diff --git a/DESCRIPTION b/DESCRIPTION
index f7030f3af8a487fca8be8a7b4d25e7a5caa27b33..db24faf1fa1a3e4939cb31dc191b911b55bb1139 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
Package: dataRetrieval
Type: Package
-Title: Retrieval functions for USGS data
+Title: Retrieval functions for hydrologic data
Version: 1.2.2
Date: 2012-12-31
Author: Robert M. Hirsch, Laura De Cicco
@@ -55,6 +55,8 @@ Collate:
'padVariable.r'
'getRDB1Data.r'
'getSTORETSampleData.R'
+ 'getWaterML2Data.r'
+ 'renameColumns.R'
Depends:
R (>= 3.0)
Imports:
diff --git a/NAMESPACE b/NAMESPACE
index b9206bbe640951f91f1c8c9b8733dd67dc99c519..a0effc82a4061ca822787666442b9667481b7b04 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -25,6 +25,7 @@ export(getSampleDataFromFile)
export(getSiteFileData)
export(getWQPData)
export(getWaterML1Data)
+export(getWaterML2Data)
export(mergeReport)
export(padVariable)
export(populateConcentrations)
@@ -35,6 +36,7 @@ export(populateSampleColumns)
export(populateSiteINFO)
export(processQWData)
export(removeDuplicates)
+export(renameColumns)
export(retrieveNWISData)
export(retrieveNWISqwData)
export(retrieveUnitNWISData)
diff --git a/R/getWaterML2Data.r b/R/getWaterML2Data.r
index ca03fdda343995d6ffe10eef2016e6d5b6488bca..4baac2f8e055364f8d675dae8c0c703538fb6cde 100644
--- a/R/getWaterML2Data.r
+++ b/R/getWaterML2Data.r
@@ -21,43 +21,40 @@ getWaterML2Data <- function(obs_url){
ns <- xmlNamespaceDefinitions(doc, simplify = TRUE)
- timeseries <- xpathApply(doc, "//wml2:MeasurementTimeseries/wml2:point/wml2:MeasurementTVP", namespaces = ns)
- DF <- xmlToDataFrame(timeseries,stringsAsFactors=FALSE)
- DF$time <- gsub(":","",DF$time)
-
- DF$time <- ifelse(nchar(DF$time) > 18,as.POSIXct(strptime(DF$time, format="%Y-%m-%dT%H%M%S%z")),
- ifelse("Z" == substr(DF$time,(nchar(DF$time)),nchar(DF$time)),as.POSIXct(strptime(DF$time, format="%Y-%m-%dT%H%M%S",tz="GMT")),
- as.POSIXct(strptime(DF$time, format="%Y-%m-%dT%H%M%S",tz=""))))
-
- DF$time <- as.POSIXct(DF$time,origin=as.POSIXct(strptime("1970-01-01 00:00:00", "%Y-%m-%d %H:%M:%S", tz="UTC")))
- DF$value<- as.numeric(DF$value)
-
+ timeseries2 <- xpathApply(doc, "//wml2:MeasurementTimeseries/wml2:point", namespaces = ns)
+
+ xp <- xpathApply(doc, "//wml2:MeasurementTimeseries/wml2:point/wml2:MeasurementTVP", xpathSApply, ".//*[not(*)]", function(x)
+ setNames(ifelse(nzchar(xmlValue(x)), xmlValue(x),
+ ifelse("qualifier" == xmlName(x),xpathSApply(x,"./@xlink:title",namespaces = ns),"")), #originally I had the "" as xmlAttr(x)
+ xmlName(x)), namespaces = ns)
+ library(plyr)
+ DF2 <- do.call(rbind.fill.matrix, lapply(xp, t))
+ DF2 <- as.data.frame(DF2,stringsAsFactors=FALSE)
+ DF2$time <- gsub(":","",DF2$time)
+ DF2$time <- with(DF2, ifelse(nchar(time) > 18,as.POSIXct(strptime(time, format="%Y-%m-%dT%H%M%S%z")),
+ ifelse("Z" == substr(time,(nchar(time)),nchar(time)),as.POSIXct(strptime(time, format="%Y-%m-%dT%H%M%S",tz="GMT")),
+ as.POSIXct(strptime(time, format="%Y-%m-%dT%H%M%S",tz="")))))
+
+ DF2$time <- with(DF2, as.POSIXct(time,origin=as.POSIXct(strptime("1970-01-01 00:00:00", "%Y-%m-%d %H:%M:%S", tz="UTC"))))
+
+ DF2$value <- as.numeric(gsub("true","",DF2$value))
+
# Very specific to USGS:
defaultQualifier <- as.character(xpathApply(doc, "//wml2:defaultPointMetadata/wml2:DefaultTVPMeasurementMetadata/wml2:qualifier/@xlink:title",namespaces = ns))
-
- defaultQualifier <- ifelse("Provisional data subject to revision." == defaultQualifier, "P",
