new branch

NAMESPACE

@@ -14,6 +14,7 @@ export(importWaterML1)
 export(importWaterML2)
 export(pCodeToName)
 export(parameterCdFile)
+export(readNGWMNdata)
 export(readNWISdata)
 export(readNWISdv)
 export(readNWISgwl)
@@ -47,6 +48,7 @@ importFrom(curl,curl_version)
 importFrom(dplyr,bind_rows)
 importFrom(dplyr,full_join)
 importFrom(dplyr,left_join)
+importFrom(dplyr,mutate)
 importFrom(dplyr,mutate_)
 importFrom(dplyr,mutate_each_)
 importFrom(dplyr,rbind_all)

R/importNGWMN_wml2.R

-#' Function to return data from the WaterML2 data
+#' Function to return data from the National Ground Water Monitoring Network waterML2 format
 #'
 #' This function accepts a url parameter for a WaterML2 getObservation. This function is still under development,
 #' but the general functionality is correct.
-#'
+#' 
 #' @param input character or raw, containing the url for the retrieval or a path to the data file, or raw XML.
 #' @param asDateTime logical, if \code{TRUE} returns date and time as POSIXct, if \code{FALSE}, character
 #' @param tz character to set timezone attribute of datetime. Default is an empty quote, which converts the 
 #' datetimes to UTC (properly accounting for daylight savings times based on the data's provided tz_cd column).
 #' Possible values to provide are "America/New_York","America/Chicago", "America/Denver","America/Los_Angeles",
 #' "America/Anchorage","America/Honolulu","America/Jamaica","America/Managua","America/Phoenix", and "America/Metlakatla"
-#' @return mergedDF a data frame time, value, description, qualifier, and identifier
+#' @return mergedDF a data frame source, time, value, uom, uomTitle, comment, gmlID
 #' @export
 #' @importFrom xml2 read_xml
 #' @importFrom xml2 xml_find_all
@@ -17,9 +17,12 @@
 #' @importFrom xml2 xml_attr
 #' @importFrom lubridate parse_date_time
 #' @examples
-#' 
+#' \dontrun{
+#' url <- "http://cida.usgs.gov/ngwmn_cache/sos?request=GetObservation&service=SOS&version=2.0.0&observedProperty=urn:ogc:def:property:OGC:GroundWaterLevel&responseFormat=text/xml&featureOfInterest=VW_GWDP_GEOSERVER.USGS.403836085374401"
+#' data <- importNGWMN_wml2(url)
+#' }
 importNGMWN_wml2 <- function(input, asDateTime=FALSE, tz=""){
-  
+  #TODO: update documentation
   if(tz != ""){
     tz <- match.arg(tz, c("America/New_York","America/Chicago",
                           "America/Denver","America/Los_Angeles",
@@ -38,58 +41,59 @@ importNGMWN_wml2 <- function(input, asDateTime=FALSE, tz=""){
     returnedDoc <- xml_root(getWebServiceData(input, encoding='gzip'))
   }
   
-  
-  
-  timeSeries <- xml_find_all(returnedDoc, "//wml2:MeasurementTimeseries") #each parameter/site combo
-  
-  if(0 == length(timeSeries)){
-    df <- data.frame()
-    if(!raw){
-      attr(df, "url") <- input
-    }
-    return(df)
-  }
-  
-  mergedDF <- NULL
-  
-  for(t in timeSeries){
-    gmlID <- xml_attr(t,"id")
-    uomTitle <- xml_attr(xml_find_all(t, ".//wml2:uom"), "title")
-    TVP <- xml_find_all(t, ".//wml2:MeasurementTVP")#time-value pairs
-    time <- xml_text(xml_find_all(TVP,".//wml2:time"))
-    if(asDateTime){
-      time <- parse_date_time(time, c("%Y","%Y-%m-%d","%Y-%m-%dT%H:%M","%Y-%m-%dT%H:%M:%S",
-                                      "%Y-%m-%dT%H:%M:%OS","%Y-%m-%dT%H:%M:%OS%z"), exact = TRUE)
-      #^^setting tz in as.POSIXct just sets the attribute, does not convert the time!
-      attr(time, 'tzone') <- tz 
+  response <- xml_name(returnedDoc)
+  if(response == "GetObservationResponse"){
+    
+    timeSeries <- xml_find_all(returnedDoc, "//wml2:MeasurementTimeseries") #each parameter/site combo
+    
+    if(0 == length(timeSeries)){
+      df <- data.frame()
+      if(!raw){
+        attr(df, "url") <- input
+      }
+      return(df)
     }
-    valueNodes <- xml_find_all(TVP,".//wml2:value")
-    values <- as.numeric(xml_text(valueNodes))
-    nVals <- length(values)
-    gmlID <- rep(gmlID, nVals)
-    uomTitle <- rep(uomTitle, nVals)
     
