Added dates and date/times to raw wqp data pulls.

DESCRIPTION

@@ -2,7 +2,7 @@ Package: dataRetrieval
 Type: Package
 Title: Retrieval functions for hydrologic data
 Version: 1.3.3
-Date: 2014-08-04
+Date: 2014-09-12
 Author: Robert M. Hirsch, Laura De Cicco
 Maintainer: Laura De Cicco <ldecicco@usgs.gov>
 Description: Collection of functions to help retrieve USGS data from either web

NAMESPACE

 # Generated by roxygen2 (4.0.2): do not edit by hand
 
+export(basicWQPData)
 export(checkStartEndDate)
 export(compressData)
 export(constructNWISURL)

R/basicWQPData.R

+#' Basic Water Quality Portal Data grabber
+#'
+#' Imports data from the Water Quality Portal based on a specified url.
+#' 
+#' @param url string URL to Water Quality Portal#' @keywords data import USGS web service
+#' @return retval dataframe raw data returned from the Water Quality Portal. Additionally, a POSIXct dateTime column is supplied for 
+#' start and end times.
+#' @export
+#' @import RCurl
+#' @examples
+#' # These examples require an internet connection to run
+#' rawSampleURL <- constructNWISURL('USGS-01594440','01075', '1985-01-01', '1985-03-31',"wqp")
+#' rawSample <- basicWQPData(rawSampleURL)
+basicWQPData <- function(url){
+  
+  h <- basicHeaderGatherer()
+  
+  retval = tryCatch({  
+    doc <- getURL(url, headerfunction = h$update)
+    
+  }, warning = function(w) {
+    message(paste("URL caused a warning:", url))
+    message(w)
+  }, error = function(e) {
+    message(paste("URL does not seem to exist:", url))
+    message(e)
+    return(NA)
+  })
+  
+  if(h$value()["Content-Type"] == "text/tab-separated-values;charset=UTF-8"){
+    
+    numToBeReturned <- as.numeric(h$value()["Total-Result-Count"])
+    
+    if (!is.na(numToBeReturned) | numToBeReturned != 0){
+      
+      
+      namesData <- read.delim(textConnection(doc), header = TRUE, quote="\"", 
+                              dec=".", sep='\t', 
+                              colClasses='character', 
+                              fill = TRUE,nrow=1)
+      classColumns <- setNames(rep('character',ncol(namesData)),names(namesData))
+      classColumns["ActivityStartDate"] <- "Date"
+      
+      classColumns[grep("MeasureValue",names(classColumns))] <- NA
+      
+      retval <- read.delim(textConnection(doc), header = TRUE, quote="\"", 
+                           dec=".", sep='\t', 
+                           colClasses=as.character(classColumns), 
+                           fill = TRUE)    
+      actualNumReturned <- nrow(retval)
+      
+      if(actualNumReturned != numToBeReturned) warning(numToBeReturned, " sample results were expected, ", actualNumReturned, " were returned")
+      
+      timeZoneLibrary <- setNames(c("America/New_York","America/New_York","America/Chicago","America/Chicago",
+                                    "America/Denver","America/Denver","America/Los_Angeles","America/Los_Angeles",
+                                    "America/Anchorage","America/Anchorage","America/Honolulu","America/Honolulu"),
+                                  c("EST","EDT","CST","CDT","MST","MDT","PST","PDT","AKST","AKDT","HAST","HST"))
+      timeZoneStart <- as.character(timeZoneLibrary[retval$ActivityStartTime.TimeZoneCode])
+      timeZoneEnd <- as.character(timeZoneLibrary[retval$ActivityEndTime.TimeZoneCode])
+      
+      if(any(!is.na(timeZoneStart))){
+        if(length(unique(timeZoneStart)) == 1){
+          retval$ActivityStartDateTime <- with(retval, as.POSIXct(paste(ActivityStartDate, ActivityStartTime.Time),format="%Y-%m-%d %H:%M:%S", tz=unique(timeZoneStart)))
+        } else {
+          warning("Mixed time zone information")
+          if(any(is.na(timeZoneStart))){
+            warning("Missing time zone information, all dateTimes default to user's local time")
+            retval$ActivityStartDateTime <- with(retval, as.POSIXct(paste(ActivityStartDate, ActivityStartTime.Time), format="%Y-%m-%d %H:%M:%S"),tz=Sys.timezone())
+          } else {
+            for(i in seq_along(row.names(retval))){
+              timeZone <- timeZoneStart[i]
+              retval$ActivityStartDateTime[i] <- with(retval, as.POSIXct(paste(ActivityStartDate[i], ActivityStartTime.Time[i]), format="%Y-%m-%d %H:%M:%S",tz=timeZone))
+            }
+          }
+        }
+      }
+      
+      if(any(!is.na(timeZoneEnd))){
+        if(length(unique(timeZoneEnd)) == 1){
+          retval$ActivityEndDateTime <- with(retval, as.POSIXct(paste(ActivityEndDate, ActivityEndTime.Time), format="%Y-%m-%d %H:%M:%S",tz=unique(timeZoneEnd)))
+        } else {
+          warning("Mixed time zone information")
+          if(any(is.na(timeZoneEnd))){
+            warning("Missing time zone information, all dateTimes default to user's local time")
+            retval$ActivityEndDateTime <- with(retval, as.POSIXct(paste(ActivityEndDate, ActivityEndTime.Time), format="%Y-%m-%d %H:%M:%S"), tz=Sys.timezone())
+          } else {
+            for(i in seq_along(row.names(retval))){
+              retval$ActivityEndDateTime[i] <- with(retval, as.POSIXct(paste(ActivityEndDate[i], ActivityEndTime.Time[i]), format="%Y-%m-%d %H:%M:%S",tz=timeZoneEnd[i]))
+            }
+          }
+        }
+      }
+      
+      if(any(retval$ActivityEndDate != "")){
+        retval$ActivityEndDate <- as.Date(retval$ActivityEndDate)
+      }
+      
+      return(retval)
+      
+    } else {
+      warning("No data to retrieve")
+      return(NA)
+    }
+  } else {
+    message(paste("URL caused an error:", url))
+    message("Content-Type=",h$value()["Content-Type"])
+    return(NA)
+  }
+}
\ No newline at end of file