- ifelse("Approved for publication. Processing and review completed." == defaultQualifier, "A", defaultQualifier))
- qualifier <- rep(defaultQualifier,nrow(DF))
-
- realQual <- as.character(xpathSApply(doc,"//wml2:TVPMeasurementMetadata/wml2:qualifier/@xlink:title", namespaces = ns))
+ if (length(defaultQualifier) == 0 && (typeof(defaultQualifier) == "character")) {
+ defaultQualifier <- "NA"
+ }
- if (length(realQual) > 0){
- timeseriesSub <- xpathApply(doc, "//wml2:MeasurementTimeseries/wml2:point/wml2:MeasurementTVP/wml2:metadata", namespaces = ns)
- DF2 <- xmlToDataFrame(timeseriesSub,stringsAsFactors=FALSE)
+ if("qualifier" %in% names(DF2)){
+ DF2$qualifier <- ifelse(defaultQualifier != DF2$qualifier,DF2$qualifier,defaultQualifier)
} else {
- if (length(qualifier) > 0){
- DF$qualifier <- qualifier
- }
+ DF2$qualifier <- rep(defaultQualifier,nrow(DF2))
}
- timeseries2 <- xpathApply(doc, "//wml2:MeasurementTimeseries/wml2:point", namespaces = ns)
- xp <- xpathApply(doc, "//wml2:MeasurementTimeseries/wml2:point/wml2:MeasurementTVP", xpathSApply, ".//*[not(*)]", function(x)
- setNames(ifelse(nzchar(xmlValue(x)), xmlValue(x),
- ifelse("qualifier" == xmlName(x),xpathSApply(x,"./@xlink:title",namespaces = ns),xmlAttrs(x))),
- xmlName(x)), namespaces = ns)
- library(plyr)
- DF <- do.call(rbind.fill.matrix, lapply(xp, t))
- return (DF)
+ DF2$qualifier <- ifelse("Provisional data subject to revision." == DF2$qualifier, "P",
+ ifelse("Approved for publication. Processing and review completed." == DF2$qualifier, "A", DF2$qualifier))
+
+ return (DF2)
}
diff --git a/R/renameColumns.R b/R/renameColumns.R
new file mode 100644
index 0000000000000000000000000000000000000000..27f98997080e9465bbfcfc6e348af9b14ba09a69
--- /dev/null
+++ b/R/renameColumns.R
@@ -0,0 +1,68 @@
+#' renameColumns
+#'
+#' Rename columns coming back from NWIS data retrievals
+#'
+#' @param rawData dataframe returned from retrieval functions
+#' @keywords data import USGS web service
+#' @return rawData dataframe with improved column names
+#' @export
+#' @examples
+#' # These examples require an internet connection to run
+#' siteNumber <- '05114000'
+#' ParameterCd <- c('00060','00065')
+#' StartDate <- as.character(Sys.Date())
+#' EndDate <- as.character(Sys.Date())
+#' # These examples require an internet connection to run
+#' rawData <- retrieveUnitNWISData(siteNumber,ParameterCd,StartDate,EndDate,interactive=FALSE)
+#' rawData <- renameColumns(rawData)
+#' rawData2 <- retrieveNWISData(siteNumber,c("00010","00060","00300"),"2001-01-01","2002-01-01",StatCd=c("00001","00003"),interactive=FALSE)
+#' rawData2 <- renameColumns(rawData2)
+#' site <- '04027000'
+#' pCodes <- c("00010","00060","00095","00300","00400","63680")
+#' rawData3 <- retrieveUnitNWISData(site,pCodes,StartDate,EndDate,interactive=FALSE)
+#' rawData3 <- renameColumns(rawData3)
+renameColumns <- function(rawData){
+
+ columnNames <- names(rawData)
+
+ dataCols <- columnNames["X" == substring(columnNames, 1, 1)]
+ dataCol_cds <- dataCols["cd" == substring(dataCols, nchar(dataCols)-1, nchar(dataCols))]
+ dataCol_names <- dataCols[!(dataCols %in% dataCol_cds)]
+
+ pCodes <- sapply(strsplit(dataCol_names, "_"), function(x) x[2])
+ statCd <- sapply(strsplit(dataCol_names, "_"), function(x) x[3])
+
+ pcodeINFO <- getParameterInfo(pCodes,interactive=FALSE)
+ multipleCodes <- anyDuplicated(pCodes)