-    uom <- removeBlanks(xml_attr(valueNodes, "uom", default = NA))
-    source <- xml_attr(xml_find_all(TVP, ".//wml2:source"), "title")
-    comment <- removeBlanks(xml_text(xml_find_all(TVP, ".//wml2:comment")))
+    mergedDF <- NULL
     
-    df <- cbind.data.frame(source, time, value=values, uom, uomTitle, comment, gmlID,
-                           stringsAsFactors=FALSE)
-    if (is.null(mergedDF)){
-      mergedDF <- df
-    } else {
-      similarNames <- intersect(colnames(mergedDF), colnames(df))
-      mergedDF <- full_join(mergedDF, df, by=similarNames)
+    for(t in timeSeries){
+      gmlID <- xml_attr(t,"id")
+      TVP <- xml_find_all(t, ".//wml2:MeasurementTVP")#time-value pairs
+      time <- xml_text(xml_find_all(TVP,".//wml2:time"))
+      if(asDateTime){
+        time <- parse_date_time(time, c("%Y","%Y-%m-%d","%Y-%m-%dT%H:%M","%Y-%m-%dT%H:%M:%S",
+                                        "%Y-%m-%dT%H:%M:%OS","%Y-%m-%dT%H:%M:%OS%z"), exact = TRUE)
+        #^^setting tz in as.POSIXct just sets the attribute, does not convert the time!
+        attr(time, 'tzone') <- tz 
+      }
+      valueNodes <- xml_find_all(TVP,".//wml2:value")
+      values <- as.numeric(xml_text(valueNodes))
+      nVals <- length(values)
+      gmlID <- rep(gmlID, nVals)
+      
+      uom <- removeBlanks(xml_attr(valueNodes, "uom", default = NA))
+      source <- xml_attr(xml_find_all(TVP, ".//wml2:source"), "title")
+      comment <- removeBlanks(xml_text(xml_find_all(TVP, ".//wml2:comment")))
+      
+      df <- cbind.data.frame(source, time, value=values, uom, comment, gmlID,
+                             stringsAsFactors=FALSE)
+      if (is.null(mergedDF)){
+        mergedDF <- df
+      } else {
+        similarNames <- intersect(colnames(mergedDF), colnames(df))
+        mergedDF <- full_join(mergedDF, df, by=similarNames)
+      }
     }
+    
+    if(!raw){
+      url <- input
+      attr(mergedDF, "url") <- url
+    }
+    attr(mergedDF, "gml:identifier") <- xml_text(xml_find_all(returnedDoc, ".//gml:identifier")) 
+    attr(mergedDF, "generationDate") <- xml_text(xml_find_all(returnedDoc, ".//wml2:generationDate")) 
+  }else if(response == "ExceptionReport"){
+    #TODO: what happens if exception?
   }
-  
-  if(!raw){
-    url <- input
-    attr(mergedDF, "url") <- url
-  }
-  attr(mergedDF, "gml:identifier") <- xml_text(xml_find_all(returnedDoc, ".//gml:identifier")) 
-  attr(mergedDF, "generationDate") <- xml_text(xml_find_all(returnedDoc, ".//wml2:generationDate")) 
-  
   return(mergedDF)
   
