTime, "%Y-%m-%d")
- data$dateTime <- as.Date(data$dateTime)
- return(data)
+
+ if(nrow(retval) > 0){
+ data <- processQWData(retval,pCodeLogic)
} else {
- warning("No data retrieved")
+ data <- NULL
}
+ return(data)
+
}
--
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