+
+ statCd <- sub("00001", "_Max", statCd)
+ statCd <- sub("00002", "_Min", statCd)
+ statCd <- sub("00003", "", statCd) # Leave mean blank
+ statCd <- sub("00011", "", statCd) # Also leaving blank
+
+ DDnum <- sapply(strsplit(dataCol_names, "_"), function(x) x[1])
+ DDnum <- gsub("X","",DDnum)
+
+ if (!any(duplicated(pCodes))){
+ dataColNames <- pcodeINFO$srsname[which(pcodeINFO$parameter_cd %in% pCodes)]
+ dataColNames <- paste(dataColNames,statCd,sep="")
+ } else {
+ dataColNames <- rep(NA,length(dataCol_names))
+ for (i in 1:length(dataCol_names)){
+ dataColNames[i] <- pcodeINFO$srsname[which(pcodeINFO$parameter_cd %in% pCodes[i])]
+ if((!(pCodes[i] %in% duplicated(pCodes))) && (pCodes[i] != pCodes[anyDuplicated(pCodes)])){
+ dataColNames[i] <- paste(dataColNames[i],statCd[i],sep="")
+ } else {
+ dataColNames[i] <- paste(dataColNames[i],statCd[i],"_",DDnum[i],sep="")
+ }
+
+ }
+
+ }
+ dataColCDS <- paste(dataColNames, "_cd")
+ columnNames[which(columnNames %in% dataCol_names)] <- dataColNames
+ columnNames[which(columnNames %in% dataCol_cds)] <- dataColCDS
+ names(rawData) <- columnNames
+
+ return(rawData)
+}
diff --git a/man/getWaterML2Data.Rd b/man/getWaterML2Data.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..3e7611bd1d4516cc91bb914fb33339def82b452d
--- /dev/null
+++ b/man/getWaterML2Data.Rd
@@ -0,0 +1,24 @@
+\name{getWaterML2Data}
+\alias{getWaterML2Data}
+\title{Function to return data from the WaterML2 data}
+\usage{
+ getWaterML2Data(obs_url)
+}
+\arguments{
+ \item{obs_url}{string containing the url for the
+ retrieval}
+}
+\value{
+ mergedDF a data frame containing columns agency, site,
+ dateTime, values, and remark codes for all requested
+ combinations
+}
+\description{
+ This function accepts a url parameter for a WaterML2
+ getObservation
+}
+\examples{
+url <- "http://webvastage6.er.usgs.gov/ogc-swie/wml2/uv/sos?request=GetObservation&featureID=01446500&observedProperty=00065&offering=UNIT&beginPosition=2013-08-20"
+dataReturned <- getWaterML2Data(urlMulti)
+}
+
diff --git a/man/renameColumns.Rd b/man/renameColumns.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..1f68f8287b74f95468fbcb9c74310e07a0d7cbb0
--- /dev/null
+++ b/man/renameColumns.Rd
@@ -0,0 +1,38 @@
+\name{renameColumns}
+\alias{renameColumns}
+\title{renameColumns}
+\usage{
+ renameColumns(rawData)
+}
+\arguments{
+ \item{rawData}{dataframe returned from retrieval
+ functions}
+}
+\value{
+ rawData dataframe with improved column names
+}
+\description{
+ Rename columns coming back from NWIS data retrievals
+}
+\examples{
+# These examples require an internet connection to run
+siteNumber <- '05114000'
+ParameterCd <- c('00060','00065')
+StartDate <- as.character(Sys.Date())
+EndDate <- as.character(Sys.Date())
+# These examples require an internet connection to run
+rawData <- retrieveUnitNWISData(siteNumber,ParameterCd,StartDate,EndDate,interactive=FALSE)
+rawData <- renameColumns(rawData)
+rawData2 <- retrieveNWISData(siteNumber,c("00010","00060","00300"),"2001-01-01","2002-01-01",StatCd=c("00001","00003"),interactive=FALSE)
+rawData2 <- renameColumns(rawData2)
+site <- '04027000'
+pCodes <- c("00010","00060","00095","00300","00400","63680")
+rawData3 <- retrieveUnitNWISData(site,pCodes,StartDate,EndDate,interactive=FALSE)
+rawData3 <- renameColumns(rawData3)
+}
+\keyword{USGS}
+\keyword{data}
+\keyword{import}
+\keyword{service}
+\keyword{web}
+