Merge pull request #24 from ldecicco-USGS/master

Fixed bug, cleaned up help files.

R/getNWISSites.R

@@ -2,11 +2,13 @@
 #'
 #' Returns a list of sites from the NWIS web service. This function gets the data from: \url{http://waterservices.usgs.gov/rest/Site-Test-Tool.html}.
 #' Arguments to the function should be based on \url{http://waterservices.usgs.gov/rest/Site-Service.html#Service}
+#' Mapper format is used
 #'
 #' @param \dots see \url{http://waterservices.usgs.gov/rest/Site-Service.html#Service} for a complete list of options
 #' @keywords data import NWIS web service
-#' @return retval dataframe 
+#' @return retval dataframe with agency_cd, site_no, station_nm, site_tp_cd, dec_lat_va, and dec_long_va.
 #' @export
+#' @import XML
 #' @examples
 #' siteListPhos <- getNWISSites(stateCd="OH",parameterCd="00665")
 getNWISSites <- function(...){
@@ -18,20 +20,53 @@ getNWISSites <- function(...){
   urlCall <- paste(paste(names(values),values,sep="="),collapse="&")
   
   
-  baseURL <- "http://waterservices.usgs.gov/nwis/site/?format=rdb&"
+  baseURL <- "http://waterservices.usgs.gov/nwis/site/?format=mapper&"
   urlCall <- paste(baseURL,
                    urlCall,sep = "")
-
-  retval <- getRDB1Data(urlCall)
-
-  if("dec_lat_va" %in% names(retval)){
-    retval$dec_lat_va <- as.numeric(retval$dec_lat_va)
-  }
   
-  if("dec_long_va" %in% names(retval)){
-    retval$dec_long_va <- as.numeric(retval$dec_long_va)
+  h <- basicHeaderGatherer()
+  doc = tryCatch({
+    returnedDoc <- getURI(urlCall, headerfunction = h$update)
+    if(h$value()["Content-Type"] == "text/xml;charset=UTF-8"){
+      xmlTreeParse(returnedDoc, getDTD = FALSE, useInternalNodes = TRUE)
+    } else {
+      message(paste("URL caused an error:", obs_url))
+      message("Content-Type=",h$value()["Content-Type"])
+      return(NA)
+    }   
+    
+  }, warning = function(w) {
+    message(paste("URL caused a warning:", obs_url))
+    message(w)
+  }, error = function(e) {
+    message(paste("URL does not seem to exist:", obs_url))
+    message(e)
+    return(NA)
+  }) 
+  
+  doc <- xmlRoot(doc)
+  numChunks <- xmlSize(doc)
+  for(i in 1:numChunks){
+    chunk <- doc[[1]]
+    site_no <- as.character(xpathApply(chunk, "site/@sno"))
+    station_nm <- as.character(xpathApply(chunk, "site/@sna"))
+    site_tp_cd <- as.character(xpathApply(chunk, "site/@cat"))
+    dec_lat_va <- as.numeric(xpathApply(chunk, "site/@lat"))
+    dec_long_va <- as.numeric(xpathApply(chunk, "site/@lng"))
+    agency_cd <- as.character(xpathApply(chunk, "site/@agc"))
+    
+    df <- data.frame(agency_cd, site_no, station_nm, site_tp_cd, 
+                     dec_lat_va, dec_long_va, stringsAsFactors=FALSE) 
+    
+    if(1==i){
+      retval <- df
+    } else {
+      retval <- rbind(retval, df)
+    }
   }
   
+  retval <- retval[!duplicated(retval),]
+  
   retval$queryTime <- Sys.time()
   
   return(retval)

R/getRDB1Data.r

@@ -40,6 +40,8 @@ getRDB1Data <- function(obs_url,asDateTime=FALSE, qw=FALSE){
   
   if(as.character(h$value()["Content-Type"]) == "text/plain;charset=UTF-8" | as.character(h$value()["Content-Type"]) == "text/plain"){
     
+#     comments <- readLines(doc)
+    
     tmp <- read.delim(  
       textConnection(doc), 
       header = TRUE, 