R/getGeneralWQPData.R

@@ -30,45 +30,7 @@ getGeneralWQPData <- function(...){
   urlCall <- paste(baseURL,
                    urlCall,
                    "&mimeType=tsv",sep = "")
-  
-  doc = tryCatch({
-    h <- basicHeaderGatherer()
-    doc <- getURL(urlCall, headerfunction = h$update)
-    
-  }, warning = function(w) {
-    message(paste("URL caused a warning:", urlCall))
-    message(w)
-  }, error = function(e) {
-    message(paste("URL does not seem to exist:", urlCall))
-    message(e)
-    return(NA)
-  })
-  
-  if(h$value()["Content-Type"] == "text/tab-separated-values;charset=UTF-8"){
-    
-    numToBeReturned <- as.numeric(h$value()["Total-Result-Count"])
-    
-    if (!is.na(numToBeReturned) | numToBeReturned != 0){
-      retval <- read.delim(textConnection(doc), header = TRUE, quote="\"", 
-                           dec=".", sep='\t', 
-                           colClasses=c('character'), 
-                           fill = TRUE)
-      
-      actualNumReturned <- nrow(retval)
-      
-      if(actualNumReturned != numToBeReturned) warning(numToBeReturned, " sample results were expected, ", actualNumReturned, " were returned")
-      
-      return(retval)
-    } else {
-      warning(paste("No data to retrieve from",urlCall))
-      return(NA)
-    }
-    
-  } else {
-    message(paste("URL caused an error:", urlCall))
-    message("Content-Type=",h$value()["Content-Type"])
-    return(NA)
-  }
-
+  retVal <- basicWQPData(urlCall)
+  return(retVal)
   
 }
\ No newline at end of file

R/getRawQWData.r

-#' Raw Data Import for USGS NWIS Water Quality Data
+#' Raw Data Import for Water Quality Portal
 #'
-#' Imports data from NWIS web service. This function gets the data from here: \url{http://www.waterqualitydata.us}
-#' A list of parameter codes can be found here: \url{http://nwis.waterdata.usgs.gov/nwis/pmcodes/}
-#' A list of statistic codes can be found here: \url{http://nwis.waterdata.usgs.gov/nwis/help/?read_file=stat&format=table}
+#' Imports data from the Water Quality Portal. This function gets the data from here: \url{http://www.waterqualitydata.us}
 #'
-#' @param siteNumber string USGS site number.  This is usually an 8 digit number
-#' @param parameterCd vector of USGS 5-digit parameter code or string of characteristicNames. Leaving this blank will return all of the measured values during the specified time period.
+#' @param siteNumber string site number. This needs to include the full agency code prefix.
+#' @param parameterCd vector of USGS 5-digit parameter code or string of characteristicNames. 
+#' Leaving this blank will return all of the measured values during the specified time period.
 #' @param startDate string starting date for data retrieval in the form YYYY-MM-DD.
 #' @param endDate string ending date for data retrieval in the form YYYY-MM-DD.
 #' @param interactive logical Option for interactive mode.  If true, there is user interaction for error handling and data checks.
 #' @keywords data import USGS web service
-#' @return retval dataframe with first column dateTime, and at least one qualifier and value columns
-#' (subsequent qualifier/value columns could follow depending on requested parameter codes)
+#' @return retval dataframe raw data returned from the Water Quality Portal. Additionally, a POSIXct dateTime column is supplied for 
+#' start and end times.
 #' @export
 #' @import RCurl
 #' @examples
@@ -23,44 +22,7 @@
 retrieveWQPqwData <- function(siteNumber,parameterCd,startDate,endDate,interactive=TRUE){
 
