diff --git a/R/getNWISSites.R b/R/getNWISSites.R
index 708a26db675d67c5e01280e3098d0c9a668aa807..fe7001f61a2877bb7ed813fb6c2518b9a2f6dbbf 100644
--- a/R/getNWISSites.R
+++ b/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)
diff --git a/R/getRDB1Data.r b/R/getRDB1Data.r
index edf14e3aff4a6d822e245bc0b3b2ab5092a4ca56..c1a470edb85fd8b99557530efb4e1752c871ec55 100644
--- a/R/getRDB1Data.r
+++ b/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,
diff --git a/R/getRawQWData.r b/R/getRawQWData.r
index 09612a068a043ed6b77d043cb088fba57eb7d08f..7589cce5bc1bf3da6d47065dedfbff440ca23735 100644
--- a/R/getRawQWData.r
+++ b/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)
diff --git a/inst/doc/dataRetrieval.R b/inst/doc/dataRetrieval.R
index 49ab3e8fdc3e7f2edfe7ece5a80d05bde400aa72..2ee4a6c27c24a6a6b14f3d5746c49ce75524d829 100644
--- a/inst/doc/dataRetrieval.R
+++ b/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,"]")
))
diff --git a/inst/doc/dataRetrieval.Rnw b/inst/doc/dataRetrieval.Rnw
index 5432158041474cfaeeb8debdda4edae8c4055160..ecd2d82431a11a2965d254b9fe479b5d9e42549e 100644
--- a/inst/doc/dataRetrieval.Rnw
+++ b/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,"]")
))
diff --git a/inst/doc/dataRetrieval.pdf b/inst/doc/dataRetrieval.pdf
index ba94ac345fe83f8ae7795b7a9e8dfd23ffee34bf..27ce75a2fd0e1b256363d8337e20c6b207176bb7 100644
Binary files a/inst/doc/dataRetrieval.pdf and b/inst/doc/dataRetrieval.pdf differ
diff --git a/man/getNWISSites.Rd b/man/getNWISSites.Rd
index 0fb2734a0e1f1f01b978d617e063ca1e149d2f71..3921badfae3d4d49bb7973b0982b07203f1cbb7e 100644
--- a/man/getNWISSites.Rd
+++ b/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")
diff --git a/man/getWQPqwData.Rd b/man/getWQPqwData.Rd
index 7c351b3b30cd248f11bbda405b216b583bf4509b..44c6244eef89d43b496826606cd61cf3dd215776 100644
--- a/man/getWQPqwData.Rd
+++ b/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}},
diff --git a/vignettes/dataRetrieval-concordance.tex b/vignettes/dataRetrieval-concordance.tex
index 7fa17698e20d5c90bf79dfa462958e1408da497d..48e40e6aabc983953b36dfca326368e1d5896a70 100644
--- a/vignettes/dataRetrieval-concordance.tex
+++ b/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 %
diff --git a/vignettes/figure/egretEx.pdf b/vignettes/figure/egretEx.pdf
index 2b74285fd7de68e5a23b1cf2c98574b89877af36..b06cd6fa6226005c41c3dff6449a573b0f09a9d7 100644
Binary files a/vignettes/figure/egretEx.pdf and b/vignettes/figure/egretEx.pdf differ
diff --git a/vignettes/figure/getNWIStemperaturePlot.pdf b/vignettes/figure/getNWIStemperaturePlot.pdf
index 86c9793ba058f459ceafe2992c7f0ee5bdff6884..b89257452f8190556a4b65ee34493c5ea5f6f4b8 100644
Binary files a/vignettes/figure/getNWIStemperaturePlot.pdf and b/vignettes/figure/getNWIStemperaturePlot.pdf differ
diff --git a/vignettes/figure/getQWtemperaturePlot.pdf b/vignettes/figure/getQWtemperaturePlot.pdf
index 02c128eb0cc6bab168544d805540ab85651ab893..9a5f1629424ea4246c17101915a887bac0eed346 100644
Binary files a/vignettes/figure/getQWtemperaturePlot.pdf and b/vignettes/figure/getQWtemperaturePlot.pdf differ