R/getRawQWData.r

@@ -22,10 +22,8 @@
 #' \code{\link{getSTORETSampleData}}, \code{\link{getNWISqwData}}, and \code{\link{readWQPData}}
 #' @examples
 #' # These examples require an internet connection to run
-#' rawSample <- getWQPqwData('USGS-01594440','01075', '1985-01-01', '1985-03-31')
-#' rawSampleAll <- getWQPqwData('USGS-05114000','', '1985-01-01', '1985-03-31')
-#' rawSampleSelect <- getWQPqwData('USGS-05114000',c('00915','00931'), '1985-01-01', '1985-04-30')
-#' rawStoret <- getWQPqwData('WIDNR_WQX-10032762','Specific conductance', '', '')
+#' rawPcode <- getWQPqwData('USGS-01594440','01075', '1985-01-01', '1985-03-31')
+#' rawCharacteristicName <- getWQPqwData('WIDNR_WQX-10032762','Specific conductance', '', '')
 getWQPqwData <- function(siteNumber,parameterCd,startDate,endDate,interactive=TRUE){
 
   url <- constructNWISURL(siteNumber,parameterCd,startDate,endDate,"wqp",interactive=interactive)

inst/doc/dataRetrieval.R

@@ -210,7 +210,7 @@ names(dissolvedNitrate)
 
 ## ----getQWtemperaturePlot, echo=TRUE, fig.cap=paste(parameterINFO$parameter_nm, "at", siteINFO$station.nm[1])----
 with(dissolvedNitrate, plot(
-  dateTime, result_va_00618,
+  startDateTime, result_va_00618,
   xlab="Date",ylab = paste(parameterINFO$srsname,
       "[",parameterINFO$parameter_units,"]")
   ))

inst/doc/dataRetrieval.Rnw

@@ -512,7 +512,7 @@ names(dissolvedNitrate)
 
 <<getQWtemperaturePlot, echo=TRUE, fig.cap=paste(parameterINFO$parameter_nm, "at", siteINFO$station.nm[1])>>=
 with(dissolvedNitrate, plot(
-  dateTime, result_va_00618,
+  startDateTime, result_va_00618,
   xlab="Date",ylab = paste(parameterINFO$srsname,
       "[",parameterINFO$parameter_units,"]")
   ))

man/getNWISSites.Rd

@@ -9,11 +9,12 @@ getNWISSites(...)
 \item{\dots}{see \url{http://waterservices.usgs.gov/rest/Site-Service.html#Service} for a complete list of options}
 }
 \value{
-retval dataframe
+retval dataframe with agency_cd, site_no, station_nm, site_tp_cd, dec_lat_va, and dec_long_va.
 }
 \description{
 Returns a list of sites from the NWIS web service. This function gets the data from: \url{http://waterservices.usgs.gov/rest/Site-Test-Tool.html}.
 Arguments to the function should be based on \url{http://waterservices.usgs.gov/rest/Site-Service.html#Service}
+Mapper format is used
 }
 \examples{
 siteListPhos <- getNWISSites(stateCd="OH",parameterCd="00665")

man/getWQPqwData.Rd

@@ -31,10 +31,8 @@ site name, such as 'USGS-01234567'.
 }
 \examples{
 # These examples require an internet connection to run
-rawSample <- getWQPqwData('USGS-01594440','01075', '1985-01-01', '1985-03-31')
-rawSampleAll <- getWQPqwData('USGS-05114000','', '1985-01-01', '1985-03-31')
-rawSampleSelect <- getWQPqwData('USGS-05114000',c('00915','00931'), '1985-01-01', '1985-04-30')
-rawStoret <- getWQPqwData('WIDNR_WQX-10032762','Specific conductance', '', '')
+rawPcode <- getWQPqwData('USGS-01594440','01075', '1985-01-01', '1985-03-31')
+rawCharacteristicName <- getWQPqwData('WIDNR_WQX-10032762','Specific conductance', '', '')
 }
 \seealso{
 \code{\link{getWQPData}}, \code{\link{getWQPSites}},

vignettes/dataRetrieval-concordance.tex

@@ -2,7 +2,7 @@
 1 127 1 49 0 1 7 15 1 1 14 55 1 3 0 36 1 2 0 8 1 9 0 %
 24 1 3 0 21 1 4 0 6 1 8 0 18 1 3 0 25 1 1 4 19 1 9 0 %
 6 1 7 0 22 1 8 0 16 1 2 0 11 1 23 0 22 1 9 0 20 1 3 0 %
-6 1 17 0 28 1 12 0 10 1 9 0 20 1 4 0 14 1 4 0 33 1 17 %
+6 1 17 0 28 1 39 0 10 1 9 0 20 1 4 0 14 1 4 0 33 1 13 %
 0 39 1 14 0 18 1 2 0 14 1 2 0 49 1 4 0 7 1 4 0 11 1 2 %
 0 17 1 7 0 22 1 8 0 21 1 4 0 9 1 4 0 79 1 1 2 9 1 1 4 %
 4 1 20 0 44 1 4 0 30 1 4 0 22 1 4 0 21 1 26 0 13 1 9 %