   url <- constructNWISURL(siteNumber,parameterCd,startDate,endDate,"wqp",interactive=interactive)
-
-  retval = tryCatch({
-    h <- basicHeaderGatherer()
-    doc <- getURL(url, headerfunction = h$update)
-
-  }, warning = function(w) {
-    message(paste("URL caused a warning:", url))
-    message(w)
-  }, error = function(e) {
-    message(paste("URL does not seem to exist:", url))
-    message(e)
-    return(NA)
-  })
-  
-  if(h$value()["Content-Type"] == "text/tab-separated-values;charset=UTF-8"){
-  
-    numToBeReturned <- as.numeric(h$value()["Total-Result-Count"])
-    
-    if (!is.na(numToBeReturned) | numToBeReturned != 0){
-    
-      retval <- read.delim(textConnection(doc), header = TRUE, quote="\"", 
-                 dec=".", sep='\t', 
-                 colClasses=c('character'), 
-                 fill = TRUE)    
-      actualNumReturned <- nrow(retval)
-      
-      if(actualNumReturned != numToBeReturned) warning(numToBeReturned, " sample results were expected, ", actualNumReturned, " were returned")
-      
-      return(retval)
-  
-    } else {
-      warning("No data to retrieve")
-      return(NA)
-    }
-  } else {
-    message(paste("URL caused an error:", url))
-    message("Content-Type=",h$value()["Content-Type"])
-    return(NA)
-  }
+  retVal <- basicWQPData(url)
+  return(retVal)
   
 }

man/basicWQPData.Rd

+% Generated by roxygen2 (4.0.2): do not edit by hand
+\name{basicWQPData}
+\alias{basicWQPData}
+\title{Basic Water Quality Portal Data grabber}
+\usage{
+basicWQPData(url)
+}
+\arguments{
+\item{url}{string URL to Water Quality Portal#'}
+}
+\value{
+retval dataframe raw data returned from the Water Quality Portal. Additionally, a POSIXct dateTime column is supplied for
+start and end times.
+}
+\description{
+Imports data from the Water Quality Portal based on a specified url.
+}
+\examples{
+# These examples require an internet connection to run
+rawSampleURL <- constructNWISURL('USGS-01594440','01075', '1985-01-01', '1985-03-31',"wqp")
+rawSample <- basicWQPData(rawSampleURL)
+}
+\keyword{USGS}
+\keyword{data}
+\keyword{import}
+\keyword{service}
+\keyword{web}
+

man/retrieveWQPqwData.Rd

 % Generated by roxygen2 (4.0.2): do not edit by hand
 \name{retrieveWQPqwData}
 \alias{retrieveWQPqwData}
-\title{Raw Data Import for USGS NWIS Water Quality Data}
+\title{Raw Data Import for Water Quality Portal}
 \usage{
 retrieveWQPqwData(siteNumber, parameterCd, startDate, endDate,
   interactive = TRUE)
 }
 \arguments{
-\item{siteNumber}{string USGS site number.  This is usually an 8 digit number}
+\item{siteNumber}{string site number. This needs to include the full agency code prefix.}
 
-\item{parameterCd}{vector of USGS 5-digit parameter code or string of characteristicNames. Leaving this blank will return all of the measured values during the specified time period.}
+\item{parameterCd}{vector of USGS 5-digit parameter code or string of characteristicNames.
+Leaving this blank will return all of the measured values during the specified time period.}
 
 \item{startDate}{string starting date for data retrieval in the form YYYY-MM-DD.}
 
@@ -18,13 +19,11 @@ retrieveWQPqwData(siteNumber, parameterCd, startDate, endDate,
 \item{interactive}{logical Option for interactive mode.  If true, there is user interaction for error handling and data checks.}
 }
 \value{
-retval dataframe with first column dateTime, and at least one qualifier and value columns
-(subsequent qualifier/value columns could follow depending on requested parameter codes)
+retval dataframe raw data returned from the Water Quality Portal. Additionally, a POSIXct dateTime column is supplied for
+start and end times.
 }
 \description{
-Imports data from NWIS web service. This function gets the data from here: \url{http://www.waterqualitydata.us}
-A list of parameter codes can be found here: \url{http://nwis.waterdata.usgs.gov/nwis/pmcodes/}
-A list of statistic codes can be found here: \url{http://nwis.waterdata.usgs.gov/nwis/help/?read_file=stat&format=table}
+Imports data from the Water Quality Portal. This function gets the data from here: \url{http://www.waterqualitydata.us}
 }
 \examples{
 # These examples require an internet connection to run