 }

R/readNGWMNdata.R

 #' import data from the National Groundwater Monitoring Network \link{http://cida.usgs.gov/ngwmn/}
 #' Only water level data and site metadata is currently available through the web service.  
-#' @param asDateTime
-#' @param sites
-#' @param request
+#' @param asDateTime logical 
+#' @param featureID character
+#' @param request character
+#' @import utils
+#' @importFrom dplyr mutate
+#' @export
 #' 
-
-readNGWMNdata <- function(sites, request = "observation", asDateTime = TRUE){
+#TODO: documentation once more solidified
+readNGWMNdata <- function(featureID, request = "observation", asDateTime = TRUE){
   
+  match.arg(request, c("observation", "featureOfInterest"))
+  
+  if(request == "observation"){
+    #allow for multiple site calls, and aggregate here?
+    #will need to contruct this more piece by piece if other versions, properties are added
+    baseURL <- "http://cida.usgs.gov/ngwmn_cache/sos?request=GetObservation&service=SOS&version=2.0.0&observedProperty=urn:ogc:def:property:OGC:GroundWaterLevel&responseFormat=text/xml&featureOfInterest=VW_GWDP_GEOSERVER."
+    url <- paste0(baseURL, featureID)
+    
+    returnData <- importNGMWN_wml2(url, asDateTime)
+    #tack on site number
+    siteNum <- rep(sub('.*\\.', '', featureID), nrow(returnData))
+    returnData <- mutate(returnData, site = siteNum)
+    returnData <- returnData[,c(7,1:6)] #move siteNum to the left
+    
+  } 
+  
+  return(returnData)
 }
-  
\ No newline at end of file

man/importNGMWN_wml2.Rd

@@ -2,7 +2,7 @@
 % Please edit documentation in R/importNGWMN_wml2.R
 \name{importNGMWN_wml2}
 \alias{importNGMWN_wml2}
-\title{Function to return data from the WaterML2 data}
+\title{Function to return data from the National Ground Water Monitoring Network waterML2 format}
 \usage{
 importNGMWN_wml2(input, asDateTime = FALSE, tz = "")
 }
@@ -17,13 +17,16 @@ Possible values to provide are "America/New_York","America/Chicago", "America/De
 "America/Anchorage","America/Honolulu","America/Jamaica","America/Managua","America/Phoenix", and "America/Metlakatla"}
 }
 \value{
-mergedDF a data frame time, value, description, qualifier, and identifier
+mergedDF a data frame source, time, value, uom, uomTitle, comment, gmlID
 }
 \description{
 This function accepts a url parameter for a WaterML2 getObservation. This function is still under development,
 but the general functionality is correct.
 }
 \examples{
-
+\dontrun{
+url <- "http://cida.usgs.gov/ngwmn_cache/sos?request=GetObservation&service=SOS&version=2.0.0&observedProperty=urn:ogc:def:property:OGC:GroundWaterLevel&responseFormat=text/xml&featureOfInterest=VW_GWDP_GEOSERVER.USGS.403836085374401"
+data <- importNGWMN_wml2(url)
+}
 }
 

man/readNGWMNdata.Rd

@@ -2,14 +2,20 @@
 % Please edit documentation in R/readNGWMNdata.R
 \name{readNGWMNdata}
 \alias{readNGWMNdata}
-\title{import data from the National Groundwater Monitoring Network \link{http://cida.usgs.gov/ngwmn/}}
+\title{import data from the National Groundwater Monitoring Network \link{http://cida.usgs.gov/ngwmn/}
+Only water level data and site metadata is currently available through the web service.}
 \usage{
-readNGWMNdata(sites, request = "observation", asDateTime = TRUE)
+readNGWMNdata(featureID, request = "observation", asDateTime = TRUE)
 }
 \arguments{
-\item{request}{}
+\item{featureID}{character}
+
+\item{request}{character}
+
+\item{asDateTime}{logical}
 }
 \description{
 import data from the National Groundwater Monitoring Network \link{http://cida.usgs.gov/ngwmn/}
+Only water level data and site metadata is currently available through the web service.
 }